<TeXmacs|1.0.3>

<style|generic>

<\body>
  <\table-of-contents|toc>
    Lecture 1<value|toc-dots><pageref|toc-1>

    <with|par-left|1.5fn|Using R<value|toc-dots><pageref|toc-2>>

    <with|par-left|1.5fn|TeXmacs<value|toc-dots><pageref|toc-3>>

    <with|par-left|3fn|<value|toc-dots><pageref|toc-4>>

    <with|par-left|3fn|The TeXmacs interface<value|toc-dots><pageref|toc-5>>

    <with|par-left|6fn|font-size|0.84|Help in
    TeXmacs<value|toc-dots><pageref|toc-6>>

    <with|par-left|6fn|font-size|0.84|Opening
    files<value|toc-dots><pageref|toc-7>>

    <with|par-left|6fn|font-size|0.84|The status
    line<value|toc-dots><pageref|toc-8>>

    <with|par-left|6fn|font-size|0.84|Starting R inside
    TeXmacs<value|toc-dots><pageref|toc-9>>

    <with|par-left|6fn|font-size|0.84|Important hints for the R interface in
    TeXmacs<value|toc-dots><pageref|toc-10>>

    <with|par-left|6fn|font-size|0.84|Managing R input and
    Text<value|toc-dots><pageref|toc-11>>

    <with|par-left|1.5fn|The basics of R<value|toc-dots><pageref|toc-12>>

    <with|par-left|6fn|font-size|0.84|More usefull functions in
    R<value|toc-dots><pageref|toc-13>>

    <with|par-left|6fn|font-size|0.84|Vectors<value|toc-dots><pageref|toc-14>>

    <with|par-left|6fn|font-size|0.84|Subsetting vectors, and operation on
    vectors<value|toc-dots><pageref|toc-15>>

    <with|par-left|1.5fn|What is statistics?<value|toc-dots><pageref|toc-16>>

    <with|par-left|6fn|font-size|0.84|So?<value|toc-dots><pageref|toc-17>>

    <with|par-left|1.5fn|Some simple random functions in
    R<value|toc-dots><pageref|toc-18>>

    <with|par-left|3fn|<value|toc-dots><pageref|toc-19>>

    <with|par-left|3fn|<value|toc-dots><pageref|toc-20>>

    <with|par-left|6fn|font-size|0.84|<value|toc-dots><pageref|toc-21>>

    <with|par-left|6fn|font-size|0.84|<with|font-family|tt|language|verbatim|sample><value|toc-dots><pageref|toc-22>>

    <with|par-left|6fn|font-size|0.84|<with|font-family|tt|language|verbatim|rnorm><value|toc-dots><pageref|toc-23>>
  </table-of-contents>

  <page-break*><section|Lecture 1>

  <subsection|Using R>

  Let us start R from the command line. First make a directory, and then run
  R inside it:

  <verbatim|ssh bio41 -X -lcourse>

  or

  <verbatim|ssh bioXX -X -lusername >

  Then, in the shell do the following:

  <with|prog-language|shell|prog-session|default|<\session>
    <\output>
      Shell session inside TeXmacs
    </output>

    <\input|shell] >
      cd class
    </input>

    <\input|shell] >
      ls -la
    </input>

    <\output>
      total 24

      drwxr-sr-x \ \ \ 2 dirk \ \ \ \ dirk \ \ \ \ \ \ \ \ 4096 Jan 25 16:15
      .

      drwxr-sr-x \ \ 79 dirk \ \ \ \ dirk \ \ \ \ \ \ \ 20480 Jan 25 16:15 ..

      \;
    </output>

    <\input|shell] >
      R
    </input>
  </session>>

  Now we start R (here I am cheating, and starting R inside texmacs)

  <with|prog-language|r|prog-session|default|<\session>
    <\output>
      library(TeXmacs,lib.loc="/usr/share/texmacs/TeXmacs/plugins/r/r/")

      \;

      \;

      R : Copyright 2003, The R Foundation for Statistical Computing

      Version 1.8.1 \ (2003-11-21), ISBN 3-900051-00-3

      \;

      R is free software and comes with ABSOLUTELY NO WARRANTY.

      You are welcome to redistribute it under certain conditions.

