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515(base-pkg.tex
516Chapter 1.
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518(C:\Users\Jeroen\AppData\Roaming\MiKTeX\2.9\tex/latex/inconsolata\t1zi4.fd
519File: t1zi4.fd 2018/01/14 T1/zi4 (Inconsolata)
520)
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539 [4]
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542/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It
543 []
544
545
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548m/m/n/10 if \T1/zi4/m/n/10 double.base
549 []
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554er-wise, it is \T1/zi4/m/n/10 (double.base
555 []
556
557
558Underfull \hbox (badness 10000) in paragraph at lines 141--149
559\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
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561 []
562
563
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567 []
568
569[5] [6]
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573 []
574
575[7] [8] [9] [10]
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577[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
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579 []
580
581[11] [12]
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596[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
597tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
598t of length
599 []
600
601[20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30]
602Overfull \hbox (26.27782pt too wide) in paragraph at lines 1953--1953
603 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
604t-date-and-times-in-MATLAB.html)[] 
605 []
606
607[31] [32] [33] [34] [35] [36]
608Underfull \hbox (badness 10000) in paragraph at lines 2394--2396
609[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
610ently) by
611 []
612
613
614Underfull \hbox (badness 10000) in paragraph at lines 2397--2402
615[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
616ngth re-sults, so at-tempt-ing to split via
617 []
618
619
620Underfull \hbox (badness 1102) in paragraph at lines 2397--2402
621\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
622-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit
623
624 []
625
626[37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
627[52] [53] [54] [55] [56]
628Underfull \hbox (badness 10000) in paragraph at lines 3776--3778
629[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
630-ited by set-ting
631 []
632
633[57] [58] [59] [60]
634Overfull \hbox (6.42029pt too wide) in paragraph at lines 4017--4017
635 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
636, recursive=recursive) 
637 []
638
639[61]
640Underfull \hbox (badness 1057) in paragraph at lines 4125--4128
641[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
642(but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m
643/n/10 expression[][][]\T1/ptm/m/n/10 s where
644 []
645
646[62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73]
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648[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
649har-ac-ter by
650 []
651
652[74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88]
653[89] [90]
654Overfull \hbox (5.27168pt too wide) in paragraph at lines 6135--6135
655 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
656_)), is.na(Im(NA_complex_)))[] 
657 []
658
659[91] [92] [93] [94] [95] [96]
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661[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
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663 []
664
665[97]
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668st gen-eral form (from RFC1738) is
669 []
670
671[98] [99] [100]
672Underfull \hbox (badness 6063) in paragraph at lines 6874--6880
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675
676 []
677
678
679Underfull \hbox (badness 2343) in paragraph at lines 6874--6880
680\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
681 and web-pages gen-er-
682 []
683
684
685Underfull \hbox (badness 1708) in paragraph at lines 6874--6880
686\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
687s not rec-om-mended) when
688 []
689
690
691Underfull \hbox (badness 1831) in paragraph at lines 6874--6880
692\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
693/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
694 []
695
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697Underfull \vbox (badness 10000) has occurred while \output is active []
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700[104] [105]
701Underfull \hbox (badness 1077) in paragraph at lines 7212--7218
702[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
7031/ptm/m/n/10 . Con-di-tions of length greater
704 []
705
706
707Underfull \hbox (badness 1231) in paragraph at lines 7212--7218
708\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
709first el-e-
710 []
711
712[106] [107] [108] [109] [110]
713Underfull \hbox (badness 2096) in paragraph at lines 7553--7557
714\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
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716[][]\T1/ptm/m/n/10 .
717 []
718
719[111]
720Underfull \hbox (badness 2351) in paragraph at lines 7671--7674
721[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
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725 []
726
727[112] [113] [114] [115] [116]
728Underfull \hbox (badness 4479) in paragraph at lines 7997--8007
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730[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
731, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
732[][] \T1/ptm/m/n/10 (for the col-umn names),
733 []
734
735[117] [118] [119] [120] [121] [122]
736Underfull \hbox (badness 1629) in paragraph at lines 8444--8456
737[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
738re ig-nored, and real times
739 []
740
741
742Underfull \hbox (badness 1609) in paragraph at lines 8444--8456
743\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
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745 []
746
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748Underfull \hbox (badness 2426) in paragraph at lines 8444--8456
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750value is on those OSes also used as an er-ror code.
751 []
752
753[123] [124] [125] [126] [127] [128] [129] [130] [131] [132]
754Underfull \hbox (badness 1178) in paragraph at lines 9179--9183
755[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
756mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
757]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
758 []
759
760[133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144]
761[145] [146] [147] [148]
762Underfull \hbox (badness 1735) in paragraph at lines 10327--10331
763\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
764en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
765zi4/m/n/10 https : / / en . wikipedia .
766 []
767
768[149] [150] [151] [152] [153] [154] [155]
769Underfull \hbox (badness 6396) in paragraph at lines 10766--10774
770[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
771t method def-i-ni-tions for
772 []
773
774
775Underfull \hbox (badness 1946) in paragraph at lines 10766--10774
776\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
777m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
778ized'' short-cut for
779 []
780
781[156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167]
782[168] [169] [170]
783Underfull \hbox (badness 4569) in paragraph at lines 11895--11899
784[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
785 passed as an ar-gu-ment
786 []
787
788
789Underfull \hbox (badness 2401) in paragraph at lines 11895--11899
790\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
791s en-vi-ron-ment, i.e., one needs
792 []
793
794[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182]
795[183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194]
796Underfull \hbox (badness 2253) in paragraph at lines 13574--13576
797[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
798 done: see
799 []
800
801[195]
802Underfull \hbox (badness 1565) in paragraph at lines 13647--13651
803[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
804lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
805le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
80610 , and
807 []
808
809
810Underfull \hbox (badness 4927) in paragraph at lines 13691--13693
811[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
812/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
813/m/n/10 fsep =
814 []
815
816[196] [197]
817Underfull \hbox (badness 3148) in paragraph at lines 13784--13789
818[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
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820/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
821/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
822 []
823
824[198]
825Underfull \hbox (badness 1466) in paragraph at lines 13833--13837
826[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
827zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
828 []
829
830[199]
831Underfull \hbox (badness 2875) in paragraph at lines 13954--13965
832[]\T1/ptm/m/n/10 A ver-sion of sym-bolic link-ing to files/directories was im-p
833le-mented more re-cently, and
834 []
835
836[200]
837Underfull \hbox (badness 10000) in paragraph at lines 13997--14001
838[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
839cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
840][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
841[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
842zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
843 []
844
845
846Underfull \hbox (badness 10000) in paragraph at lines 14008--14011
847[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
848] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
849i /
850 []
851
852[201] [202] [203] [204]
853Underfull \hbox (badness 3965) in paragraph at lines 14297--14301
854[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
855i-bu-tion func-tion, and in-deed,
856 []
857
858[205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215]
859Underfull \hbox (badness 4429) in paragraph at lines 15072--15075
860[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
861\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
862 []
863
864[216] [217]
865Underfull \hbox (badness 10000) in paragraph at lines 15194--15198
866[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
867ers on the dec-i-mal point, so
868 []
869
870
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873ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
874 []
875
876[218]
877Underfull \hbox (badness 2035) in paragraph at lines 15233--15237
878[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
879 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
880m/m/n/10 3.2.0: for use within
881 []
882
883[219] [220] [221] [222] [223] [224] [225] [226]
884Underfull \hbox (badness 2452) in paragraph at lines 15825--15829
885[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
886ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-
887 []
888
889
890Underfull \hbox (badness 1147) in paragraph at lines 15825--15829
891\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
892 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
893WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
894 []
895
896[227] [228] [229]
897Underfull \hbox (badness 1092) in paragraph at lines 15998--16003
898[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
899he DLL has been loaded us-ing
900 []
901
902[230] [231] [232]
903Underfull \hbox (badness 6741) in paragraph at lines 16248--16252
904\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
905T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
906 ,
907 []
908
909[233] [234] [235] [236] [237] [238] [239] [240] [241]
910Underfull \vbox (badness 10000) has occurred while \output is active []
911
912 [242]
913[243] [244] [245] [246] [247] [248] [249] [250]
914Underfull \hbox (badness 1478) in paragraph at lines 17537--17540
915[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
916r-ac-ter vec-tor
917 []
918
919[251] [252] [253] [254]
920Underfull \hbox (badness 10000) in paragraph at lines 17792--17794
921[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
922 . unicode . org / reports / tr35 /
923 []
924
925[255] [256] [257] [258] [259] [260] [261] [262]
926Underfull \hbox (badness 1442) in paragraph at lines 18390--18392
927[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
928and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
929 []
930
931[263]
932Underfull \hbox (badness 2452) in paragraph at lines 18482--18498
933[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
934omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
935 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
936cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
937T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
938 []
939
940[264] [265] [266] [267] [268] [269]
941Underfull \hbox (badness 1248) in paragraph at lines 18901--18904
942[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
943s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
944/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
945m/n/10 ,
946 []
947
948[270] [271] [272] [273]
949Underfull \hbox (badness 4739) in paragraph at lines 19159--19161
950[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
951d, see
952 []
953
954[274] [275] [276] [277]
955LaTeX Font Info:    Font shape `T1/ptm/bx/it' in size <10> not available
956(Font)              Font shape `T1/ptm/b/it' tried instead on input line 19357.
957
958 [278] [279] [280]
959Underfull \hbox (badness 1596) in paragraph at lines 19589--19594
960\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
961 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
962/m/n/10 .
963 []
964
965[281] [282] [283] [284] [285] [286] [287] [288] [289]
966Underfull \hbox (badness 2469) in paragraph at lines 20193--20198
967[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
968a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
969n/10 and
970 []
971
972[290]
973Underfull \hbox (badness 10000) in paragraph at lines 20207--20214
974[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
975 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
976 []
977
978[291] [292] [293]
979Underfull \hbox (badness 1014) in paragraph at lines 20450--20455
980[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
981s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
9820 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
983 []
984
985[294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304]
986Underfull \hbox (badness 1264) in paragraph at lines 21252--21257
987[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
988be sup-ported:
989 []
990
991[305]
992Underfull \hbox (badness 4441) in paragraph at lines 21281--21284
993[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
994m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
995i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
996 []
997
998[306] [307] [308] [309] [310] [311] [312] [313] [314] [315]
999Underfull \hbox (badness 6047) in paragraph at lines 22028--22030
1000[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
1001/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
1002 []
1003
1004[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
1005[328] [329] [330] [331]
1006Underfull \hbox (badness 1077) in paragraph at lines 23069--23075
1007\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
1008]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
10091/zi4/m/n/10 https : / / en . wikipedia .
1010 []
1011
1012[332] [333] [334] [335] [336] [337] [338] [339]
1013Underfull \hbox (badness 2790) in paragraph at lines 23574--23577
1014[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
1015ages can be sup-pressed sep-a-rately by
1016 []
1017
1018
1019Underfull \hbox (badness 1571) in paragraph at lines 23574--23577
1020\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
1021es-sages, so can be sup-pressed by
1022 []
1023
1024[340] [341] [342] [343]
1025Underfull \hbox (badness 1194) in paragraph at lines 23856--23859
1026[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
1027n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
1028 It calls
1029 []
1030
1031[344] [345]
1032Underfull \hbox (badness 2368) in paragraph at lines 24062--24068
1033[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
1034, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
1035ing list, i.e.,
1036 []
1037
1038
1039Underfull \hbox (badness 4981) in paragraph at lines 24062--24068
1040\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
1041so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
1042 []
1043
1044[346] [347] [348] [349] [350] [351]
1045Underfull \hbox (badness 10000) in paragraph at lines 24447--24450
1046[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
1047tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
1048 []
1049
1050[352] [353] [354] [355] [356] [357] [358] [359]
1051! Undefined control sequence.
1052l.25018 \bsl{}item\dotsfurther
1053                               arguments to be passed to \code{loadNamespace}.
1054The control sequence at the end of the top line
1055of your error message was never \def'ed. If you have
1056misspelled it (e.g., `\hobx'), type `I' and the correct
1057spelling (e.g., `I\hbox'). Otherwise just continue,
1058and I'll forget about whatever was undefined.
1059
1060
1061Underfull \hbox (badness 10000) in paragraph at lines 25017--25019
1062[]\T1/ptm/m/n/10 character vec-tors; see [][]\T1/zi4/m/n/10 library[][][]. \T1/
1063ptm/m/n/10 \itemar-gu-ments to be passed to
1064 []
1065
1066[360]
1067Underfull \hbox (badness 10000) in paragraph at lines 25095--25099
1068[]\T1/ptm/m/n/10 ## The string "foo" and the sym-bol 'foo' can be used in-ter-
1069 []
1070
1071
1072Underfull \hbox (badness 10000) in paragraph at lines 25095--25099
1073\T1/ptm/m/n/10 changably here: stopifnot( iden-ti-cal(isNamespaceLoaded( "foo" 
1074),
1075 []
1076
1077
1078Underfull \hbox (badness 10000) in paragraph at lines 25095--25099
1079\T1/ptm/m/n/10 FALSE), iden-ti-cal(isNamespaceLoaded(quote(foo)), FALSE), iden-
1080ti-
1081 []
1082
1083
1084Underfull \hbox (badness 2181) in paragraph at lines 25100--25106
1085[]\T1/ptm/m/n/10 hasS <- is-Names-paceLoaded("splines") # (to re-store if neede
1086d) Sns <-
1087 []
1088
1089
1090Underfull \hbox (badness 5022) in paragraph at lines 25100--25106
1091\T1/ptm/m/n/10 as-Names-pace("splines") # loads it if not al-ready stopifnot( i
1092s-Names-
1093 []
1094
1095
1096Underfull \hbox (badness 2894) in paragraph at lines 25100--25106
1097\T1/ptm/m/n/10 paceLoaded("splines")) un-load-Names-pace(Sns) # un-load-ing the
1098 NS 'ob-
1099 []
1100
1101
1102Underfull \hbox (badness 2213) in paragraph at lines 25100--25106
1103\T1/ptm/m/n/10 ject' stopifnot( ! is-Names-paceLoaded("splines")) if (hasS) loa
1104d-Names-
1105 []
1106
1107[361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371]
1108Underfull \hbox (badness 1038) in paragraph at lines 25887--25895
1109[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
111010 R \T1/ptm/m/n/10 starts up. Ini-tially
1111 []
1112
1113
1114Underfull \hbox (badness 1735) in paragraph at lines 25887--25895
1115\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
1116DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-
1117 []
1118
1119
1120Underfull \hbox (badness 1292) in paragraph at lines 25887--25895
1121\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
1122","stats","methods")\T1/ptm/m/n/10 . (Set
1123 []
1124
1125
1126Underfull \hbox (badness 1881) in paragraph at lines 25896--25899
1127[]\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str
1128ucts which are
1129 []
1130
1131
1132Underfull \hbox (badness 6220) in paragraph at lines 25915--25917
1133[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see
1134
1135 []
1136
1137[372] [373]
1138Underfull \hbox (badness 2142) in paragraph at lines 26056--26060
1139[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
1140ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able
1141 []
1142
1143
1144Underfull \hbox (badness 1968) in paragraph at lines 26106--26111
1145[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
1146tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able
1147 []
1148
1149[374] [375] [376]
1150Underfull \hbox (badness 10000) in paragraph at lines 26394--26400
1151[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/
1152n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
1153 []
1154
1155
1156Underfull \hbox (badness 10000) in paragraph at lines 26394--26400
1157\T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/
1158ptm/m/n/10 ' or the Eu-ro-pean mir-ror
1159 []
1160
1161
1162Underfull \hbox (badness 10000) in paragraph at lines 26394--26400
1163\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
1164T1/ptm/m/n/10 '. Can be set by
1165 []
1166
1167[377]
1168Underfull \hbox (badness 10000) in paragraph at lines 26407--26410
1169[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
1170][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
1171 and
1172 []
1173
1174
1175Underfull \hbox (badness 2689) in paragraph at lines 26433--26435
1176[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
1177l HTTP server, see
1178 []
1179
1180
1181Underfull \hbox (badness 10000) in paragraph at lines 26468--26473
1182[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
118310 (and in-di-rectly
1184 []
1185
1186
1187Underfull \hbox (badness 2529) in paragraph at lines 26474--26485
1188\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
1189/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-
1190 []
1191
1192
1193Underfull \hbox (badness 2512) in paragraph at lines 26474--26485
1194\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
1195/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
1196 []
1197
1198
1199Underfull \hbox (badness 7203) in paragraph at lines 26486--26489
1200[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
1201t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
1202n/10 and
1203 []
1204
1205[378]
1206Underfull \hbox (badness 10000) in paragraph at lines 26510--26515
1207[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
1208-cOS build),
1209 []
1210
1211
1212Underfull \hbox (badness 2057) in paragraph at lines 26510--26515
1213\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
1214 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).