      Type 'license()' or 'licence()' for distribution details.

      \;

      R is a collaborative project with many contributors.

      Type 'contributors()' for more information and

      'citation()' on how to cite R in publications.

      \;

      Type 'demo()' for some demos, 'help()' for on-line help, or

      'help.start()' for a HTML browser interface to help.

      Type 'q()' to quit R.

      \;

      \;

      \;

      \<gtr\>\ 
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a=5
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      q()
    </input>

    <\input|<with|color|red|Save workspace image? [y/n/c]:
    <with|color|black|>>>
      y
    </input>

    \;
  </session>>

  To quit R use the function <verbatim|q()>.

  After we quit, look at the directory again:

  <with|prog-language|shell|prog-session|default|<\session>
    <\input|shell] >
      ls -la
    </input>

    <\output>
      total 32

      drwxr-sr-x \ \ \ 2 dirk \ \ \ \ dirk \ \ \ \ \ \ \ \ 4096 Jan 25 16:17
      .

      drwxr-sr-x \ \ 79 dirk \ \ \ \ dirk \ \ \ \ \ \ \ 20480 Jan 25 16:15 ..

      -rw-r--r-- \ \ \ 1 dirk \ \ \ \ dirk \ \ \ \ \ \ \ \ \ \ 56 Jan 25
      16:17 .RData

      -rw------- \ \ \ 1 dirk \ \ \ \ dirk \ \ \ \ \ \ \ \ \ \ \ 8 Jan 25
      16:17 .Rhistory

      \;
    </output>

    <\input|shell] >
      \;
    </input>
  </session>>

  When you quit R asks whether to save everything. If you say yes, then all
  the data is saved, and loaded next time you start R from the same
  directory. The data is stored in the file .RData

  <with|prog-language|r|prog-session|default|<\session>
    <\output>
      library(TeXmacs,lib.loc="/usr/share/texmacs/TeXmacs/plugins/r/r/")

      \;

      \;

      R : Copyright 2003, The R Foundation for Statistical Computing

      Version 1.8.1 \ (2003-11-21), ISBN 3-900051-00-3

      \;

      R is free software and comes with ABSOLUTELY NO WARRANTY.

      You are welcome to redistribute it under certain conditions.

      Type 'license()' or 'licence()' for distribution details.

      \;

      R is a collaborative project with many contributors.

      Type 'contributors()' for more information and

      'citation()' on how to cite R in publications.

      \;

      Type 'demo()' for some demos, 'help()' for on-line help, or

      'help.start()' for a HTML browser interface to help.

      Type 'q()' to quit R.

      \;

      <with|color|red|[Previously saved workspace restored]>

      \;

      \;

      \;

      \<gtr\>\ 
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a
    </input>

    <\output>
      [1] 5
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  As you see, after restarting, R loaded the data, and thus the variable 'a'
  was restored.

  <page-break*><subsection|TeXmacs>

  TeXmacs provides a nice interface for working with R.

  Do the same as before, but now start texmacs instead of R

  <with|prog-language|shell|prog-session|default|<\session>
    <\input|shell] >
      cd ~/class
    </input>

    <\input|shell] >
      texmacs
    </input>
  </session>>

  <subsubsection|>

  <subsubsection|The TeXmacs interface>

  TeXmacs is very similar to Emacs, so if you know Emacs keystrokes, they
  usually work in TeXmacs.

  \;

  <paragraph|Help in TeXmacs>

  To get help in TeXmacs, click on the Help menu

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  <paragraph|The status line>

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  <paragraph|Starting R inside TeXmacs>