1215 []
1216
1217[379] [380] [381] [382]
1218Underfull \vbox (badness 10000) has occurred while \output is active []
1219
1220 [383]
1221[384] [385] [386] [387] [388] [389] [390] [391] [392] [393] [394] [395]
1222[396]
1223Underfull \hbox (badness 2726) in paragraph at lines 27777--27780
1224[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
1225-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
1226 see
1227 []
1228
1229[397] [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408]
1230[409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] [420]
1231[421]
1232Underfull \hbox (badness 1533) in paragraph at lines 29470--29473
1233[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
1234n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
1235 []
1236
1237[422] [423]
1238Underfull \hbox (badness 1163) in paragraph at lines 29633--29644
1239[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
1240T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
1241 []
1242
1243[424] [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435]
1244[436] [437] [438] [439] [440] [441] [442] [443] [444] [445]
1245Underfull \hbox (badness 10000) in paragraph at lines 31176--31180
1246[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
1247/10 sup-port `named cap-ture'. If groups are named, e.g.,
1248 []
1249
1250
1251Underfull \hbox (badness 1221) in paragraph at lines 31176--31180
1252\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
1253he matches are also re-turned by name.
1254 []
1255
1256[446]
1257Underfull \hbox (badness 6188) in paragraph at lines 31198--31200
1258[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
1259ubs . opengroup . org / onlinepubs / 9699919799 /
1260 []
1261
1262[447] [448] [449] [450] [451] [452] [453] [454]
1263Underfull \hbox (badness 1655) in paragraph at lines 31754--31756
1264[]\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm
1265/m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for
1266 []
1267
1268[455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466]
1269[467] [468] [469] [470]
1270Underfull \hbox (badness 2261) in paragraph at lines 32875--32880
1271[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
1272t ap-plies to all fields; oth-er-wise, if
1273 []
1274
1275[471]
1276Underfull \hbox (badness 10000) in paragraph at lines 32902--32908
1277[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
1278ters
1279 []
1280
1281
1282Underfull \hbox (badness 1484) in paragraph at lines 32902--32908
1283\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
1284and hex-adec-i-mal rep-re-sen-ta-tions like
1285 []
1286
1287[472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483]
1288[484] [485]
1289Underfull \hbox (badness 10000) in paragraph at lines 33902--33904
1290[]\T1/ptm/m/n/10 Encoded `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs should be
1291 in the Win-dows stan-dard form,
1292 []
1293
1294[486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497]
1295[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
1296[510] [511] [512] [513] [514] [515] [516]
1297Underfull \hbox (badness 1072) in paragraph at lines 36146--36150
1298[]\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea
1299d from the file spec-i-fied by
1300 []
1301
1302
1303Underfull \hbox (badness 10000) in paragraph at lines 36151--36157
1304[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
130510 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
1306-no-init-file\T1/ptm/m/n/10 ',
1307 []
1308
1309
1310Underfull \hbox (badness 1681) in paragraph at lines 36151--36157
1311\T1/ptm/m/n/10 `\T1/zi4/m/n/10 --no-environ\T1/ptm/m/n/10 ' and (ex-cept for \T
13121/zi4/m/n/10 R CMD\T1/ptm/m/n/10 ) `\T1/zi4/m/n/10 --no-restore\T1/ptm/m/n/10 '
1313 Un-der Win-dows, it also im-plies
1314 []
1315
1316[517]
1317Underfull \hbox (badness 10000) in paragraph at lines 36181--36187
1318[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
1319s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 '
1320 []
1321
1322
1323Underfull \hbox (badness 10000) in paragraph at lines 36181--36187
1324\T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
1325 first in architecture-specific di-rec-to-ries,
1326 []
1327
1328
1329Underfull \hbox (badness 1320) in paragraph at lines 36181--36187
1330\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
1331environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
1332n/10 ' will be used in
1333 []
1334
1335[518] [519] [520] [521] [522]
1336Underfull \hbox (badness 1142) in paragraph at lines 36543--36549
1337[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
1338at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d
1339 []
1340
1341[523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534]
1342[535] [536] [537] [538] [539] [540] [541]
1343Underfull \hbox (badness 1565) in paragraph at lines 37816--37818
1344[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
1345ype) \T1/ptm/m/n/10 for the de-fault
1346 []
1347
1348[542] [543] [544] [545] [546] [547] [548] [549] [550] [551]
1349Underfull \hbox (badness 1616) in paragraph at lines 38518--38523
1350\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
1351, pro-vided only the POSIX op-tions
1352 []
1353
1354[552] [553] [554] [555] [556] [557] [558] [559]
1355Underfull \hbox (badness 1472) in paragraph at lines 39044--39047
1356[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
1357p their source in-clud-ing com-ments, see
1358 []
1359
1360[560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571]
1361[572] [573]
1362Underfull \hbox (badness 10000) in paragraph at lines 39982--39986
1363[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
1364e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10
1365 length(bin) >
1366 []
1367
1368[574] [575] [576] [577]
1369Underfull \hbox (badness 10000) in paragraph at lines 40233--40236
1370[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
1371][]$https : / / developer . r-[]project . org /
1372 []
1373
1374[578] [579]
1375Underfull \hbox (badness 10000) in paragraph at lines 40351--40355
1376[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
1377emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
1378[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
1379 []
1380
1381
1382Underfull \hbox (badness 10000) in paragraph at lines 40413--40417
1383[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
1384emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
1385][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
1386 []
1387
1388[580] [581] [582] [583] [584] [585] [586] [587]
1389Underfull \hbox (badness 10000) in paragraph at lines 40988--40991
1390[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
1391] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
1392]zones /
1393 []
1394
1395[588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599]
1396[600]
1397Underfull \hbox (badness 1990) in paragraph at lines 41891--41899
1398[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
1399r-rors that oc-cur dur-ing the eval-u-a-tion. If
1400 []
1401
1402
1403Underfull \hbox (badness 4846) in paragraph at lines 41891--41899
1404\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
1405]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
1406 []
1407
1408[601] [602] [603] [604] [605] [606] [607]
1409Underfull \hbox (badness 1917) in paragraph at lines 42380--42387
1410[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
1411ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
1412 []
1413
1414[608] [609] [610] [611] [612] [613] [614] [615] [616] [617] [618]
1415Underfull \hbox (badness 3668) in paragraph at lines 43109--43111
1416[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
1417ately, even if
1418 []
1419
1420[619]
1421Underfull \hbox (badness 2401) in paragraph at lines 43237--43241
1422[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
1423n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
1424 []
1425
1426[620] [621] [622]
1427Underfull \hbox (badness 2111) in paragraph at lines 43426--43431
1428\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
1429ot empty, these are used as col-umn names.
1430 []
1431
1432
1433Underfull \hbox (badness 10000) in paragraph at lines 43447--43452
1434[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
1435/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
1436 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
1437 []
1438
1439[623] [624] [625] [626] [627] [628] [629] [630] [631]
1440Underfull \hbox (badness 5417) in paragraph at lines 44029--44033
1441[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
1442y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
1443 []
1444
1445[632]
1446Underfull \hbox (badness 10000) in paragraph at lines 44090--44094
1447[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
1448' reg-exps, in-clud-ing el-e-ments named
1449 []
1450
1451[633]) (compiler-pkg.tex [634
1452
1453
1454]
1455Chapter 2.
1456[635] [636] [637] [638]) (datasets-pkg.tex
1457Chapter 3.
1458[639
1459
1460
1461] [640] [641] [642] [643] [644]
1462Underfull \vbox (badness 1472) has occurred while \output is active []
1463
1464 [645]
1465[646] [647] [648] [649] [650] [651] [652] [653]
1466Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
1467[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
1468e iden-ti-fi-ca-tion of crim-i-nals.
1469 []
1470
1471[654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
1472[666] [667] [668] [669] [670] [671] [672] [673] [674] [675]
1473Overfull \vbox (4.26088pt too high) has occurred while \output is active []
1474
1475
1476[676] [677] [678] [679] [680] [681]
1477Overfull \vbox (13.87083pt too high) has occurred while \output is active []
1478
1479
1480[682]
1481Underfull \vbox (badness 2376) has occurred while \output is active []
1482
1483 [683]
1484[684]
1485Overfull \vbox (12.25539pt too high) has occurred while \output is active []
1486
1487
1488[685] [686]
1489Overfull \vbox (17.12102pt too high) has occurred while \output is active []
1490
1491
1492[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697]
1493Overfull \vbox (10.49593pt too high) has occurred while \output is active []
1494
1495
1496[698]
1497Overfull \vbox (15.49593pt too high) has occurred while \output is active []
1498
1499
1500[699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710]
1501[711] [712] [713]) (grDevices-pkg.tex [714
1502
1503
1504]
1505Chapter 4.
1506[715] [716] [717] [718]
1507Underfull \hbox (badness 3158) in paragraph at lines 282--286
1508[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
1509/m/n/10 , with iden-ti-cal mean-ing to
1510 []
1511
1512
1513Underfull \hbox (badness 10000) in paragraph at lines 298--303
1514[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
1515m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
15160 in
1517 []
1518
1519
1520Underfull \hbox (badness 1852) in paragraph at lines 298--303
1521\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
1522also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
1523ion
1524 []
1525
1526[719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730]
1527[731]
1528Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
1529[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
1530. The source code is in
1531 []
1532
1533[732] [733] [734]
1534Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
1535[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
1536ors that will be used in plot-ting, call-ing
1537 []
1538
1539[735] [736] [737]
1540Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
1541\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
1542T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
154310 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
1544 []
1545
1546[738] [739] [740] [741] [742] [743]
1547Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
1548\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
1549 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
155010 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
1551/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
1552 []
1553
1554[744]
1555Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
1556[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
1557set-ting of
1558 []
1559
1560[745] [746] [747]
1561Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
1562[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
1563 doc-u-men-ta-tion) are
1564 []
1565
1566[748] [749] [750] [751] [752] [753] [754] [755] [756]
1567Underfull \hbox (badness 10000) in paragraph at lines 2826--2827
1568
1569 []
1570
1571
1572Underfull \vbox (badness 10000) has occurred while \output is active []
1573
1574 [757]
1575[758] [759] [760] [761] [762] [763] [764]
1576Underfull \hbox (badness 10000) in paragraph at lines 3382--3387
1577[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
1578ed on the inter-quartile range
1579 []
1580
1581[765] [766] [767] [768]
1582Underfull \hbox (badness 10000) in paragraph at lines 3648--3651
1583[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
1584e a C in-te-ger for-mat such as
1585 []
1586
1587[769] [770] [771] [772] [773] [774] [775] [776] [777] [778]
1588Underfull \hbox (badness 10000) in paragraph at lines 4377--4382
1589[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
1590 / devnet / actionscript / articles / PLRM . pdf$[][]
1591 []
1592
1593
1594Underfull \hbox (badness 4181) in paragraph at lines 4377--4382
1595\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
1596t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
1597 []
1598
1599[779] [780] [781] [782]
1600Underfull \hbox (badness 3364) in paragraph at lines 4676--4678
1601[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
1602\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
1603 []
1604
1605[783] [784]
1606Underfull \hbox (badness 1377) in paragraph at lines 4810--4815
1607[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
1608al-lowed val-ues
1609 []
1610
1611[785]
1612Underfull \hbox (badness 1418) in paragraph at lines 4886--4893
1613\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
1614/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
1615zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
1616/m/n/10 ,
1617 []
1618
1619
1620Underfull \hbox (badness 1755) in paragraph at lines 4904--4906
1621[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
1622Asian lan-guages -- see
1623 []
1624
1625[786] [787]
1626Underfull \hbox (badness 1377) in paragraph at lines 5015--5020
1627[]\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \
1628T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and
1629 []
1630
1631
1632Underfull \hbox (badness 7344) in paragraph at lines 5084--5086
1633[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
1634ion by Brian D'Urso
1635 []
1636
1637[788] [789] [790]
1638Underfull \hbox (badness 2035) in paragraph at lines 5219--5228
1639[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
1640-a-lents) are also pro-
1641 []
1642
1643
1644Underfull \hbox (badness 10000) in paragraph at lines 5219--5228
1645\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
16460 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
1647n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
16480 ,
1649 []
1650
1651
1652Underfull \hbox (badness 10000) in paragraph at lines 5219--5228
1653\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
1654 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
1655othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
1656 []
1657
1658[791]
1659Underfull \hbox (badness 10000) in paragraph at lines 5287--5294
1660[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
1661/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
1662 []
1663
1664
1665Underfull \hbox (badness 2189) in paragraph at lines 5287--5294
1666\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
1667V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
1668 []
1669
1670[792] [793]
1671Underfull \hbox (badness 1546) in paragraph at lines 5429--5437
1672[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
16730 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
1674nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
16751/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
1676n/10 ,
1677 []
1678
1679[794] [795] [796] [797] [798] [799] [800] [801]
1680Underfull \hbox (badness 10000) in paragraph at lines 5964--5967
1681[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
1682/green/blue) into HSV space
1683 []
1684
1685[802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813]
1686Underfull \hbox (badness 1189) in paragraph at lines 6800--6802
1687[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
1688. One of
1689 []
1690
1691[814]
1692Underfull \hbox (badness 10000) in paragraph at lines 6898--6900
1693[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
1694lan-guages and
1695 []
1696
1697[815] [816] [817] [818] [819]
1698Underfull \hbox (badness 3780) in paragraph at lines 7198--7204
1699[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
17000 "AvantGarde"\T1/ptm/m/n/10 ,
1701 []
1702
1703[820] [821]
1704Underfull \hbox (badness 2680) in paragraph at lines 7399--7401
1705[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
1706umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
1707 []
1708
1709[822] [823] [824]) (graphics-pkg.tex
1710Chapter 5.
1711[825
1712
1713
1714] [826] [827] [828] [829] [830] [831] [832] [833] [834] [835] [836]
1715[837] [838] [839] [840] [841] [842] [843] [844]
1716Underfull \hbox (badness 4634) in paragraph at lines 1307--1310
1717[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
1718nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
1719/10 ,
1720 []
1721
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1724Underfull \hbox (badness 1009) in paragraph at lines 2346--2353
1725\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
1726ot ap-ply to
1727 []
1728
1729[861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] [872]
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1738Underfull \hbox (badness 3229) in paragraph at lines 4489--4494
1739[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
1740to be used, see
1741 []
1742
1743[893] [894] [895] [896] [897]
1744Underfull \hbox (badness 10000) in paragraph at lines 4846--4852
1745[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
1746/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
1747 []
1748
1749
1750Underfull \hbox (badness 5908) in paragraph at lines 4846--4852
1751\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
1752) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
1753 []
1754
1755[898] [899]
1756Underfull \hbox (badness 10000) in paragraph at lines 4977--4980
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1787[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
1788:6\T1/ptm/m/n/10 ) cor-re-spond to
1789 []
1790
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1808[][] 
1809 []
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1818[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
1819rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi
1820nt
1821 []
1822
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1824[950] [951] [952] [953] [954] [955] [956]
1825Underfull \hbox (badness 10000) in paragraph at lines 8790--8792
1826[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
1827 []
1828
1829
1830Underfull \hbox (badness 10000) in paragraph at lines 8792--8794
1831[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
1832 []
1833
1834[957]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
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1837                   \relax 
1838l.8872 \HeaderA{units}{Graphical Units}{units}
1839                                               [958] [959] [960] [961])
1840(grid-pkg.tex [962
1841
1842
1843]
1844Chapter 6.
1845[963] [964] [965] [966] [967] [968] [969] [970]
1846Underfull \hbox (badness 2680) in paragraph at lines 483--486
1847[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
1848/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
1849n of
1850 []
1851
1852[971] [972] [973] [974] [975] [976] [977] [978] [979]
1853Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
1854[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
1855/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
1856 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
1857m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
185810 unit[][][]\T1/ptm/m/n/10 ,
1859 []
1860
1861[980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991]
1862[992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003]
1863[1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014]
1864[1015] [1016] [1017] [1018] [1019]
1865Underfull \vbox (badness 10000) has occurred while \output is active []
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1867 [1020]
1868[1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031]
1869[1032]
1870Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
1871[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
1872t de-scrib-ing seg-ments), but only
1873 []
1874
1875[1033] [1034] [1035] [1036]
1876Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
1877[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
1878s are co-erced by
1879 []
1880
1881[1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047]
1882[1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058]
1883[1059] [1060] [1061] [1062] [1063] [1064]
1884Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
1885[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
1886 do-ing some-thing like \T1/zi4/m/n/10 depth
1887 []
1888
1889[1065] [1066] [1067] [1068]) (methods-pkg.tex
1890Chapter 7.
1891[1069
1892
1893
1894] [1070] [1071] [1072] [1073] [1074] [1075] [1076]
1895Underfull \vbox (badness 10000) has occurred while \output is active []
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1902Underfull \hbox (badness 2237) in paragraph at lines 1385--1387
1903[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
1904T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
1905"\T1/ptm/m/n/10 , also of class
1906 []
1907
1908[1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094]
1909Underfull \hbox (badness 2181) in paragraph at lines 1932--1939
1910[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
1911jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests
1912 []
1913
1914
1915Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
1916[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
1917an be an ob-ject of class
1918 []
1919
1920
1921Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
1922\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
19230 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
1924 []
1925
1926[1095] [1096] [1097]
1927Underfull \hbox (badness 2213) in paragraph at lines 2214--2219
1928[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
1929, use \T1/zi4/m/n/10 where =
1930 []
1931
1932[1098] [1099] [1100] [1101] [1102]
1933Underfull \hbox (badness 10000) in paragraph at lines 2574--2577
1934[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
1935tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
1936b-jects of class
1937 []
1938
1939[1103] [1104]
1940Underfull \hbox (badness 1132) in paragraph at lines 2714--2718
1941[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
19420 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
1943-turned re-sult is in
1944 []
1945
1946
1947Underfull \hbox (badness 1033) in paragraph at lines 2746--2751
1948\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
1949ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
1950s the
1951 []
1952
1953[1105] [1106] [1107] [1108] [1109] [1110] [1111]
1954Underfull \hbox (badness 1102) in paragraph at lines 3303--3305
1955[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
1956me of the pack-age (with-out the ex-tra-ne-ous
1957 []
1958
1959[1112] [1113] [1114] [1115] [1116]
1960Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
1961[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
1962classes takes spe-cial ar-gu-ments
1963 []
1964
1965
1966Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
1967[]\T1/ptm/m/n/10 The
1968 []
1969
1970[1117] [1118]
1971Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
1972[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
1973 = "numeric",altitude
1974 []
1975
1976[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127]
1977Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
1978[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
1979the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar
1980 []
1981
1982
1983Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
1984\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
19851/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
1986 []
1987
1988[1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136]
1989Underfull \vbox (badness 10000) has occurred while \output is active []
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1992Underfull \vbox (badness 10000) has occurred while \output is active []
1993
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1995[1139] [1140]
1996Underfull \hbox (badness 4036) in paragraph at lines 5437--5440
1997[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
1998 the method to use in re-sponse to a
1999 []
2000
2001[1141]
2002Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
2003[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
2004assed to
2005 []
2006
2007[1142] [1143] [1144]
2008Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
2009[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
2010ds for this class are found (us-ing
2011 []
2012
2013[1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152]
2014Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
2015\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
2016od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
2017 []
2018
2019[1153] [1154] [1155] [1156]
2020Underfull \vbox (badness 10000) has occurred while \output is active []
2021
2022 [1157]
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2026                   \relax 
2027l.6973 \aliasA{S4}{S3Part}{S4}
2028                               [1160] [1161] [1162]pdfTeX warning (ext4): desti
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2032                   \relax 
2033l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
2034                                                pdfTeX warning (ext4): destinat
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2039l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
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2044                   \relax 
2045l.7232 \aliasA{Math}{S4groupGeneric}{Math}
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2050                   \relax 
2051l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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2057l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
2058                                                 [1163]
2059Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
2060[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
2061can be ob-tained by call-ing
2062 []
2063
2064[1164] [1165]
2065Underfull \hbox (badness 1286) in paragraph at lines 7484--7486
2066[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
2067a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
2068ly
2069 []
2070
2071[1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176]
2072[1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187]
2073[1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198]
2074Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
2075[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
2076w("signature",functionDef,...)\T1/ptm/m/n/10 . The
2077 []
2078
2079[1199] [1200] [1201] [1202] [1203] [1204] [1205]
2080Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
2081[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
2082ass, from the data part; e.g.,
2083 []
2084
2085[1206] [1207] [1208]) (parallel-pkg.tex
2086Chapter 8.
2087
2088Underfull \hbox (badness 5490) in paragraph at lines 14--16
2089[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
2090/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
2091][][]: see
2092 []
2093
2094[1209
2095
2096
2097] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
2098Underfull \hbox (badness 3386) in paragraph at lines 595--598
2099[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
2100andom.seed \T1/ptm/m/n/10 when the
2101 []
2102
2103[1217] [1218] [1219]) (splines-pkg.tex [1220
2104
2105
2106]
2107Chapter 9.
2108
2109Underfull \hbox (badness 10000) in paragraph at lines 22--24
2110[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
2111m/n/10 and William N. Ven-ables
2112 []
2113
2114[1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231]
2115[1232] [1233] [1234]) (stats-pkg.tex
2116Chapter 10.
2117[1235
2118
2119
2120] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]
2121[1246] [1247]
2122Underfull \hbox (badness 1412) in paragraph at lines 847--849
2123[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
2124\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
2125 []
2126
2127[1248] [1249] [1250] [1251] [1252] [1253] [1254]
2128Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
2129[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
2130\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
2131 []
2132
2133[1255] [1256]
2134Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
2135[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
21360 or for mul-ti-ple re-sponses of class
2137 []
2138
2139[1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267]
2140[1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278]
2141[1279] [1280] [1281] [1282] [1283] [1284]
2142Underfull \hbox (badness 2503) in paragraph at lines 3407--3410
2143[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
2144\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
2145 []
2146
2147[1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295]
2148[1296] [1297] [1298]
2149Underfull \hbox (badness 1127) in paragraph at lines 4321--4324
2150[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
2151/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
2152 []
2153
2154[1299] [1300] [1301] [1302] [1303]
2155Underfull \hbox (badness 3989) in paragraph at lines 4651--4658
2156[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
2157(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
2158it/10 g[] \OT1/cmr/m/n/10 =
2159 []
2160
2161[1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312]
2162Underfull \hbox (badness 2556) in paragraph at lines 5287--5290
2163[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
2164ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
2165tm/m/n/10 . For
2166 []
2167
2168
2169Underfull \hbox (badness 2932) in paragraph at lines 5304--5306
2170[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
2171quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
2172given by
2173 []
2174
2175[1313] [1314] [1315] [1316] [1317] [1318]
2176Underfull \hbox (badness 2503) in paragraph at lines 5696--5700
2177[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
2178\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
2179 []
2180
2181[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
2182[1330]
2183Underfull \hbox (badness 7081) in paragraph at lines 6478--6481
2184[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
2185 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
2186 []
2187
2188
2189Underfull \hbox (badness 10000) in paragraph at lines 6482--6484
2190[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
2191m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
2192 []
2193
2194[1331] [1332] [1333] [1334] [1335]
2195Underfull \vbox (badness 10000) has occurred while \output is active []
2196
2197 [1336]
2198[1337] [1338]
2199Underfull \vbox (badness 10000) has occurred while \output is active []
2200
2201 [1339]
2202[1340] [1341] [1342] [1343]
2203Underfull \hbox (badness 10000) in paragraph at lines 7327--7330
2204[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
22051/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
2206 []
2207
2208[1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354]
2209[1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363]
2210Underfull \vbox (badness 10000) has occurred while \output is active []
2211
2212 [1364]
2213[1365] [1366] [1367]
2214Underfull \hbox (badness 2626) in paragraph at lines 9004--9007
2215[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
2216m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
2217 []
2218
2219[1368] [1369]
2220Underfull \hbox (badness 2503) in paragraph at lines 9111--9115
2221[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
2222\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
2223 []
2224
2225[1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380]
2226[1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388]
2227Underfull \hbox (badness 4518) in paragraph at lines 10421--10426
2228[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
2229-ercible by
2230 []
2231
2232[1389] [1390] [1391] [1392] [1393]
2233Underfull \hbox (badness 2142) in paragraph at lines 10781--10784
2234[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 $\T1/ptm
2235/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/10 
2236dev \OMS/cmsy/m/n/10  
2237 []
2238
2239
2240Underfull \hbox (badness 1253) in paragraph at lines 10800--10803
2241[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][
2242]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it-
2243er-a-tion. Hence,
2244 []
2245
2246[1394]
2247Underfull \hbox (badness 1708) in paragraph at lines 10862--10866
2248[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
2249na-tives are:
2250 []
2251
2252[1395] [1396] [1397] [1398] [1399]
2253Underfull \hbox (badness 1694) in paragraph at lines 11258--11261
2254[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
2255de-fault to
2256 []
2257
2258[1400] [1401] [1402] [1403] [1404] [1405]
2259Underfull \hbox (badness 10000) in paragraph at lines 11585--11588
2260[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
2261[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
2262uiv-a-lent of
2263 []
2264
2265
2266Underfull \hbox (badness 1281) in paragraph at lines 11585--11588
2267\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
2268l ap-prox-i-ma-tion may be con-sid-er-ably
2269 []
2270
2271[1406] [1407]pdfTeX warning (ext4): destination with the same identifier (name{
2272Rfn.hat}) has been already used, duplicate ignored
2273<to be read again> 
2274                   \relax 
2275l.11739 \aliasA{hat}{influence.measures}{hat}
2276                                              [1408] [1409]
2277Underfull \hbox (badness 1484) in paragraph at lines 11874--11876
2278[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
2279ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
2280 []
2281
2282[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418]
2283Underfull \hbox (badness 10000) in paragraph at lines 12467--12469
2284[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
2285ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit =
2286 []
2287
2288[1419] [1420] [1421] [1422] [1423]
2289Underfull \hbox (badness 2894) in paragraph at lines 12803--12807
2290[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
2291ault method
2292 []
2293
2294[1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434]
2295[1435]
2296Underfull \hbox (badness 4518) in paragraph at lines 13553--13558
2297[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
2298-ercible by
2299 []
2300
2301[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444]
2302Underfull \hbox (badness 4518) in paragraph at lines 14205--14210
2303[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
2304-ercible by
2305 []
2306
2307[1445] [1446]
2308Underfull \hbox (badness 8151) in paragraph at lines 14343--14347
2309[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
2310olate",statistics =
2311 []
2312
2313
2314Underfull \hbox (badness 1199) in paragraph at lines 14350--14352
2315[]\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on
2316ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is
2317 []
2318
2319[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
2320[1458] [1459] [1460] [1461] [1462] [1463]
2321Underfull \hbox (badness 2503) in paragraph at lines 15421--15425
2322[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
2323\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
2324 []
2325
2326[1464] [1465] [1466] [1467] [1468] [1469] [1470]
2327Underfull \hbox (badness 4621) in paragraph at lines 15933--15939
2328[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
2329\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/
2330ptm/m/n/10 and
2331 []
2332
2333[1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481]
2334[1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492]
2335[1493] [1494] [1495] [1496] [1497]
2336Underfull \vbox (badness 10000) has occurred while \output is active []
2337
2338 [1498]
2339[1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509]
2340[1510]
2341Underfull \hbox (badness 1377) in paragraph at lines 18527--18532
2342[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
2343a-tion is per-formed on
2344 []
2345
2346
2347Underfull \hbox (badness 1735) in paragraph at lines 18532--18535
2348[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
2349-tion to the gra-di-ent, on
2350 []
2351
2352
2353Underfull \hbox (badness 2343) in paragraph at lines 18545--18549
2354[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
2355t is un-able to re-duce
2356 []
2357
2358
2359Underfull \hbox (badness 3471) in paragraph at lines 18545--18549
2360\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
2361ltol) \T1/ptm/m/n/10 at a step. De-faults to
2362 []
2363
2364[1511]
2365Underfull \hbox (badness 2662) in paragraph at lines 18553--18557
2366[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
2367m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
2368T1/ptm/m/n/10 meth-ods if
2369 []
2370
2371[1512] [1513]
2372Underfull \vbox (badness 10000) has occurred while \output is active []
2373
2374 [1514]
2375Overfull \hbox (15.73795pt too wide) in paragraph at lines 18778--18778
2376 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
2377ut NM may be ok and "unavoidable",[] 
2378 []
2379
2380
2381Overfull \hbox (3.75941pt too wide) in paragraph at lines 18781--18781
2382 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
2383warn.1d.NelderMead = FALSE)))[] 
2384 []
2385
2386[1515] [1516] [1517] [1518] [1519] [1520]
2387Underfull \hbox (badness 1337) in paragraph at lines 19203--19206
2388[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
2389e-sis, must be one of
2390 []
2391
2392[1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529]
2393Underfull \hbox (badness 3049) in paragraph at lines 19699--19703
2394[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
2395rs of stan-dard-ized resid-u-als
2396 []
2397
2398[1530] [1531] [1532] [1533]
2399Underfull \hbox (badness 1194) in paragraph at lines 19957--19960
2400[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
2401 of the con-fi-dence
2402 []
2403
2404[1534] [1535] [1536] [1537] [1538]
2405Underfull \hbox (badness 2503) in paragraph at lines 20332--20335
2406[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
2407\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
2408 []
2409
2410[1539]
2411Underfull \hbox (badness 3919) in paragraph at lines 20359--20361
2412[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
2413/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
2414 []
2415
2416[1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550]
2417[1551] [1552] [1553] [1554] [1555]
2418Underfull \hbox (badness 10000) in paragraph at lines 21436--21442
2419[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
2420][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
2421\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
2422 []
2423
2424[1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566]
2425[1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576]
2426Underfull \hbox (badness 1337) in paragraph at lines 22783--22789
2427[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
2428e-sis, must be one of
2429 []
2430
2431[1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585]
2432Overfull \hbox (27.74408pt too wide) in paragraph at lines 23348--23348
2433 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
2434p, ...), quantile(x, prob, type=1)))[] 
2435 []
2436
2437[1586] [1587] [1588]
2438Underfull \hbox (badness 10000) in paragraph at lines 23599--23602
2439[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
2440 []
2441
2442
2443Underfull \hbox (badness 4205) in paragraph at lines 23599--23602
2444\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
2445ef-fi-ciency if al-ready
2446 []
2447
2448[1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597]
2449Underfull \hbox (badness 10000) in paragraph at lines 24184--24187
2450[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
2451med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] =
2452 []
2453
2454[1598]
2455Underfull \hbox (badness 3690) in paragraph at lines 24236--24240
2456[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
2457 end point rule and is called by de-fault from
2458 []
2459
2460[1599] [1600] [1601] [1602] [1603] [1604] [1605]
2461Underfull \hbox (badness 2165) in paragraph at lines 24713--24718
2462[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
2463/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
24640 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
2465 []
2466
2467[1606] [1607] [1608] [1609]
2468Underfull \hbox (badness 1867) in paragraph at lines 24918--24920
2469[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
2470Passed to
2471 []
2472
2473
2474Underfull \hbox (badness 10000) in paragraph at lines 24931--24935
2475\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
2476se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
2477 []
2478
2479[1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619]
2480Underfull \vbox (badness 10000) has occurred while \output is active []
2481
2482 [1620]
2483[1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630]
2484Underfull \vbox (badness 10000) has occurred while \output is active []
2485
2486 [1631]
2487Underfull \hbox (badness 3514) in paragraph at lines 26470--26475
2488[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
2489T1/ptm/m/n/10 . It is the value of the ex-pres-sion
2490 []
2491
2492[1632] [1633] [1634] [1635]
2493Overfull \hbox (2.23795pt too wide) in paragraph at lines 26704--26704
2494 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
2495 == frac(log(2), e^{phi[2]})}),[] 
2496 []
2497
2498[1636]
2499Underfull \hbox (badness 3514) in paragraph at lines 26740--26746
2500[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
2501T1/ptm/m/n/10 . It is the value of the ex-pres-sion
2502 []
2503
2504[1637] [1638] [1639]
2505Underfull \hbox (badness 3514) in paragraph at lines 26954--26959
2506[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
2507T1/ptm/m/n/10 . It is the value of the ex-pres-sion
2508 []
2509
2510[1640] [1641]
2511Underfull \hbox (badness 3514) in paragraph at lines 27041--27046
2512[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
2513T1/ptm/m/n/10 . It is the value of the ex-pres-sion
2514 []
2515
2516[1642]
2517Underfull \hbox (badness 3514) in paragraph at lines 27106--27111
2518[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
2519T1/ptm/m/n/10 . It is the value of the ex-pres-sion
2520 []
2521
2522[1643]
2523Underfull \hbox (badness 3514) in paragraph at lines 27200--27205
2524[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
2525T1/ptm/m/n/10 . It is the value of the ex-pres-sion
2526 []
2527
2528[1644] [1645]
2529Underfull \hbox (badness 6691) in paragraph at lines 27292--27297
2530[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
2531tm/m/n/10 . It is the value of the ex-pres-sion
2532 []
2533
2534[1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653]
2535Underfull \hbox (badness 4024) in paragraph at lines 27822--27825
2536[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
2537, which
2538 []
2539
2540[1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662]
2541Underfull \hbox (badness 5431) in paragraph at lines 28428--28430
2542[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
2543i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
2544 []
2545
2546[1663] [1664] [1665] [1666]
2547Underfull \hbox (badness 5431) in paragraph at lines 28638--28641
2548[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
2549i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
2550 []
2551
2552[1667] [1668] [1669] [1670] [1671]
2553Underfull \hbox (badness 1337) in paragraph at lines 28952--28956
2554[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
2555e-sis, must be one of
2556 []
2557
2558[1672] [1673] [1674] [1675]
2559Underfull \hbox (badness 1616) in paragraph at lines 29254--29257
2560[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
2561 resid-u-als, when
2562 []
2563
2564[1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686]
2565[1687] [1688] [1689] [1690] [1691] [1692] [1693]
2566Underfull \hbox (badness 3557) in paragraph at lines 30384--30388
2567[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
2568i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4
2569/m/n/10 interval =
2570 []
2571
2572[1694] [1695]
2573Underfull \vbox (badness 10000) has occurred while \output is active []
2574
2575 [1696]
2576[1697] [1698]
2577Underfull \hbox (badness 1337) in paragraph at lines 30748--30752
2578[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
2579e-sis, must be one of
2580 []
2581
2582[1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706]
2583Underfull \hbox (badness 1337) in paragraph at lines 31275--31279
2584[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
2585e-sis, must be one of
2586 []
2587
2588[1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715]) (stats4-pkg.tex
2589[1716
2590
2591
2592]
2593Chapter 11.