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  QQܠ\t.e\nϵ Tsɠxc9mct8\nj[SP%%͡exn%ĐY\\HhvhˈP`\>=Nޣ0\n@7ă8\\e?B9g"d=\0)4,3@v\<h)rAϪ,SD@i7
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  p !{hrl6F\0r.OT@:pV$\>gHwu!Ɇy"ŰuF,2-"-U-tq,2vd('\0@"x{dlq
  AT&A08\>pe9jv"8&f̽Gp"a7pץ\0H0\<4\0(+xa]('\|\\GyAqZ-#RJwzg.rء0X\0g\|qac}#1TJC14!2N\t+'g\|Tqhr\0%a2xHfMqTCBM\|l%\<"h\n2.@\>1q#;#j):h,D՘0:\\n7q$1"C,BS\|nCg4E&/&))7V##B":b"&!,"'2%v-$E:\>#+#%Q'K0-7M\<LX+C@\t"w)yc\>p#IТH0`xD.",윣/*\nJJ+R'R\n\\D\0$$/=\0$3Vj4D.&n)/o2_e"l\nB?'rK"3.2\0\>NZ~Е@@34Gq4IsyGa%1ڑK1jE(R23`da#;/cJvBc9`lglR'!aܫrtj)#p))rbp1\<QLXjiZK(v3GqA訡ć\nK{Bv~+q4ES%-]$vFm%̉lq\nhJD+sEr\0OϮhlȧVpNPGVEzq4+'^BZRKI2c\>\0odoXqr¬qMAyrN$BvHn)9u2"47j"cGm2N3@7Xc*ۢ2+K&QT4zDd\nb808TKT;UTF?i4/6^ܴZJ`3WG0S{+]'o6*]*"USR$/ک6'lH_ߓ_#U.a'Tc`au9!D*Fl23-3@\>[fq]Ig=7+ɵ[ӆM]eG1fTbbdR$nmJ{g1d@t9JN\0"6ui$f#CB:72
  E[6TJk n\<?Reݖ)"odfP
  Guf!p4qN@e\>6rA*4t?\tPhz1wZ̊Rp7ipECbFN+QX"\0lpY78%u
  BfDk7llx÷"'OK1p`gtS0,ZgLUM)U*3M)IksB1{WL\|e-N'ico-?+uJg\>hZpO/NS0r&l6(%Z=/,;yDga%sXpCc\tRrG8b&̯2EXq.F6I.#^zBIRn-e]5ADg_7[.d\>ѓvϱߔW2gW%6W`T0/74KAl#cDD\|'Ȋro7n.XfW*&"t늢cDJ:RNMT٘ۊXb.2Q2!۰ٗJ.Cn$y}%,G9cmImoBiRW.T١\tGW
  wVR-٣k,'4s!r'u9tƦgs=zg+\\w?4wKѾfx\|z14ӾgGz"pTm5paM."t%
  T4MW@\0NǬwXMsMMݶaUi#)F:pBPAT'!\0ǚv'uS,l@pa\\Spbt(BaڡBc#dZuZ
  8@mC2"zB0qڣcgGR6kW.q#2,r9By&bQzQy\<[.dֵYz6bv1-)Ҍ{Ab3{1¹"4k\n)x,I:6/;c[+'#nQkϑś$A\n0Î5eo\n(`m;'Bª;%a\0h\\_;~\nÓc;{ؾ:I-[(\\uR\>cۺW'lͫ7,\n.y8":\\\<S˕s\nLS
  ~m0܋JݼFx7O!ߜ\>\<;9,߶Ɖ\<nHkkxѹ=/T\|ڝ)CWhG}oi2ʨٽݣһ\\.kKݹ=-4j%/\tݥRBE\n=3E\<9^5ڟ$}5IK8_~#?E]w_WqIS+a.@0^1[;3Yȥ9\tI=B~ۇ=cYBR~AYqv^3\05cpm?YԘz59˳dK\|\>5aR+OaѼ!\>cdr@&7?#\\anWK񧿘#c7.ƩslXos1n0{z:wЙ.1ĉ+Z1ƍ;z2ȑ$K\<2ʕ,=R\n2̙4kڼAqȳaD;y.\<4ҥL\|\n5ԩ-)ᡊ5֭\\[:L8G~-1Z]ۺ}%ܹt%9hJl\n8w\>UČ;pW)]93ǜ;S5ӳў:[%;Jne۾vegY3{\0}[\03}"AS=\0"xvc\<\>\tg6O&\|ADqD`=-xXh\>
  ~\tDA_Ust^{AH"\\u5\0ā733\>q\>?1\tBbY9hdu\0\<A8zUz\0z#*\t&N'IfcU=Ah\<=ߠ3YzƄ~u^ba=-x[\\q$
  BIcfV酏A揶8OUz'u\nG}J+T$tb7UQPYJ\>Ki鸎
  j$\0=\0@$\<Iނ:*n+ݧנ\\ڦOBXeɋ~\>\tEzÕ{«q(O\0oO\0(i/KH@6%n#o\|r;\|VˀdTYA?g\|uC-Go}2۝\\Q,K=5$c:@~9[B`N@\<g#lFxL_.kDz袏B3HKާj:n\>\<Q}톧{rEo݀E{7lexH{SzţJIu_O6b_SJ5\|joOYt\|#8\<;W\|kaEap{\\,
  iY!x4x*hp4bw\n5,ϱ"2"F
  d9"ʶ߬Fw#,;rtE1AbAeU!N\0UYZȋc)1W\\{&0礧!8=*\t$990УI&)DUJY$%K\>۽i
  jQ=`KAa=_U~NIBM\nQXJJ
  \\%)iSbBCB(4]B3K urNw')f]i,\>JGϘ'uzqZ3g\\H\<a#tH-(}MUA1TzQ$)'e2Qѣoi$MG6'a~"J\nH!jBA]#S;Rk@P*\tT%b%cX`Jϴ\<+6c6\tol\n5r0̚1}3'6sVYʿ&b+V\|\\X\\iUVKl,BE\>MX%nkӆG/p\t7
  [[@O(qLS`uIeMnr\tw.-sBwt.uGawCn^-՟wˋ^7\>_đ6E{_7}xC.pkj\nnp,a28M@\0\0;>|gif>|*5/8|*5/8||||>

  Which should give you the following:

  <with|prog-language|r|prog-session|default|<\session>
    <\output>
      library(TeXmacs,lib.loc="/usr/share/texmacs/TeXmacs/plugins/r/r/")

      \;

      \;

      R : Copyright 2003, The R Foundation for Statistical Computing

      Version 1.8.1 \ (2003-11-21), ISBN 3-900051-00-3

      \;

      R is free software and comes with ABSOLUTELY NO WARRANTY.

      You are welcome to redistribute it under certain conditions.

      Type 'license()' or 'licence()' for distribution details.

      \;

      R is a collaborative project with many contributors.

      Type 'contributors()' for more information and

      'citation()' on how to cite R in publications.

      \;

      Type 'demo()' for some demos, 'help()' for on-line help, or

      'help.start()' for a HTML browser interface to help.

      Type 'q()' to quit R.

      \;

      [Previously saved workspace restored]

      \;

      \;

      \;

      \<gtr\>\ 
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <paragraph|Important hints for the R interface in TeXmacs>

  There are two important icons: the 'STOP' and the 'scissors':

  <postscript|<tuple|<raw-data|GIF87a\0\0\0\0\0\0\0\0%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ023/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XYYZk\\Z[[[_`N8`abdaOe[6ghhghhhhlhiiijlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{\|\|}hP~xajLkLlNx\\ĿſƗ^f8Su`md`⮪ϲj\|ָnvsztíjŦhIǩ~ɬ̮̱ЬӰӰӸԹԺָ׷ٽܹݾŦġǥ˫̬ѷҶӹ}~ր\0\0tt\0\0\0\0
  \0N\0\0X\|(=@\0PP\0tt\0\0\0(\|\0=D\0\0@@\0PPtt(N\|GD@@Pt\0\0\0
  Pt-@XL{\|`D!@@`P t\|\0@\0\0\0\0\0\0-\0\0@\0Tt0\0X\0\0\0\0\0\0\0P\0qt\0!\0@
  (=@`\|D`\0\0\0\0\0\0Pzt\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0`H*\\ȰÇ#JHŋ3jȱǏ
  Dɓ(S\\ɲ˗0cʜI͛8sɳϟ@$"ѣH*]ʴӧPSJ$LU]ʵׯ`NtkUdӪ]˶ʱ;ȝ\\twK&/\t\<X(`+^.\0#Kv_([\\Y3g$LZJ6g@ukbG0mƸs\tfN{VYR3VQ\t`unhwv/7Pvw={(68tʹS:t@&)]З\0%@]v}yVywJ]Yf~K"hwP})%g^$I"-eIrxt(5
  g\0Bf]\<]xF)WT"h+^L.%u5"a\nr)ɨ'@9#rx\0蹞c(]wLPUy2}p?5u_nJLY着'Jr2kbP@m0G9ư+ǂ阂0B[X07cK\td\0lkRA\0z.ohPl$oREiJ\|JҦb\\Ӟ&#$@\|5p\t``Jg!\<Ot4ϴI\0$KYj=i*DG;P-&ˡy"sgx$
  'F}P58sl\<\|,,(=a^ז\\rx-FnQ2piJzh"L#?`e"&%4Y㧚m*yK_sQ@)IWv&i:g){Yh5
  V\0Źo\t%d p#,Ȃ\\PzTKX"E\>#Y%U_]Jp=C"EAG`8`I,ȭN̓\>a^g%R~2b54~a1G$qBBp5\0pW\|tqUB{I
  /D'KD$E4tv5` cbiʪ\0x=$a;a\nPTd$j^ˤ3LfJٶcřʌ&2)jZ?&6nH8IrL:v\<Iz2̧\>~6JHJЂMBІ:
  }D'JъZͨF\0;>|gif>|*5/8|*5/8||||>