2594[1717] [1718] [1719] [1720] [1721] [1722]pdfTeX warning (ext4): destination wit
2595h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
2596licate ignored
2597<to be read again> 
2598                   \relax 
2599l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
2600                                                   [1723] [1724] [1725])
2601(tcltk-pkg.tex [1726
2602
2603
2604]
2605Chapter 12.
2606[1727] [1728] [1729] [1730] [1731] [1732] [1733]
2607Underfull \vbox (badness 10000) has occurred while \output is active []
2608
2609 [1734]
2610Underfull \hbox (badness 1546) in paragraph at lines 660--667
2611[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
2612 any Tk or Tcl com-mand by sim-ply run-ning
2613 []
2614
2615[1735] [1736] [1737] [1738] [1739]
2616Underfull \vbox (badness 10000) has occurred while \output is active []
2617
2618 [1740]
2619[1741] [1742] [1743] [1744] [1745] [1746]) (tools-pkg.tex
2620Chapter 13.
2621[1747
2622
2623
2624]
2625
2626LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
2627(Font)              using `T1/zi4/m/n' instead on input line 72.
2628
2629[1748]
2630Underfull \hbox (badness 3039) in paragraph at lines 164--167
2631[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
2632e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
2633 []
2634
2635[1749] [1750]
2636Underfull \hbox (badness 1308) in paragraph at lines 285--298
2637[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
2638o ren-der each of the 12 types
2639 []
2640
2641
2642Underfull \hbox (badness 4967) in paragraph at lines 285--298
2643\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
2644ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-
2645 []
2646
2647
2648Underfull \hbox (badness 10000) in paragraph at lines 285--298
2649\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
2650dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
26510 formatMastersthesis\T1/ptm/m/n/10 ,
2652 []
2653
2654
2655Underfull \hbox (badness 10000) in paragraph at lines 285--298
2656\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
2657/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
2658tTechreport \T1/ptm/m/n/10 and
2659 []
2660
2661[1751]
2662Underfull \hbox (badness 3039) in paragraph at lines 389--391
2663[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
2664to use. Over-rides any
2665 []
2666
2667[1752] [1753] [1754] [1755] [1756] [1757] [1758]
2668Overfull \vbox (7.18602pt too high) has occurred while \output is active []
2669
2670
2671[1759] [1760] [1761] [1762] [1763]
2672Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
2673\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
2674n-den-cies (de-
2675 []
2676
2677[1764]
2678Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
2679[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
2680erse de-pen-den-cies
2681 []
2682
2683
2684Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
2685[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
2686pre-vi-ous
2687 []
2688
2689
2690Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
2691[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing
2692
2693 []
2694
2695
2696Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
2697\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
2698i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
2699 []
2700
2701[1765] [1766] [1767] [1768] [1769]
2702Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
2703[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
2704its func-tion-al-ity in-te-grated into that of
2705 []
2706
2707[1770] [1771]
2708Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
2709[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
2710 sub-set of
2711 []
2712
2713[1772]
2714Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
2715[]\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br
2716ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see
2717 []
2718
2719[1773] [1774] [1775]pdfTeX warning (ext4): destination with the same identifier
2720 (name{Rfn.GSC}) has been already used, duplicate ignored
2721<to be read again> 
2722                   \relax 
2723l.1899 \aliasA{GSC}{find\_gs\_cmd}{GSC}
2724                                       pdfTeX warning (ext4): destination with 
2725the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig
2726nored
2727<to be read again> 
2728                   \relax 
2729l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
2730                                                   [1776] [1777] [1778]
2731[1779]
2732Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
2733 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
2734ogo.svg}{options: width=100}",[] 
2735 []
2736
2737[1780] [1781] [1782]
2738Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
2739[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
2740 sub-set of
2741 []
2742
2743[1783] [1784] [1785] [1786] [1787] [1788] [1789]
2744
2745LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
2746(Font)              using `T1/zi4/m/n' instead on input line 2837.
2747
2748LaTeX Font Info:    Font shape `T1/zi4/m/sl' will be
2749(Font)              scaled to size 10.0pt on input line 2838.
2750[1790] [1791] [1792] [1793]
2751Underfull \hbox (badness 1424) in paragraph at lines 3119--3121
2752[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
2753or of links, as re-turned by
2754 []
2755
2756[1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803]
2757Underfull \hbox (badness 10000) in paragraph at lines 3825--3827
2758[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
2759,
2760 []
2761
2762[1804] [1805]
2763Underfull \hbox (badness 10000) in paragraph at lines 3963--3966
2764[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
2765and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
2766 []
2767
2768[1806] [1807]
2769Underfull \hbox (badness 1137) in paragraph at lines 4065--4067
2770[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
2771 sys-tem, as from
2772 []
2773
2774[1808] [1809] [1810]
2775Underfull \hbox (badness 1838) in paragraph at lines 4277--4283
2776[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
2777o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
2778 The
2779 []
2780
2781
2782Underfull \hbox (badness 10000) in paragraph at lines 4277--4283
2783\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
2784the pack-age are ex-am-ined to cre-ate a file
2785 []
2786
2787[1811] [1812] [1813]
2788Underfull \hbox (badness 2197) in paragraph at lines 4493--4503
2789[]\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
2790/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :
2791 []
2792
2793[1814]
2794Underfull \hbox (badness 1571) in paragraph at lines 4556--4560
2795[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
2796load speed and time spent by
2797 []
2798
2799[1815] [1816] [1817]) (utils-pkg.tex [1818
2800
2801
2802]
2803Chapter 14.
2804
2805Underfull \hbox (badness 2556) in paragraph at lines 47--52
2806[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
28071/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
2808 []
2809
2810[1819] [1820] [1821] [1822] [1823]
2811Underfull \hbox (badness 10000) in paragraph at lines 376--381
2812\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
2813tm/m/n/10 with
2814 []
2815
2816[1824] [1825] [1826] [1827] [1828]
2817Underfull \hbox (badness 10000) in paragraph at lines 717--723
2818[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
28190 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
2820 []
2821
2822
2823Underfull \hbox (badness 3343) in paragraph at lines 717--723
2824\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
2825l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
2826 []
2827
2828[1829] [1830]
2829Underfull \hbox (badness 5847) in paragraph at lines 850--856
2830[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
2831 se-lect which of the pack-ages on the repos-i-to-
2832 []
2833
2834
2835Underfull \hbox (badness 4229) in paragraph at lines 850--856
2836\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
28374/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
2838 []
2839
2840[1831]
2841Underfull \hbox (badness 3861) in paragraph at lines 918--923
2842[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
2843S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
284410 "License_is_FOSS"\T1/ptm/m/n/10 ,
2845 []
2846
2847[1832] [1833] [1834]
2848Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
2849[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
28500 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
2851/ptm/m/n/10 , in-di-cat-
2852 []
2853
2854
2855Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
2856\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
2857or-mat-
2858 []
2859
2860
2861Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
2862\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
2863han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is
2864 []
2865
2866
2867Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
2868\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
2869x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.
2870 []
2871
2872
2873Underfull \hbox (badness 1817) in paragraph at lines 1089--1097
2874\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
2875ault by
2876 []
2877
2878
2879Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
2880[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
2881 []
2882
2883[1835] [1836] [1837] [1838] [1839] [1840] [1841]
2884Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
2885[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
28861/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
2887 []
2888
2889[1842] [1843] [1844] [1845] [1846] [1847] [1848] [1849] [1850]
2890Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
2891[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
2892is func-tion is in-voked for its side ef-fect of up-dat-ing
2893 []
2894
2895[1851] [1852] [1853] [1854] [1855]pdfTeX warning (ext4): destination with the s
2896ame identifier (name{Rfn.clipboard}) has been already used, duplicate ignored
2897<to be read again> 
2898                   \relax 
2899l.2566 ... the Clipboard in MS Windows}{clipboard}
2900                                                   [1856] [1857]
2901Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
2902[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
2903/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
2904/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
2905 []
2906
2907[1858] [1859] [1860] [1861] [1862] [1863]
2908Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
2909[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
2910m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
2911us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header =
2912 []
2913
2914
2915Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
2916[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
29174/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
2918[][](...,header = TRUE,sep =
2919 []
2920
2921[1864] [1865] [1866] [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874]
2922Underfull \hbox (badness 1430) in paragraph at lines 3915--3923
2923[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
2924 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
2925 []
2926
2927[1875]
2928Underfull \hbox (badness 1231) in paragraph at lines 3992--4004
2929[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
2930via en-vi-ron-ment vari-able
2931 []
2932
2933[1876] [1877]
2934Underfull \hbox (badness 10000) in paragraph at lines 4152--4154
2935[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
2936nload.file[][][] \T1/ptm/m/n/10 and
2937 []
2938
2939[1878] [1879] [1880] [1881] [1882] [1883] [1884] [1885] [1886] [1887] [1888]pdf
2940TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has
2941 been already used, duplicate ignored
2942<to be read again> 
2943                   \relax 
2944l.4850 ...mat Unordered and Ordered Lists}{format}
2945                                                  pdfTeX warning (ext4): destin
2946ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
2947icate ignored
2948<to be read again> 
2949                   \relax 
2950l.4850 ...mat Unordered and Ordered Lists}{format}
2951                                                   [1889] [1890] [1891]
2952[1892] [1893] [1894] [1895] [1896]
2953Underfull \hbox (badness 1622) in paragraph at lines 5369--5373
2954[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
2955 to ex-ter-nal GUIs or to the
2956 []
2957
2958[1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905]
2959Underfull \hbox (badness 1371) in paragraph at lines 6005--6007
2960[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
29611/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
2962 []
2963
2964[1906]
2965Underfull \hbox (badness 1502) in paragraph at lines 6094--6099
2966[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
2967'. `Key-
2968 []
2969
2970
2971Underfull \hbox (badness 2103) in paragraph at lines 6094--6099
2972\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
2973listed in file
2974 []
2975
2976[1907] [1908] [1909]
2977Underfull \hbox (badness 10000) in paragraph at lines 6267--6276
2978[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
2979x,
2980 []
2981
2982[1910]
2983Underfull \hbox (badness 2150) in paragraph at lines 6331--6334
2984[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
2985to search. See
2986 []
2987
2988[1911]
2989Underfull \hbox (badness 3118) in paragraph at lines 6462--6464
2990[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
2991Lock-ing' in the help for
2992 []
2993
2994[1912] [1913] [1914]
2995Underfull \hbox (badness 1325) in paragraph at lines 6626--6630
2996[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
2997es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able
2998 []
2999
3000
3001Underfull \hbox (badness 4726) in paragraph at lines 6638--6644
3002\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
3003 a char-ac-ter vec-tor, a sub-set of
3004 []
3005
3006
3007Underfull \hbox (badness 10000) in paragraph at lines 6710--6713
3008[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
3009 be
3010 []
3011
3012
3013Underfull \hbox (badness 10000) in paragraph at lines 6710--6713
3014\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
3015rce pack-age in-stall. E.g.,
3016 []
3017
3018[1915]
3019Underfull \hbox (badness 3219) in paragraph at lines 6786--6793
3020[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
302110 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
3022 []
3023
3024
3025Underfull \hbox (badness 5175) in paragraph at lines 6786--6793
3026\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
3027 are source pack-ages
3028 []
3029
3030
3031Underfull \hbox (badness 1342) in paragraph at lines 6786--6793
3032\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
3033-piled is con-trolled by
3034 []
3035
3036
3037Underfull \hbox (badness 1596) in paragraph at lines 6786--6793
3038[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
3039ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently
3040 []
3041
3042[1916]
3043Underfull \hbox (badness 2932) in paragraph at lines 6794--6797
3044[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
3045/n/10 al-ways works pro-vided the pack-age con-tains no
3046 []
3047
3048[1917]
3049Underfull \hbox (badness 10000) in paragraph at lines 6928--6933
3050[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
3051 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
3052[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
305310 ,
3054 []
3055
3056[1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928]
3057[1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939]
3058[1940]
3059Underfull \hbox (badness 10000) in paragraph at lines 8429--8431
3060[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
30614/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from
3062 []
3063
3064[1941]
3065Underfull \hbox (badness 2310) in paragraph at lines 8451--8456
3066[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
3067 given pack-age is found and can suc-cess-fully be read,
3068 []
3069
3070[1942] [1943] [1944] [1945] [1946] [1947] [1948]
3071Underfull \hbox (badness 1248) in paragraph at lines 8975--8979
3072[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
3073n/10 source tar-balls. The name(s) of the pack-ages are taken from the
3074 []
3075
3076[1949]
3077Underfull \hbox (badness 1789) in paragraph at lines 9053--9055
3078[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
3079 more dis-cus-sion of the
3080 []
3081
3082[1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958]
3083Underfull \vbox (badness 5533) has occurred while \output is active []
3084
3085 [1959]
3086[1960] [1961]
3087Underfull \hbox (badness 1097) in paragraph at lines 9890--9893
3088[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
3089e used on Win-dows, in which case
3090 []
3091
3092[1962] [1963]
3093Underfull \hbox (badness 3000) in paragraph at lines 10026--10031
3094[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
3095rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
3096read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
3097dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
3098able[][][]\T1/ptm/m/n/10 ;
3099 []
3100
3101[1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971]
3102Underfull \hbox (badness 2134) in paragraph at lines 10609--10614
3103[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
3104rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
3105read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
3106dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
3107table[][][]\T1/ptm/m/n/10 ;
3108 []
3109
3110[1972]
3111Underfull \hbox (badness 10000) in paragraph at lines 10665--10670
3112[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for
3113
3114 []
3115
3116
3117Underfull \hbox (badness 10000) in paragraph at lines 10665--10670
3118\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
3119_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
3120 []
3121
3122[1973] [1974] [1975] [1976] [1977] [1978] [1979]
3123Underfull \hbox (badness 2469) in paragraph at lines 11139--11143
3124[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
3125, The Free En-cy-clo-pe-dia.