  You see them only when you are inside the R session.

  The <postscript|<tuple|<raw-data|GIF87a\0\0\0\0\0\0\0\0\0%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ023/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XYYZk\\Z[[[_`N8`abdaOe[6ghhghhhhlhiiijlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{\|\|}hP~xajLkLlNx\\ĿſƗ^f8Su`md`⮪ϲj\|ָnvsztíjŦhIǩ~ɬ̮̱ЬӰӰӸԹԺָ׷ٽܹݾŦġǥ˫̬ѷҶӹ}~ր\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0\0\tH*TpC/I8`C3J4xQƏ;fDdFG,yR`ʉ+cRQ"8srD\0$\nK71\tUQPس&ҥ9^\tb̕3vQdYkcQmAû˷/\0;>|gif>|*5/8|*5/8||||>
  will stop the current R session, maybe in a long calculation.

  The <postscript|<tuple|<raw-data|GIF87a\0\0\0\0\0\0\0\0\0%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ023/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XYYZk\\Z[[[_`N8`abdaOe[6ghhghhhhlhiiijlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{\|\|}hP~xajLkLlNx\\ĿſƗ^f8Su`md`⮪ϲj\|ָnvsztíjŦhIǩ~ɬ̮̱ЬӰӰӸԹԺָ׷ٽܹݾŦġǥ˫̬ѷҶӹ}~ր\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0n\0\tH*\\Ȱ!K&pxqaF\0h"kFZǍ0ntē#C1J&\teBSv4jpFzǝ\<bʵW\0;>|gif>|*5/8|*5/8||||>
  will exit the current R session, and a new one will be started when another
  R command is entered.

  If, for some reason the output from the R session becomes uncoordinated
  with your input, just enter @@@ on \ an empty input line:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      @@@
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a=6
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  \ (You might then need to hit the <postscript|<tuple|<raw-data|GIF87a\0\0\0\0\0\0\0\0\0%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ023/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XYYZk\\Z[[[_`N8`abdaOe[6ghhghhhhlhiiijlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{\|\|}hP~xajLkLlNx\\ĿſƗ^f8Su`md`⮪ϲj\|ָnvsztíjŦhIǩ~ɬ̮̱ЬӰӰӸԹԺָ׷ٽܹݾŦġǥ˫̬ѷҶӹ}~ր\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0\0\tH*TpC/I8`C3J4xQƏ;fDdFG,yR`ʉ+cRQ"8srD\0$\nK71\tUQPس&ҥ9^\tb̕3vQdYkcQmAû˷/\0;>|gif>|*5/8|*5/8||||>
  to regain the input)

  <paragraph|Managing R input and Text>

  To enter text (i.e. non-R input), just click beyond the blue lines that
  deliniate the R session. To continue with the R session, just select R from
  the menu on the monitor icon.

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a
    </input>

    <\output>
      [1] 6
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <page-break*><subsection|The basics of R>

  When you enter an exression without parentheses at the end, R prints the
  expression

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a
    </input>

    <\output>
      [1] 6
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      q
    </input>

    <\output>
      function (save = "default", status = 0, runLast = TRUE)\ 

      .Internal(quit(save, status, runLast))

      \<less\>environment: namespace:base\<gtr\>
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  as you see, when we entered '<verbatim|q>', and not '<verbatim|q()>', R
  printed the function <verbatim|q()>. To actually call that function, we
  have to call it with '<verbatim|q()>'.