3126 []
3127
3128
3129Underfull \hbox (badness 3428) in paragraph at lines 11139--11143
3130[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
3131 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
3132 []
3133
3134[1980] [1981] [1982] [1983]
3135Underfull \hbox (badness 4060) in paragraph at lines 11443--11446
3136[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
3137used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
3138i-able
3139 []
3140
3141[1984]
3142Overfull \hbox (18.77168pt too wide) in paragraph at lines 11471--11471
3143 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
3144aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
3145 []
3146
3147[1985] [1986] [1987]
3148Underfull \hbox (badness 2150) in paragraph at lines 11710--11712
3149[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
3150ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
3151s / manual /
3152 []
3153
3154[1988] [1989] [1990] [1991]
3155Underfull \hbox (badness 10000) in paragraph at lines 11929--11933
3156[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
3157ow taken from the en-vi-ron-ment vari-able
3158 []
3159
3160
3161Underfull \hbox (badness 10000) in paragraph at lines 11960--11966
3162[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
3163ou can add a
3164 []
3165
3166[1992] [1993]
3167Underfull \hbox (badness 1009) in paragraph at lines 12154--12166
3168[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
3169tions can be ex-e-cuted. If
3170 []
3171
3172[1994]
3173Underfull \hbox (badness 4779) in paragraph at lines 12191--12193
3174[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
3175s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
3176nd
3177 []
3178
3179
3180Underfull \hbox (badness 1077) in paragraph at lines 12221--12228
3181\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
3182er-sonal' di-rec-tory, oth-er-wise to
3183 []
3184
3185[1995] [1996] [1997] [1998] [1999] [2000]
3186Underfull \hbox (badness 3780) in paragraph at lines 12622--12626
3187[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
3188/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via
3189 []
3190
3191
3192Underfull \hbox (badness 2635) in paragraph at lines 12638--12641
3193[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
3194e-cially: the value is taken from the cur-rent set-ting of
3195 []
3196
3197[2001] [2002] [2003]
3198Underfull \hbox (badness 2302) in paragraph at lines 12842--12844
3199[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
3200o the Win-dows API call
3201 []
3202
3203[2004] [2005] [2006] [2007] [2008]
3204Underfull \hbox (badness 10000) in paragraph at lines 13138--13143
3205[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
3206[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
3207 []
3208
3209
3210Underfull \hbox (badness 5970) in paragraph at lines 13147--13150
3211[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
3212ive
3213 []
3214
3215[2009]
3216Underfull \vbox (badness 10000) has occurred while \output is active []
3217
3218 [2010]
3219[2011] [2012] [2013] [2014]
3220Underfull \hbox (badness 2932) in paragraph at lines 13567--13574
3221[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
3222 then the avail-able syn-tax ob-jects are con-sulted in turn,
3223 []
3224
3225
3226Underfull \hbox (badness 1688) in paragraph at lines 13567--13574
3227\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
3228com-po-nent matches (as a reg-exp) the file name. Ob-
3229 []
3230
3231[2015] [2016] [2017] [2018]
3232Underfull \hbox (badness 6510) in paragraph at lines 13876--13880
3233[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
3234he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
3235ble
3236 []
3237
3238
3239Underfull \hbox (badness 10000) in paragraph at lines 13883--13886
3240[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
3241format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
3242 org /
3243 []
3244
3245
3246Underfull \hbox (badness 2245) in paragraph at lines 13883--13886
3247\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
32482 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
3249 []
3250
3251[2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027]
3252Underfull \hbox (badness 10000) in paragraph at lines 14547--14552
3253[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
3254T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to
3255 []
3256
3257
3258Underfull \hbox (badness 3861) in paragraph at lines 14547--14552
3259[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
3260gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
3261/10 and
3262 []
3263
3264[2028]
3265Underfull \hbox (badness 1052) in paragraph at lines 14553--14555
3266[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
3267 in-stall. See
3268 []
3269
3270
3271Underfull \hbox (badness 10000) in paragraph at lines 14612--14615
3272[][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
32730 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package
3274s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n
3275/10 ,
3276 []
3277
3278[2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039]
3279[2040]
3280Underfull \hbox (badness 10000) in paragraph at lines 15385--15387
3281[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
3282tion e.g. \T1/zi4/m/sl/10 file =
3283 []
3284
3285[2041] [2042] [2043]) [2044
3286
3287
3288] [2045] [2046] (KernSmooth-pkg.tex
3289Chapter 15.
3290[2047
3291
3292] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056])
3293(MASS-pkg.tex
3294Chapter 16.
3295[2057
3296
3297
3298] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067]
3299[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078]
3300[2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089]
3301[2090] [2091] [2092] [2093]
3302Underfull \hbox (badness 7944) in paragraph at lines 2694--2697
3303[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an
3304d graph-i-cal pa-ram-e-ters. Note that
3305 []
3306
3307[2094] [2095] [2096]
3308Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
3309\T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm
3310/m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic
3311"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative
3312 []
3313
3314[2097] [2098]
3315Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
3316[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
3317na-tor ex-ceeds
3318 []
3319
3320[2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109]
3321[2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120]
3322[2121] [2122] [2123]
3323Underfull \hbox (badness 1117) in paragraph at lines 4791--4794
3324[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
3325rm \T1/zi4/m/sl/10 response ~
3326 []
3327
3328[2124]
3329Underfull \hbox (badness 1117) in paragraph at lines 4869--4872
3330[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
3331rm \T1/zi4/m/sl/10 response ~
3332 []
3333
3334[2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135]
3335[2136] [2137] [2138] [2139] [2140] [2141]pdfTeX warning (ext4): destination wit
3336h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored
3337<to be read again> 
3338                   \relax 
3339l.6111 ...sical N, P, K Factorial Experiment}{npk}
3340                                                  pdfTeX warning (ext4): destin
3341ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
3342te ignored
3343<to be read again> 
3344                   \relax 
3345l.6111 ...sical N, P, K Factorial Experiment}{npk}
3346                                                   [2142] [2143] [2144]
3347[2145] [2146]
3348Underfull \vbox (badness 10000) has occurred while \output is active []
3349
3350 [2147]
3351[2148] [2149] [2150] [2151] [2152] [2153] [2154]
3352Underfull \hbox (badness 1117) in paragraph at lines 7078--7085
3353[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
3354rm \T1/zi4/m/sl/10 response ~
3355 []
3356
3357[2155]
3358Underfull \hbox (badness 3138) in paragraph at lines 7149--7155
3359[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
3360s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
3361mr/m/n/10 ) =
3362 []
3363
3364[2156] [2157] [2158]
3365Underfull \hbox (badness 6775) in paragraph at lines 7328--7331
3366\T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n
3367ant com-po-nents are used (ex-cept for
3368 []
3369
3370[2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167]
3371Underfull \hbox (badness 4686) in paragraph at lines 7961--7963
3372[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
3373na-tor ex-ceeds
3374 []
3375
3376[2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178]
3377[2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189]
3378[2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200]
3379[2201] [2202] [2203] [2204]) (Matrix-pkg.tex
3380Chapter 17.
3381
3382Underfull \hbox (badness 10000) in paragraph at lines 41--44
3383[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
3384t to change, and if you
3385 []
3386
3387
3388Underfull \hbox (badness 10000) in paragraph at lines 41--44
3389\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
3390age main-tain-ers
3391 []
3392
3393[2205
3394
3395
3396]
3397Underfull \hbox (badness 1769) in paragraph at lines 95--98
3398[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
3399wn code. Please con-tact us
3400 []
3401
3402[2206] [2207] [2208] [2209]
3403Underfull \hbox (badness 5119) in paragraph at lines 508--512
3404[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
3405g from class
3406 []
3407
3408[2210] [2211]
3409Underfull \hbox (badness 2418) in paragraph at lines 597--600
3410[]\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f
3411rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z
3412i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a
3413 []
3414
3415[2212] [2213] [2214] [2215] [2216]
3416Underfull \hbox (badness 10000) in paragraph at lines 1022--1024
3417[]\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n
3418/10 (or equiv-a-lently, \T1/zi4/m/sl/10 to =
3419 []
3420
3421[2217] [2218]pdfTeX warning (ext4): destination with the same identifier (name{
3422Rfn.chol}) has been already used, duplicate ignored
3423<to be read again> 
3424                   \relax 
3425l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
3426                                                  pdfTeX warning (ext4): destin
3427ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
3428ate ignored
3429<to be read again> 
3430                   \relax 
3431l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
3432                                                  
3433Underfull \hbox (badness 1117) in paragraph at lines 1189--1195
3434\T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc
3435h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t
3436he same al-go-rithm
3437 []
3438
3439[2219pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol
3440,dsCMatrix.Rdash.method}) has been already used, duplicate ignored
3441
3442\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
3443                                                  \fi \fi 
3444l.1209 \item[chol]
3445                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
3446ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth
3447od}) has been already used, duplicate ignored
3448
3449\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
3450                                                  \fi \fi 
3451l.1209 \item[chol]
3452                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
3453ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth
3454od}) has been already used, duplicate ignored
3455
3456\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
3457                                                  \fi \fi 
3458l.1209 \item[chol]
3459                   \code{signature(x = "dgeMatrix")}: works via] [2220]
3460[2221]
3461Underfull \hbox (badness 2277) in paragraph at lines 1388--1391
3462[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
3463-ent types of ma-tri-ces. Use
3464 []
3465
3466[2222] [2223]
3467Underfull \hbox (badness 1097) in paragraph at lines 1560--1563
3468[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and
3469 \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 "
3470dgeMatrix"\T1/ptm/m/n/10 , by class
3471 []
3472
3473
3474Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
3475[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
3476/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
3477 []
3478
3479[2224]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
3480Sums}) has been already used, duplicate ignored
3481<to be read again> 
3482                   \relax 
3483l.1623 ... Row and Column Sums and Means}{colSums}
3484                                                  pdfTeX warning (ext4): destin
3485ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
3486licate ignored
3487<to be read again> 
3488                   \relax 
3489l.1623 ... Row and Column Sums and Means}{colSums}
3490                                                  pdfTeX warning (ext4): destin
3491ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
3492icate ignored
3493<to be read again> 
3494                   \relax 
3495l.1624 \aliasA{colMeans}{colSums}{colMeans}
3496                                           pdfTeX warning (ext4): destination w
3497ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
3498gnored
3499<to be read again> 
3500                   \relax 
3501l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
3502                                           pdfTeX warning (ext4): destination w
3503ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
3504nored
3505<to be read again> 
3506                   \relax 
3507l.1656 \aliasA{rowSums}{colSums}{rowSums}
3508                                          [2225] [2226] [2227]
3509Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
3510[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
3511 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
3512 []
3513
3514[2228] [2229] [2230] [2231] [2232]
3515Underfull \hbox (badness 1360) in paragraph at lines 2295--2299
3516[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n
3517ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via
3518 []
3519
3520[2233] [2234] [2235] [2236]
3521Underfull \hbox (badness 2368) in paragraph at lines 2610--2614
3522[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
3523n more than one pos-si-ble
3524 []
3525
3526[2237] [2238]
3527Underfull \hbox (badness 6842) in paragraph at lines 2700--2703
3528[]\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T
35291/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[]
3530[][] \T1/ptm/m/n/10 (with ``su-per-class''
3531 []
3532
3533[2239]
3534Underfull \hbox (badness 10000) in paragraph at lines 2986--2990
3535[]\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro
3536up meth-ods re-turn a
3537 []
3538
3539[2240] [2241] [2242]
3540Underfull \hbox (badness 1173) in paragraph at lines 3196--3198
3541[]\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t
3542his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and
3543 []
3544
3545
3546Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
3547[][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre
3548fer-able to (and more ef-fi-cient than)
3549 []
3550
3551[2243] [2244]
3552Underfull \hbox (badness 1354) in paragraph at lines 3442--3445
3553[]\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex
3554-plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in
3555-her-it-ing from
3556 []
3557
3558[2245] [2246] [2247] [2248] [2249]
3559Underfull \hbox (badness 6188) in paragraph at lines 3852--3855
3560[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
3561 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =
3562 []
3563
3564
3565Underfull \hbox (badness 5147) in paragraph at lines 3855--3858
3566[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
3567 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =
3568 []
3569
3570[2250] [2251]
3571Underfull \hbox (badness 2318) in paragraph at lines 3969--3973
3572[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C
3573lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi
35744/m/sl/10 "dMatrix"\T1/ptm/m/n/10 ,
3575 []
3576
3577[2252] [2253]
3578Underfull \hbox (badness 5245) in paragraph at lines 4105--4109
3579[]\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1
35800 : the [][]\T1/zi4/m/sl/10 determinant[][][](x)
3581 []
3582
3583[2254] [2255] [2256] [2257] [2258] [2259]
3584Overfull \hbox (3.77782pt too wide) in paragraph at lines 4527--4527
3585 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
3586Boeing/msc00726.tar.gz"))))[] 
3587 []
3588
3589
3590Overfull \hbox (48.77782pt too wide) in paragraph at lines 4530--4530
3591 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
3592ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
3593 []
3594
3595[2260] [2261]
3596Underfull \hbox (badness 1931) in paragraph at lines 4762--4764
3597[]\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/
3598ptm/m/n/10 codes should be aligned, see
3599 []
3600
3601[2262] [2263] [2264] [2265] [2266]
3602Underfull \hbox (badness 1005) in paragraph at lines 5068--5073
3603[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA 
3604\T1/ptm/m/n/10 means no bor-der is drawn.
3605 []
3606
3607
3608Underfull \hbox (badness 1655) in paragraph at lines 5068--5073
3609\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4
3610/m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is
3611 []
3612
3613
3614Underfull \hbox (badness 5862) in paragraph at lines 5087--5090
3615[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
3616]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
3617 []
3618
3619[2267]
3620Overfull \hbox (42.75635pt too wide) in paragraph at lines 5134--5134
3621 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
3622der.col = adjustcolor("skyblue", 1/2))[] 
3623 []
3624
3625[2268]
3626Underfull \hbox (badness 3229) in paragraph at lines 5235--5244
3627[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
3628r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
3629 the
3630 []
3631
3632
3633Underfull \hbox (badness 10000) in paragraph at lines 5277--5279
3634[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot
3635her sig-na-tures (use
3636 []
3637
3638[2269]
3639Underfull \hbox (badness 4995) in paragraph at lines 5282--5285
3640[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : 
3641a user con-ve-nience, to al-low
3642 []
3643
3644
3645Underfull \hbox (badness 10000) in paragraph at lines 5292--5295
3646[]\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c
3647o-er-cion to a tra-di-tional
3648 []
3649
3650[2270] [2271] [2272] [2273] [2274]
3651Underfull \hbox (badness 1014) in paragraph at lines 5669--5672
3652[]\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10
3653 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10
3654 is a tri-an-gu-lar ma-trix. Anal-o-gously,
3655 []
3656
3657[2275] [2276] [2277] [2278]
3658Underfull \hbox (badness 10000) in paragraph at lines 5984--5987
3659[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
3660 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
3661 []
3662
3663[2279]
3664Underfull \hbox (badness 2478) in paragraph at lines 6096--6101
3665[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly
3666. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde
3667nseMatrix"\T1/ptm/m/n/10 . Class
3668 []
3669
3670[2280]
3671Underfull \hbox (badness 10000) in paragraph at lines 6104--6107
3672[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
3673 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
3674use, e.g.,
3675 []
3676
3677[2281]
3678Underfull \hbox (badness 10000) in paragraph at lines 6296--6299
3679[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
3680y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
3681 []
3682
3683[2282]
3684Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
3685[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
3686 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
3687se, e.g.,
3688 []
3689
3690[2283]
3691Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
3692[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
3693 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
3694se, e.g.,
3695 []
3696
3697[2284]
3698Underfull \hbox (badness 2050) in paragraph at lines 6545--6548
3699[]\T1/zi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth
3700-ods for dif-fer-ent types of ma-tri-ces. Use
3701 []
3702
3703[2285] [2286] [2287]
3704Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
3705[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
3706e-mat-i-cally''),
3707 []
3708
3709[2288]
3710Underfull \hbox (badness 6268) in paragraph at lines 6775--6779
3711[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
3712/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1
37130 . How-ever,
3714 []
3715
3716[2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
3717}) has been already used, duplicate ignored
3718<to be read again> 
3719                   \relax 
3720l.6868 \aliasA{det}{Matrix-class}{det}
3721                                      
3722Underfull \hbox (badness 1527) in paragraph at lines 6961--6963
3723[]\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \
3724T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode
3725 []
3726
3727
3728Underfull \hbox (badness 4846) in paragraph at lines 6966--6969
3729[]\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1
3730/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing
3731 []
3732
3733
3734Underfull \hbox (badness 10000) in paragraph at lines 6971--6974
3735
3736 []
3737
3738[2290]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
3739cent.*.Rpcent.}) has been already used, duplicate ignored
3740<to be read again> 
3741                   \relax 
3742l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
3743                                                  pdfTeX warning (ext4): destin
3744ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
3745licate ignored
3746<to be read again> 
3747                   \relax 
3748l.7152 ...A{crossprod}{matrix-products}{crossprod}
3749                                                  pdfTeX warning (ext4): destin
3750ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
3751plicate ignored
3752<to be read again> 
3753                   \relax 
3754l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
3755                                                   [2291pdfTeX warning (ext4): 
3756destination with the same identifier (name{Rfn.crossprod.Rdash.methods}) has be
3757en already used, duplicate ignored
3758
3759\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
3760                                                  \fi \fi 
3761l.7356 
3762       pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc
3763rossprod.Rdash.methods}) has been already used, duplicate ignored
3764
3765\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
3766                                                  \fi \fi 
3767l.7356 
3768       ] [2292]
3769Underfull \hbox (badness 10000) in paragraph at lines 7426--7431
3770[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
3771her sig-na-tures (use
3772 []
3773
3774
3775Underfull \hbox (badness 1448) in paragraph at lines 7426--7431
3776\T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m
3777ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of
3778 []
3779
3780
3781Underfull \hbox (badness 10000) in paragraph at lines 7435--7437
3782[]\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
3783e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an
3784 []
3785
3786
3787Underfull \hbox (badness 10000) in paragraph at lines 7437--7439
3788[]\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
3789e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an
3790 []
3791
3792
3793Underfull \hbox (badness 1264) in paragraph at lines 7441--7442
3794[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
3795her sig-na-tures, see
3796 []
3797
3798[2293] [2294]
3799Underfull \hbox (badness 1430) in paragraph at lines 7585--7590
3800[]\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio
3801n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1
3802/zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][]
3803\T1/ptm/m/n/10 , and
3804 []
3805
3806[2295]
3807Underfull \hbox (badness 10000) in paragraph at lines 7656--7659
3808[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
3809 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
3810 []
3811
3812[2296]
3813Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
3814[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/
3815ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X
3816 []
3817
3818[2297] [2298]
3819Underfull \vbox (badness 10000) has occurred while \output is active []
3820
3821 [2299]
3822Underfull \hbox (badness 2478) in paragraph at lines 7911--7916
3823[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly
3824. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde
3825nseMatrix"\T1/ptm/m/n/10 . Class
3826 []
3827
3828
3829Underfull \hbox (badness 10000) in paragraph at lines 7919--7922
3830[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
3831 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
3832use, e.g.,
3833 []
3834
3835[2300] [2301]
3836Underfull \hbox (badness 5924) in paragraph at lines 8113--8115
3837[]\T1/ptm/m/n/10 fast sim-ple meth-ods
3838 []
3839
3840[2302]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
3841m}) has been already used, duplicate ignored
3842<to be read again> 
3843                   \relax 
3844l.8153 \HeaderA{norm}{Matrix Norms}{norm}
3845                                         pdfTeX warning (ext4): destination wit
3846h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
3847ed
3848<to be read again> 
3849                   \relax 
3850l.8153 \HeaderA{norm}{Matrix Norms}{norm}
3851                                          [2303] [2304]
3852Underfull \hbox (badness 10000) in paragraph at lines 8426--8429
3853[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
3854y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
3855 []
3856
3857[2305]
3858Underfull \hbox (badness 10000) in paragraph at lines 8516--8519
3859[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
3860 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
3861se, e.g.,
3862 []
3863
3864[2306]
3865Underfull \hbox (badness 10000) in paragraph at lines 8592--8595
3866[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
3867 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
3868se, e.g.,
3869 []
3870
3871[2307]
3872Underfull \vbox (badness 10000) has occurred while \output is active []
3873
3874 [2308]
3875Underfull \hbox (badness 10000) in paragraph at lines 8718--8720
3876[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe
3877r sig-na-tures (use
3878 []
3879
3880
3881Underfull \hbox (badness 10000) in paragraph at lines 8723--8726
3882[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a 
3883user con-ve-nience, to al-low
3884 []
3885
3886[2309] [2310] [2311] [2312]pdfTeX warning (ext4): destination with the same ide
3887ntifier (name{Rfn.qr}) has been already used, duplicate ignored
3888<to be read again> 
3889                   \relax 
3890l.8955 \aliasA{qr}{qr-methods}{qr}
3891                                   [2313] [2314] [2315] [2316]pdfTeX warning (e
3892xt4): destination with the same identifier (name{Rfn.rcond}) has been already u
3893sed, duplicate ignored
3894<to be read again> 
3895                   \relax 
3896l.9251 ... the Reciprocal Condition Number}{rcond}
3897                                                   [2317] [2318] [2319]
3898[2320]
3899Underfull \hbox (badness 2351) in paragraph at lines 9555--9563
3900[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
3901\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
3902 via one di-men-sional
3903 []
3904
3905
3906Underfull \hbox (badness 1852) in paragraph at lines 9555--9563
3907\T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][](
3908nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 
3909is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 ---
3910 []
3911
3912
3913Underfull \hbox (badness 2343) in paragraph at lines 9555--9563
3914\T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls []
3915[]\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z
3916i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 ,
3917 []
3918
3919[2321] [2322] [2323] [2324]pdfTeX warning (ext4): destination with the same ide
3920ntifier (name{Rfn.solve}) has been already used, duplicate ignored
3921<to be read again> 
3922                   \relax 
3923l.9828 \aliasA{solve}{solve-methods}{solve}
3924                                            [2325]
3925Underfull \hbox (badness 10000) in paragraph at lines 9991--9998
3926[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse =
3927 []
3928
3929[2326]
3930Underfull \hbox (badness 4403) in paragraph at lines 10052--10055
3931[]\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing 
3932\T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and
3933 []
3934
3935
3936Underfull \hbox (badness 10000) in paragraph at lines 10122--10125
3937[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
3938la and data frame
3939 []
3940
3941[2327]
3942Underfull \hbox (badness 10000) in paragraph at lines 10158--10161
3943[]\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co
3944-er-ca-ble to)
3945 []
3946
3947
3948Underfull \hbox (badness 10000) in paragraph at lines 10169--10173
3949[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
3950
3951 []
3952
3953[2328] [2329] [2330] [2331] [2332] [2333] [2334] [2335]
3954Underfull \hbox (badness 10000) in paragraph at lines 10757--10765
3955[]\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 
3956: Co-er-cion of a fac-tor to
3957 []
3958
3959
3960Underfull \hbox (badness 1112) in paragraph at lines 10757--10765
3961\T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca
3962-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class
3963 []
3964
3965[2336]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
3966Q}) has been already used, duplicate ignored
3967<to be read again> 
3968                   \relax 
3969l.10823 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
3970                                            [2337] [2338]
3971Underfull \hbox (badness 5036) in paragraph at lines 11009--11011
3972[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
3973 a
3974 []
3975
3976[2339] [2340]
3977Underfull \hbox (badness 10000) in paragraph at lines 11215--11218
3978[]\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/
3979m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
3980 []
3981
3982[2341]
3983Underfull \vbox (badness 10000) has occurred while \output is active []
3984
3985 [2342]
3986[2343] [2344]
3987Underfull \hbox (badness 10000) in paragraph at lines 11484--11489
3988[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/
3989sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
3990 []
3991
3992[2345]
3993Underfull \hbox (badness 2057) in paragraph at lines 11564--11566
3994[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
3995r-ent ma-trix classes, use e.g.,
3996 []
3997
3998[2346] [2347]
3999Underfull \hbox (badness 1831) in paragraph at lines 11739--11745
4000[]\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1
4001/zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar
4002e de-fined
4003 []
4004
4005[2348]
4006Underfull \hbox (badness 1902) in paragraph at lines 11774--11778
4007[]\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m
4008/sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] 
4009\T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a
4010nd other
4011 []
4012
4013[2349] [2350] [2351] [2352] [2353] [2354]
4014Underfull \hbox (badness 6910) in paragraph at lines 12287--12289
4015[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
4016 []
4017
4018[2355] [2356] [2357]) (boot-pkg.tex [2358
4019
4020
4021]
4022Chapter 18.
4023[2359] [2360] [2361] [2362] [2363] [2364] [2365] [2366] [2367] [2368]
4024Underfull \hbox (badness 1297) in paragraph at lines 797--807
4025[]\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce
4026sses, the de-fault be-haviour
4027 []
4028
4029[2369]
4030Underfull \hbox (badness 1881) in paragraph at lines 824--826
4031[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
4032-cient boot-strap sim-u-la-tion.
4033 []
4034
4035[2370]
4036Underfull \vbox (badness 10000) has occurred while \output is active []
4037
4038 [2371]
4039[2372]
4040Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
4041[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
4042n-ter-
4043 []
4044
4045
4046Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
4047\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
4048 []
4049
4050
4051Underfull \hbox (badness 1859) in paragraph at lines 1066--1070
4052\T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
4053 \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will
4054 []
4055
4056[2373]
4057Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
4058[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
4059ult value is
4060 []
4061
4062[2374] [2375] [2376] [2377]
4063Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
4064[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
4065al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
4066 []
4067
4068[2378] [2379] [2380] [2381] [2382] [2383]
4069Underfull \hbox (badness 1005) in paragraph at lines 1797--1804
4070[]\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 "
4071ordinary" \T1/ptm/m/n/10 (case re-sam-pling),
4072 []
4073
4074[2384] [2385]
4075Underfull \vbox (badness 10000) has occurred while \output is active []
4076
4077 [2386]
4078Underfull \hbox (badness 7379) in paragraph at lines 2081--2083
4079[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
4080an-ning House.
4081 []
4082
4083[2387] [2388] [2389] [2390]
4084Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
4085[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
4086g-i-nal data set
4087 []
4088
4089[2391]
4090Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
4091[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
4092-cient boot-strap sim-u-la-tion.
4093 []
4094
4095[2392] [2393]
4096Underfull \hbox (badness 2970) in paragraph at lines 2533--2537
4097[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/zi4/m/s
4098l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t
4099he sam-ple
4100 []
4101
4102
4103Underfull \hbox (badness 2310) in paragraph at lines 2533--2537
4104\T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl
4105/10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n
4106/10 is used. This is mul-ti-plied by
4107 []
4108
4109[2394] [2395] [2396] [2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404]
4110[2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
4111[2416]
4112Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
4113[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
4114is
4115 []
4116
4117[2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427]
4118Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
4119[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
4120of a call to
4121 []
4122
4123[2428] [2429] [2430] [2431]
4124Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
4125[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
4126boot-strap
4127 []
4128
4129
4130Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
4131\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
4132os-est to
4133 []
4134
4135[2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] [2442]
4136Underfull \hbox (badness 4954) in paragraph at lines 6018--6021
4137[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa
4138ddle.distn"\T1/ptm/m/n/10 . See the help file for
4139 []
4140
4141[2443] [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451]
4142Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
4143[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
4144ent ex-pected by
4145 []
4146
4147[2452] [2453] [2454] [2455] [2456] [2457] [2458] [2459] [2460] [2461])
4148(class-pkg.tex [2462
4149
4150
4151]
4152Chapter 19.
4153[2463] [2464] [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473]
4154[2474] [2475] [2476] [2477] [2478]) (cluster-pkg.tex
4155Chapter 20.
4156[2479
4157
4158
4159] [2480] [2481] [2482] [2483]
4160Underfull \vbox (badness 7777) has occurred while \output is active []
4161
4162 [2484]
4163[2485] [2486] [2487] [2488]
4164Underfull \hbox (badness 4144) in paragraph at lines 688--691
4165[]\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem
4166-ory (and hence time), but dis-ables
4167 []
4168
4169[2489] [2490] [2491]
4170Underfull \hbox (badness 10000) in paragraph at lines 863--865
4171[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
4172le, see
4173 []
4174
4175[2492] [2493]
4176Underfull \hbox (badness 10000) in paragraph at lines 974--976
4177[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
4178 []
4179
4180
4181Underfull \hbox (badness 1342) in paragraph at lines 988--992
4182[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
4183 2012,
4184 []
4185
4186[2494] [2495] [2496]
4187Underfull \hbox (badness 6110) in paragraph at lines 1182--1186
4188[]\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/
4189m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne
4190nt, e.g., for
4191 []
4192
4193[2497] [2498] [2499]
4194Underfull \hbox (badness 10000) in paragraph at lines 1451--1454
4195
4196 []
4197
4198[2500] [2501]
4199Underfull \hbox (badness 2503) in paragraph at lines 1563--1566
4200[]\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or
4201 \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of
4202 []
4203
4204[2502] [2503] [2504] [2505] [2506] [2507] [2508] [2509]
4205Underfull \hbox (badness 10000) in paragraph at lines 2154--2157
4206
4207 []
4208
4209
4210Underfull \hbox (badness 10000) in paragraph at lines 2168--2174
4211[][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the 
4212[][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell
4213ipsoid \T1/ptm/m/n/10 ob-jects.
4214 []
4215
4216[2510] [2511] [2512] [2513]
4217Underfull \hbox (badness 6675) in paragraph at lines 2403--2405
4218[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
4219us-ter-ing, see
4220 []
4221
4222[2514] [2515] [2516] [2517] [2518] [2519] [2520]
4223Underfull \hbox (badness 2980) in paragraph at lines 2871--2875
4224[][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc
4225es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl
4226ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\
4227T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 ,
4228 []
4229
4230[2521] [2522] [2523] [2524] [2525]
4231Underfull \hbox (badness 1142) in paragraph at lines 3212--3215
4232[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
4233ptm/m/n/10 ) may also be sup-plied and are passed to
4234 []
4235
4236[2526] [2527]
4237Underfull \hbox (badness 1142) in paragraph at lines 3331--3334
4238[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
4239ptm/m/n/10 ) may also be sup-plied and are passed to
4240 []
4241
4242[2528] [2529] [2530] [2531]
4243Underfull \hbox (badness 2582) in paragraph at lines 3554--3559
4244[][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
42450 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default
4246[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi
42474/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p
4248tm/m/n/10 ,
4249 []
4250
4251[2532]
4252Underfull \hbox (badness 3209) in paragraph at lines 3616--3621
4253[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi
42544/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which
4255 []
4256
4257
4258Underfull \hbox (badness 8019) in paragraph at lines 3616--3621
4259\T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/
4260m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx
4261 []
4262
4263[2533] [2534] [2535] [2536]
4264Underfull \hbox (badness 10000) in paragraph at lines 3908--3910
4265[]\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T
42661/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for
4267 []
4268
4269[2537] [2538] [2539] [2540]
4270Underfull \hbox (badness 2626) in paragraph at lines 4132--4137
4271[]\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/
4272n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col =
4273 []
4274
4275[2541]
4276Underfull \hbox (badness 1383) in paragraph at lines 4210--4215
4277[]\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m
4278/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T
42791/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial)
4280 []
4281
4282[2542] [2543] [2544] [2545] [2546] [2547] [2548]
4283Underfull \hbox (badness 10000) in paragraph at lines 4638--4640
4284[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
4285`\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side
4286 []
4287
4288[2549]) (codetools-pkg.tex [2550
4289
4290
4291]
4292Chapter 21.
4293[2551] [2552] [2553] [2554] [2555]) (foreign-pkg.tex [2556
4294
4295
4296]
4297Chapter 22.
4298[2557] [2558] [2559] [2560] [2561] [2562] [2563] [2564]
4299Underfull \hbox (badness 10000) in paragraph at lines 506--515
4300[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
4301fer-
4302 []
4303
4304
4305Underfull \hbox (badness 10000) in paragraph at lines 506--515
4306\T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de
4307-fault), the first orig-i-nal value
4308 []
4309
4310
4311Underfull \hbox (badness 10000) in paragraph at lines 506--515
4312\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
4313to
4314 []
4315
4316[2565]
4317Overfull \hbox (6.73795pt too wide) in paragraph at lines 625--625
4318 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
4319R factor labels) are uncomplete,[] 
4320 []
4321
4322[2566] [2567] [2568]
4323Underfull \hbox (badness 10000) in paragraph at lines 813--814
4324
4325 []
4326
4327[2569] [2570] [2571] [2572] [2573] [2574] [2575]
4328Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
4329[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign
4330:::writeForeignStata\T1/ptm/m/n/10 ,
4331 []
4332
4333[2576] [2577]) (lattice-pkg.tex [2578
4334
4335
4336]
4337Chapter 23.
4338[2579] [2580] [2581] [2582] [2583] [2584] [2585] [2586] [2587] [2588] [2589]
4339[2590] [2591] [2592] [2593] [2594]
4340Underfull \hbox (badness 1062) in paragraph at lines 1398--1402
4341\T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta
4342-tion for
4343 []
4344
4345[2595]
4346Underfull \vbox (badness 4416) has occurred while \output is active []
4347
4348 [2596]
4349Underfull \hbox (badness 1803) in paragraph at lines 1566--1583
4350[][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack-
4351age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T
43521/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 ,
4353 []
4354
4355
4356Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
4357[][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p
4358anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p
4359tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
4360/m/sl/10 strip.default[][][]\T1/ptm/m/n/10 ,
4361 []
4362
4363[2597] [2598] [2599]
4364Underfull \hbox (badness 3009) in paragraph at lines 1725--1727
4365[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][
4366][]\T1/ptm/m/n/10 , which may pass them on to
4367 []
4368
4369
4370Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
4371[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
4372assed to
4373 []
4374
4375[2600] [2601] [2602] [2603] [2604]
4376Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
4377[]\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, 
4378the value of
4379 []
4380
4381[2605] [2606] [2607] [2608] [2609] [2610] [2611] [2612] [2613] [2614]
4382Underfull \hbox (badness 2781) in paragraph at lines 2848--2850
4383[]\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col.
4384regions \T1/ptm/m/n/10 ar-gu-ment in
4385 []
4386
4387[2615]
4388Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
4389[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
4390the de-fault panel func-tion
4391 []
4392
4393[2616] [2617] [2618] [2619] [2620] [2621] [2622]pdfTeX warning (ext4): destinat
4394ion with the same identifier (name{Rfn.parallel}) has been already used, duplic
4395ate ignored
4396<to be read again> 
4397                   \relax 
4398l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
4399                                                 [2623] [2624] [2625] [2626]
4400[2627] [2628] [2629]
4401Underfull \hbox (badness 5696) in paragraph at lines 3922--3926
4402[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
4403set-tings
4404 []
4405
4406
4407Underfull \hbox (badness 10000) in paragraph at lines 3922--3926
4408\T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme =
4409 "col.whitebg")\T1/ptm/m/n/10 .
4410 []
4411
4412
4413Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
4414\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
4415ded) set to
4416 []
4417
4418[2630] [2631]
4419Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
4420[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
4421spec-i-fied in
4422 []
4423
4424
4425Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
4426[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
4427s-sued when
4428 []
4429
4430[2632] [2633] [2634]
4431Underfull \hbox (badness 3492) in paragraph at lines 4284--4294
4432[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 
4433is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 ,
4434 []
4435
4436
4437Underfull \hbox (badness 10000) in paragraph at lines 4309--4312
4438[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo
4439t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 ,
4440 []
4441
4442
4443Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
4444[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p
4445lot.polygon \T1/ptm/m/n/10 and
4446 []
4447
4448[2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
4449Underfull \hbox (badness 6157) in paragraph at lines 5035--5038
4450[]\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
4451 via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and
4452 []
4453
4454[2645] [2646] [2647] [2648] [2649] [2650]
4455Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
4456[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
4457-zon-tal.
4458 []
4459
4460
4461Underfull \hbox (badness 5592) in paragraph at lines 5486--5489
4462\T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le
4463ft of pan-els us-ing
4464 []
4465
4466[2651] [2652] [2653] [2654] [2655]
4467Underfull \hbox (badness 4805) in paragraph at lines 5846--5850
4468[]\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should 
4469be high-
4470 []
4471
4472
4473Underfull \hbox (badness 10000) in paragraph at lines 5857--5864
4474[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t
4475ra pa-ram-e-ters are passed on to
4476 []
4477
4478
4479Underfull \hbox (badness 1226) in paragraph at lines 5857--5864
4480\T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi
4481fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as
4482 []
4483
4484
4485Underfull \hbox (badness 2418) in paragraph at lines 5857--5864
4486\T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z
4487i4/m/sl/10 trellis.focus
4488 []
4489
4490
4491Underfull \hbox (badness 10000) in paragraph at lines 5857--5864
4492\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar
4493e used (in com-bi-na-tion with
4494 []
4495
4496
4497Underfull \hbox (badness 1259) in paragraph at lines 5857--5864
4498[][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th
4499e cho-sen view-port if so re-quested.
4500 []
4501
4502[2656] [2657] [2658] [2659]
4503Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
4504[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
4505s pa-ram-e-
4506 []
4507
4508
4509Underfull \hbox (badness 2529) in paragraph at lines 6157--6162
4510\T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there
4511 is no group-ing vari-able, oth-er-wise
4512 []
4513
4514[2660] [2661]
4515Underfull \hbox (badness 2310) in paragraph at lines 6273--6278
4516[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/
451710 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round
4518 if
4519 []
4520
4521[2662] [2663] [2664] [2665] [2666] [2667] [2668] [2669] [2670] [2671] [2672]
4522Underfull \hbox (badness 3168) in paragraph at lines 7055--7059
4523\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U
4524se
4525 []
4526
4527[2673] [2674] [2675] [2676]
4528Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
4529[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
4530-ally passed on to
4531 []
4532
4533[2677] [2678]
4534Underfull \hbox (badness 3333) in paragraph at lines 7498--7500
4535[]\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol
4536 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing
4537 []
4538
4539[2679] [2680] [2681]
4540Underfull \vbox (badness 10000) has occurred while \output is active []
4541
4542 [2682]
4543[2683] [2684]
4544Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
4545[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
4546al pa-ram-e-ters for
4547 []
4548
4549[2685] [2686] [2687] [2688] [2689] [2690] [2691] [2692]
4550Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
4551[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp
4552ose \T1/ptm/m/n/10 from
4553 []
4554
4555[2693]
4556Underfull \hbox (badness 1092) in paragraph at lines 8516--8518
4557[]\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 <Deepayan.Sarkar@R-project.org
4558> \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally
4559 con-
4560 []
4561
4562[2694] [2695]
4563Underfull \hbox (badness 3895) in paragraph at lines 8677--8680
4564[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T
45651/ptm/m/n/10 has a dif-fer-ent mean-ing in
4566 []
4567
4568[2696]
4569Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
4570[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
4571es. If used with
4572 []
4573
4574[2697] [2698]
4575Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
4576[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
4577ibed in
4578 []
4579
4580
4581Underfull \hbox (badness 5908) in paragraph at lines 8876--8879
4582[]\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c
4583omponents.default \T1/ptm/m/n/10 and
4584 []
4585
4586[2699] [2700] [2701] [2702]
4587Overfull \hbox (1.94879pt too wide) in paragraph at lines 9164--9168
4588[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4
4589/m/sl/10 left,right,left.name,right.name,condition
4590 []
4591
4592[2703] [2704] [2705] [2706] [2707] [2708] [2709]
4593Underfull \hbox (badness 2310) in paragraph at lines 9622--9626
4594[]\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 ,
4595 \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m
4596/n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p
4597tm/m/n/10 ,
4598 []
4599
4600
4601Underfull \hbox (badness 3701) in paragraph at lines 9627--9630
4602[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m
4603/n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa
4604rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 ,
4605 []
4606
4607[2710] [2711] [2712]pdfTeX warning (ext4): destination with the same identifier
4608 (name{Rfn.melanoma}) has been already used, duplicate ignored
4609<to be read again> 
4610                   \relax 
4611l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
4612                                                [2713] [2714] [2715]
4613Underfull \hbox (badness 4144) in paragraph at lines 10077--10080
4614[]\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R
4615u-ral and Ur-ban Mor-tal-
4616 []
4617
4618
4619Underfull \hbox (badness 1509) in paragraph at lines 10077--10080
4620\T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl
4621/10 https : / / ruralhealth . und . edu / projects /
4622 []
4623
4624[2716] [2717]) (mgcv-pkg.tex [2718
4625
4626
4627]
4628Chapter 24.
4629[2719] [2720] [2721]
4630Underfull \hbox (badness 1142) in paragraph at lines 171--175
4631\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
4632aken from
4633 []
4634
4635
4636Underfull \hbox (badness 1043) in paragraph at lines 196--201
4637\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
4638scale.
4639 []
4640
4641[2722] [2723] [2724] [2725]
4642Underfull \hbox (badness 10000) in paragraph at lines 361--368
4643[][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m
4644gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/
4645n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
4646 smooth.terms[][][]\T1/ptm/m/n/10 ,
4647 []
4648
4649
4650Underfull \hbox (badness 7168) in paragraph at lines 361--368
4651[][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m
4652/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][]
4653[]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z
4654i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][]
4655\T1/ptm/m/n/10 ,
4656 []
4657
4658[2726] [2727] [2728] [2729] [2730] [2731] [2732]
4659Underfull \hbox (badness 1158) in paragraph at lines 749--751
4660[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
4661n us-ing pe-nal-ized re-gres-sion
4662 []
4663
4664[2733]
4665Underfull \hbox (badness 1259) in paragraph at lines 812--813
4666[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
4667-duc-tion with R (2nd edi-tion).
4668 []
4669
4670[2734]
4671Underfull \vbox (badness 10000) has occurred while \output is active []
4672
4673 [2735]
4674[2736] [2737] [2738] [2739] [2740] [2741] [2742] [2743] [2744] [2745] [2746]
4675[2747] [2748] [2749] [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757]
4676Underfull \hbox (badness 1142) in paragraph at lines 2235--2239
4677\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
4678aken from
4679 []
4680
4681[2758]
4682Underfull \hbox (badness 1043) in paragraph at lines 2261--2266
4683\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
4684scale.
4685 []
4686
4687[2759] [2760] [2761] [2762] [2763]
4688Underfull \vbox (badness 10000) has occurred while \output is active []
4689
4690 [2764]
4691Underfull \vbox (badness 10000) has occurred while \output is active []
4692
4693 [2765]
4694Underfull \vbox (badness 10000) has occurred while \output is active []
4695
4696 [2766]
4697[2767] [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777]
4698[2778] [2779]
4699Underfull \hbox (badness 10000) in paragraph at lines 3580--3584
4700[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/
4701n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
4702 []
4703
4704[2780] [2781]
4705Underfull \vbox (badness 10000) has occurred while \output is active []
4706
4707 [2782]
4708[2783] [2784]
4709Underfull \hbox (badness 1184) in paragraph at lines 3866--3870
4710[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
4711ed penalty, if
4712 []
4713
4714[2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] [2794] [2795]
4715[2796]
4716Underfull \hbox (badness 1142) in paragraph at lines 4587--4591
4717\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
4718aken from
4719 []
4720
4721[2797]
4722Underfull \hbox (badness 1231) in paragraph at lines 4688--4690
4723[]\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since
4724 it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with
4725 []
4726
4727[2798] [2799] [2800]
4728Underfull \vbox (badness 10000) has occurred while \output is active []
4729
4730 [2801]
4731[2802] [2803]
4732Underfull \hbox (badness 2181) in paragraph at lines 5060--5061
4733[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
4734tion, used by
4735 []
4736
4737[2804] [2805] [2806] [2807] [2808] [2809] [2810]
4738Underfull \hbox (badness 10000) in paragraph at lines 5449--5450
4739[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(...
4740,fit=FALSE) \T1/ptm/m/n/10 or
4741 []
4742
4743[2811] [2812]
4744Underfull \vbox (badness 10000) has occurred while \output is active []
4745
4746 [2813]
4747[2814] [2815] [2816] [2817] [2818] [2819]
4748Underfull \hbox (badness 1142) in paragraph at lines 5952--5956
4749\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
4750aken from
4751 []
4752
4753[2820] [2821] [2822]
4754Underfull \vbox (badness 10000) has occurred while \output is active []
4755
4756 [2823]
4757[2824] [2825] [2826]
4758Underfull \hbox (badness 1087) in paragraph at lines 6320--6321
4759[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet
4760a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas
4761e, and if
4762 []
4763
4764[2827] [2828] [2829]
4765Underfull \vbox (badness 10000) has occurred while \output is active []
4766
4767 [2830]
4768Underfull \vbox (badness 10000) has occurred while \output is active []
4769
4770 [2831]
4771[2832] [2833] [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842]
4772Underfull \hbox (badness 1242) in paragraph at lines 7266--7267
4773[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
4774nts EP/K005251/1 and
4775 []
4776
4777[2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853]
4778Underfull \hbox (badness 6001) in paragraph at lines 7906--7908
4779[]\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 <simon.wood@r-project.org> \T1/p
4780tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's
4781 []
4782
4783[2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861] [2862] [2863]
4784Underfull \vbox (badness 10000) has occurred while \output is active []
4785
4786 [2864]
4787[2865]
4788Underfull \hbox (badness 1038) in paragraph at lines 8655--8658
4789[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim.
4790pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
4791sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 ,
4792 []
4793
4794
4795Underfull \hbox (badness 10000) in paragraph at lines 8655--8658
4796\T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId
4797not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
4798sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 ,
4799 []
4800
4801[2866]
4802Underfull \hbox (badness 10000) in paragraph at lines 8711--8714
4803[]\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z
4804i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T
48051/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 ,
4806 []
4807
4808[2867] [2868] [2869] [2870] [2871] [2872] [2873] [2874] [2875] [2876] [2877]
4809Underfull \hbox (badness 1852) in paragraph at lines 9381--9384
4810[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
4811[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
4812tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
4813 []
4814
4815[2878] [2879]
4816Underfull \hbox (badness 1852) in paragraph at lines 9545--9548
4817[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
4818[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
4819tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
4820 []
4821
4822[2880] [2881]
4823Underfull \vbox (badness 10000) has occurred while \output is active []
4824
4825 [2882]
4826Underfull \vbox (badness 10000) has occurred while \output is active []
4827
4828 [2883]
4829Underfull \hbox (badness 1205) in paragraph at lines 9774--9776
4830[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
4831tes at which
4832 []
4833
4834
4835Underfull \hbox (badness 2689) in paragraph at lines 9774--9776
4836\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
4837as for
4838 []
4839
4840
4841Underfull \hbox (badness 1975) in paragraph at lines 9780--9785
4842[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
4843i-ca-tion ob-jects of class
4844 []
4845
4846[2884] [2885]
4847Underfull \hbox (badness 1205) in paragraph at lines 9864--9866
4848[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
4849tes at which
4850 []
4851
4852
4853Underfull \hbox (badness 2689) in paragraph at lines 9864--9866
4854\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
4855as for
4856 []
4857
4858[2886] [2887] [2888]
4859Underfull \hbox (badness 1253) in paragraph at lines 10063--10065
4860[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
4861cri-te-rion re-ported is one of GCV,
4862 []
4863
4864[2889] [2890] [2891]
4865Underfull \hbox (badness 4792) in paragraph at lines 10249--10252
4866[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/
486710 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m
4868/n/10 can be used:
4869 []
4870
4871
4872Underfull \hbox (badness 10000) in paragraph at lines 10249--10252
4873\T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo
4874th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
4875 []
4876
4877[2892] [2893]
4878Underfull \hbox (badness 10000) in paragraph at lines 10344--10347
4879[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1
48800 "deviance"\T1/ptm/m/n/10 ,
4881 []
4882
4883[2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903]
4884Underfull \vbox (badness 10000) has occurred while \output is active []
4885
4886 [2904]
4887Underfull \hbox (badness 3861) in paragraph at lines 10972--10975
4888[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
4889 model ma-trix X, or, if
4890 []
4891
4892[2905] [2906]
4893Underfull \hbox (badness 1320) in paragraph at lines 11078--11083
4894\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T
48951/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If
4896 ma-
4897 []
4898
4899[2907]
4900Underfull \hbox (badness 1975) in paragraph at lines 11184--11189
4901[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
4902i-ca-tion ob-jects of class
4903 []
4904
4905[2908] [2909]
4906Underfull \hbox (badness 1762) in paragraph at lines 11273--11285
4907\T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T
49081/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr
4909es-sion splines with
4910 []
4911
4912[2910] [2911] [2912]
4913Underfull \hbox (badness 7667) in paragraph at lines 11485--11491
4914[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
4915 or two vari-ables, spec-i-fied via terms like
4916 []
4917
4918[2913]
4919Underfull \hbox (badness 10000) in paragraph at lines 11526--11527
4920[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
4921term
4922 []
4923
4924[2914] [2915] [2916] [2917]
4925Underfull \vbox (badness 10000) has occurred while \output is active []
4926
4927 [2918]
4928Underfull \hbox (badness 10000) in paragraph at lines 11802--11804
4929[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
4930term
4931 []
4932
4933[2919] [2920]
4934Underfull \hbox (badness 10000) in paragraph at lines 11930--11931
4935[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
4936term
4937 []
4938
4939[2921] [2922] [2923]
4940Underfull \hbox (badness 1436) in paragraph at lines 12068--12075
4941\T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i
4942) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one
4943 []
4944
4945[2924] [2925]
4946Underfull \hbox (badness 10000) in paragraph at lines 12162--12163
4947[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
4948term
4949 []
4950
4951[2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933] [2934] [2935]
4952Underfull \hbox (badness 10000) in paragraph at lines 12748--12754
4953[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
4954 []
4955
4956
4957Underfull \hbox (badness 1292) in paragraph at lines 12748--12754
4958\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T
49591/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note
4960 []
4961
4962[2936] [2937] [2938]
4963Underfull \vbox (badness 10000) has occurred while \output is active []
4964
4965 [2939]
4966Underfull \vbox (badness 10000) has occurred while \output is active []
4967
4968 [2940]
4969[2941]
4970Underfull \hbox (badness 10000) in paragraph at lines 13091--13092
4971[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
4972term
4973 []
4974
4975[2942] [2943] [2944] [2945]
4976Underfull \hbox (badness 3895) in paragraph at lines 13352--13355
4977[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
4978 num-ber of vari-ables, spec-i-fied via terms like
4979 []
4980
4981[2946]
4982Underfull \hbox (badness 10000) in paragraph at lines 13397--13399
4983[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
4984term
4985 []
4986
4987[2947] [2948] [2949] [2950]
4988Underfull \hbox (badness 1371) in paragraph at lines 13614--13620
4989[]\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive
4990 smooths are avail-able (see
4991 []
4992
4993
4994Underfull \hbox (badness 10000) in paragraph at lines 13654--13658
4995[][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p
4996tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/
4997zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre
4998ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n
4999/10 ,
5000 []
5001
5002
5003Underfull \hbox (badness 10000) in paragraph at lines 13654--13658
5004[][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1
5005/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T
50061/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de
5007fined.smooth[][][]\T1/ptm/m/n/10 ,
5008 []
5009
5010
5011Overfull \hbox (46.8009pt too wide) in paragraph at lines 13654--13658
5012[][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\
5013T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4
5014/m/sl/10 factor.smooth.interaction[][][] 
5015 []
5016
5017[2951] [2952] [2953] [2954]
5018Underfull \hbox (badness 2326) in paragraph at lines 13859--13866
5019[]\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied
5020 us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and
5021 []
5022
5023[2955]
5024Underfull \hbox (badness 2158) in paragraph at lines 13944--13944
5025[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
5026trix from
5027 []
5028
5029[2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966]
5030Underfull \vbox (badness 10000) has occurred while \output is active []
5031
5032 [2967]
5033[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
5034[2979] [2980] [2981] [2982]
5035Underfull \hbox (badness 1796) in paragraph at lines 15588--15591
5036[]\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T
50371/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/
5038sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar
5039 []
5040
5041[2983] [2984] [2985] [2986] [2987] [2988]) (nlme-pkg.tex
5042Chapter 25.
5043[2989
5044
5045
5046] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999]
5047[3000] [3001] [3002] [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010]
5048[3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018]
5049Underfull \hbox (badness 2875) in paragraph at lines 1994--2000
5050[]\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat-
5051ing a co-vari-ate
5052 []
5053
5054
5055Underfull \hbox (badness 1466) in paragraph at lines 1994--2000
5056\T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1
50570 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 ,
5058 []
5059
5060[3019] [3020] [3021] [3022]
5061Underfull \hbox (badness 10000) in paragraph at lines 2255--2261
5062[][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA
5063[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][
5064]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi
5065alize.corStruct[][][]\T1/ptm/m/n/10 ,
5066 []
5067
5068[3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033]
5069[3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044]
5070[3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055]
5071Underfull \hbox (badness 1067) in paragraph at lines 4413--4418
5072\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
5073), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
5074 []
5075
5076[3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066]
5077[3067]
5078Underfull \hbox (badness 10000) in paragraph at lines 5159--5163
5079[][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
5080m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo
5081variate.varFunc[][][]\T1/ptm/m/n/10 ,
5082 []
5083
5084[3068] [3069] [3070] [3071] [3072] [3073] [3074]
5085Underfull \hbox (badness 10000) in paragraph at lines 5591--5594
5086[][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
50870 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[
5088][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 
5089,
5090 []
5091
5092[3075] [3076] [3077] [3078] [3079] [3080] [3081]
5093Underfull \hbox (badness 10000) in paragraph at lines 5972--5977
5094[][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
5095sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou
5096psFormula.lme[][][]\T1/ptm/m/n/10 ,
5097 []
5098
5099[3082] [3083] [3084] [3085]
5100Underfull \hbox (badness 1490) in paragraph at lines 6242--6253
5101[][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC
5102ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 
5103, [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.
5104gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 ,
5105 [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 ,
5106 []
5107
5108[3086]
5109Underfull \hbox (badness 10000) in paragraph at lines 6306--6308
5110[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
5111e-fault is
5112 []
5113
5114[3087] [3088] [3089] [3090] [3091] [3092]
5115Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
5116[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
5117e-fault is
5118 []
5119
5120[3093] [3094] [3095] [3096]
5121Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
5122[][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[
5123][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T
51241/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData
5125[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n
5126/10 ,
5127 []
5128
5129[3097] [3098] [3099] [3100]
5130Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
5131[][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
5132sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize
5133.glsStruct[][][]\T1/ptm/m/n/10 ,
5134 []
5135
5136[3101] [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111]
5137[3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119]
5138Underfull \hbox (badness 10000) in paragraph at lines 8520--8522
5139[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
5140e-fault is
5141 []
5142
5143[3120]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sig
5144ma}) has been already used, duplicate ignored
5145<to be read again> 
5146                   \relax 
5147l.8565 \aliasA{sigma}{lmeObject}{sigma}
5148                                        [3121] [3122] [3123] [3124]
5149Underfull \hbox (badness 10000) in paragraph at lines 8795--8802
5150[][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[]
5151[][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][]
5152\T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi
5153st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/
515410 ,
5155 []
5156
5157[3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132]
5158Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
5159[][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1
5160/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T
51611/zi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik
5162.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm
5163/m/n/10 ,
5164 []
5165
5166[3133] [3134] [3135] [3136] [3137]pdfTeX warning (ext4): destination with the s
5167ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored
5168<to be read again> 
5169                   \relax 
5170l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
5171                                                  pdfTeX warning (ext4): destin
5172ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
5173icate ignored
5174<to be read again> 
5175                   \relax 
5176l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
5177                                                   [3138] [3139] [3140]
5178[3141] [3142] [3143] [3144] [3145] [3146] [3147] [3148] [3149]
5179Underfull \hbox (badness 1596) in paragraph at lines 10452--10478
5180[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
5181f the form
5182 []
5183
5184[3150] [3151]
5185Underfull \hbox (badness 1490) in paragraph at lines 10590--10596
5186[][][]\T1/zi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
5187e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n
5188/10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
5189eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10
5190 , [][]\T1/zi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 ,
5191 []
5192
5193[3152] [3153] [3154] [3155]
5194Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
5195[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
5196e-fault is
5197 []
5198
5199[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166]
5200[3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177]
5201[3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188]
5202[3189] [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197]
5203Underfull \hbox (badness 1286) in paragraph at lines 13728--13735
5204[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/zi4/m/sl
5205/10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/zi4/m/sl/10 inner \T1/ptm/m/n/10 or
5206 []
5207
5208[3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205]
5209Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
5210[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
5211 De-faults to
5212 []
5213
5214[3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] [3216]
5215[3217] [3218]pdfTeX warning (ext4): destination with the same identifier (name{
5216Rfn.random.effects}) has been already used, duplicate ignored
5217<to be read again> 
5218                   \relax 
5219l.15153 ...Extract Random Effects}{random.effects}
5220                                                  pdfTeX warning (ext4): destin
5221ation with the same identifier (name{Rfn.random.effects.1}) has been already us
5222ed, duplicate ignored
5223<to be read again> 
5224                   \relax 
5225l.15153 ...Extract Random Effects}{random.effects}
5226                                                   [3219] [3220] [3221]
5227[3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
5228Underfull \hbox (badness 1067) in paragraph at lines 15864--15869
5229\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
5230), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
5231 []
5232
5233[3230] [3231] [3232] [3233]
5234Underfull \hbox (badness 1448) in paragraph at lines 16107--16116
5235\T1/ptm/m/n/10 Op-tions in-clude \T1/zi4/m/sl/10 "response" \T1/ptm/m/n/10 for 
5236the "raw" resid-u-als (ob-served - fit-ted),
5237 []
5238
5239[3234] [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243]
5240Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
5241[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
5242t-put in the
5243 []
5244
5245[3244] [3245] [3246] [3247] [3248]
5246Underfull \hbox (badness 8056) in paragraph at lines 17147--17156
5247\T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/
5248m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T
52491/ptm/m/n/10 , \T1/zi4/m/sl/10 "Multiple of
5250 []
5251
5252
5253Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
5254\T1/zi4/m/sl/10 an Identity" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdIdent\T1/ptm/
5255m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite,Natural
5256 []
5257
5258
5259Underfull \hbox (badness 5756) in paragraph at lines 17147--17156
5260\T1/zi4/m/sl/10 Parametrization" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdNatural\T
52611/ptm/m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite" \T1/ptm/m/n/10 for
5262 []
5263
5264[3249]
5265Underfull \hbox (badness 2913) in paragraph at lines 17211--17219
5266\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Con
5267stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower
5268\T1/ptm/m/n/10 ,
5269 []
5270
5271[3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] [3259] [3260]
5272Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
5273[][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
52740 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[
5275][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1
52760 ,
5277 []
5278
5279
5280Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
5281[][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl
5282/10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa
5283ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10
5284 ,
5285 []
5286
5287[3261] [3262] [3263] [3264] [3265]
5288Underfull \hbox (badness 5036) in paragraph at lines 18317--18326
5289[][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari
5290ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/
5291m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
5292/m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 ,
5293 []
5294
5295[3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]
5296[3277] [3278]) (nnet-pkg.tex
5297Chapter 26.
5298pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
5299) has been already used, duplicate ignored
5300<to be read again> 
5301                   \relax 
5302l.47 ...t Multinomial Log-linear Models}{multinom}
5303                                                  pdfTeX warning (ext4): destin
5304ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
5305plicate ignored
5306<to be read again> 
5307                   \relax 
5308l.47 ...t Multinomial Log-linear Models}{multinom}
5309                                                   [3279
5310
5311
5312]
5313Underfull \hbox (badness 1117) in paragraph at lines 78--87
5314[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
5315rm \T1/zi4/m/sl/10 response ~
5316 []
5317
5318[3280] [3281] [3282] [3283] [3284] [3285] [3286]) (rpart-pkg.tex
5319Chapter 27.
5320[3287
5321
5322
5323] [3288] [3289] [3290] [3291] [3292] [3293] [3294] [3295] [3296] [3297]
5324[3298] [3299] [3300] [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308]
5325[3309] [3310] [3311] [3312] [3313] [3314] [3315]) (spatial-pkg.tex [3316
5326
5327
5328]
5329Chapter 28.
5330[3317] [3318] [3319] [3320] [3321] [3322]
5331Underfull \hbox (badness 10000) in paragraph at lines 423--427
5332
5333 []
5334
5335[3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333]
5336[3334] [3335]) (survival-pkg.tex [3336
5337
5338
5339]
5340Chapter 29.
5341[3337] [3338] [3339] [3340]pdfTeX warning (ext4): destination with the same ide
5342ntifier (name{Rfn.aml}) has been already used, duplicate ignored
5343<to be read again> 
5344                   \relax 
5345l.326 ... Myelogenous Leukemia survival data}{aml}
5346                                                  pdfTeX warning (ext4): destin
5347ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
5348te ignored
5349<to be read again> 
5350                   \relax 
5351l.326 ... Myelogenous Leukemia survival data}{aml}
5352                                                   [3341] [3342] [3343]
5353[3344] [3345]
5354Underfull \vbox (badness 10000) has occurred while \output is active []
5355
5356 [3346]
5357[3347] [3348] [3349] [3350] [3351]
5358Underfull \hbox (badness 1097) in paragraph at lines 975--977
5359[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
5360al and negative-binomial data.
5361 []
5362
5363[3352] [3353] [3354]pdfTeX warning (ext4): destination with the same identifier
5364 (name{Rfn.colon}) has been already used, duplicate ignored
5365<to be read again> 
5366                   \relax 
5367l.1178 ...erapy for Stage B/C colon cancer}{colon}
5368                                                  
5369Underfull \vbox (badness 2698) has occurred while \output is active []
5370
5371 [3355]
5372[3356] [3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365] [3366]
5373[3367] [3368] [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376]
5374Underfull \vbox (badness 5359) has occurred while \output is active []
5375
5376 [3377]
5377Underfull \hbox (badness 1389) in paragraph at lines 2862--2864
5378[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
5379-Meier plot gen-er-ated with
5380 []
5381
5382[3378]
5383Underfull \hbox (badness 1048) in paragraph at lines 2917--2919
5384[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
5385e the note in
5386 []
5387
5388[3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389]
5389Underfull \vbox (badness 10000) has occurred while \output is active []
5390
5391 [3390]
5392[3391] [3392] [3393] [3394] [3395] [3396] [3397] [3398] [3399] [3400] [3401]
5393[3402]
5394Underfull \hbox (badness 5274) in paragraph at lines 4487--4489
5395[]\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "summary.survfit"\T1/ptm/m
5396/n/10 , which is the re-sult of the
5397 []
5398
5399[3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413]
5400Underfull \vbox (badness 2126) has occurred while \output is active []
5401
5402 [3414]
5403[3415]
5404Underfull \hbox (badness 1281) in paragraph at lines 5399--5402
5405[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/zi4/m/sl/10 "response
5406"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "d
5407fbeta"\T1/ptm/m/n/10 ,
5408 []
5409
5410[3416] [3417] [3418] [3419] [3420]pdfTeX warning (ext4): destination with the s
5411ame identifier (name{Rfn.solder}) has been already used, duplicate ignored
5412<to be read again> 
5413                   \relax 
5414l.5705 ...ata from a soldering experiment}{solder}
5415                                                  pdfTeX warning (ext4): destin
5416ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl
5417icate ignored
5418<to be read again> 
5419                   \relax 
5420l.5705 ...ata from a soldering experiment}{solder}
5421                                                   [3421] [3422] [3423]
5422[3424] [3425] [3426] [3427] [3428] [3429] [3430] [3431] [3432] [3433]
5423Underfull \vbox (badness 10000) has occurred while \output is active []
5424
5425 [3434]
5426[3435] [3436]
5427Underfull \hbox (badness 10000) in paragraph at lines 6876--6885
5428[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
5429 form
5430 []
5431
5432[3437] [3438]
5433Underfull \hbox (badness 1038) in paragraph at lines 7032--7038
5434\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
5435icted sur-vival
5436 []
5437
5438[3439] [3440] [3441] [3442] [3443]
5439Underfull \hbox (badness 10000) in paragraph at lines 7395--7400
5440[][][]\T1/zi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
5441 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.object[][][]\T
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