  <paragraph|More usefull functions in R>

  h<verbatim|elp.start()> - brings up a help system:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      help.start()
    </input>

    <\output>
      Making links in per-session dir ...

      \;

      If netscape is already running, it is *not* restarted, and you must

      \ \ \ \ switch to its window.

      Otherwise, be patient ...
    </output>

    \;

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <verbatim|ls()> lists all objects in memory:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      ls()
    </input>

    <\output>
      [1] "a"
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b=5
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      ls()
    </input>

    <\output>
      [1] "a" "b"
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <verbatim|rm()> removes an object:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      rm(b)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      ls()
    </input>

    <\output>
      [1] "a"
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>

    \;
  </session>>

  <paragraph|Vectors>

  Data in R is in general stored as vectors, or lists. First we'll learn
  about vectors.

  When we printed the value of <verbatim|a<verbatim|>> before, we also saw
  '<verbatim|[1]>':

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a
    </input>

    <\output>
      [1] 5
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  That is because a is actually a vector that contains one element, 5. There
  are many methods to create longer vectors:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      3:9
    </input>

    <\output>
      [1] 3 4 5 6 7 8 9
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  the collon creates a vector in ascending order. The '[1]' in front of the
  first element tells us that 3 is element number 1. This is usefull for
  longer vectors:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      -50:50
    </input>

    <\output>
      \ \ [1] -50 -49 -48 -47 -46 -45 -44 -43 -42 -41 -40 -39 -38 -37 -36 -35
      -34 -33

      \ [19] -32 -31 -30 -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -17
      -16 -15

      \ [37] -14 -13 -12 -11 -10 \ -9 \ -8 \ -7 \ -6 \ -5 \ -4 \ -3 \ -2 \ -1
      \ \ 0 \ \ 1 \ \ 2 \ \ 3

      \ [55] \ \ 4 \ \ 5 \ \ 6 \ \ 7 \ \ 8 \ \ 9 \ 10 \ 11 \ 12 \ 13 \ 14
      \ 15 \ 16 \ 17 \ 18 \ 19 \ 20 \ 21

      \ [73] \ 22 \ 23 \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34
      \ 35 \ 36 \ 37 \ 38 \ 39

      \ [91] \ 40 \ 41 \ 42 \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  Here we see that -32 is the 19th element of the vector.

  We can store a vector in a variable:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b = 5:100
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b
    </input>

    <\output>
      \ [1] \ \ 5 \ \ 6 \ \ 7 \ \ 8 \ \ 9 \ 10 \ 11 \ 12 \ 13 \ 14 \ 15 \ 16
      \ 17 \ 18 \ 19 \ 20 \ 21 \ 22 \ 23

      [20] \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34 \ 35 \ 36
      \ 37 \ 38 \ 39 \ 40 \ 41 \ 42

      [39] \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50 \ 51 \ 52 \ 53 \ 54 \ 55
      \ 56 \ 57 \ 58 \ 59 \ 60 \ 61

      [58] \ 62 \ 63 \ 64 \ 65 \ 66 \ 67 \ 68 \ 69 \ 70 \ 71 \ 72 \ 73 \ 74
      \ 75 \ 76 \ 77 \ 78 \ 79 \ 80

      [77] \ 81 \ 82 \ 83 \ 84 \ 85 \ 86 \ 87 \ 88 \ 89 \ 90 \ 91 \ 92 \ 93
      \ 94 \ 95 \ 96 \ 97 \ 98 \ 99

      [96] 100
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      length(b)
    </input>

    <\output>
      [1] 96
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      ls()
    </input>

    <\output>
      [1] "a" "b"
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  length() tells us home many elements are in a vector. We can also see that
  the result of ls() is also a vector, a vector of strings.

  The function c() allows us to list elements in the vector one after the
  other:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(1,4,10,2)
    </input>

    <\output>
      [1] \ 1 \ 4 10 \ 2
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  With c() you can also join several vectors to one longer one

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(1,4:9,2)
    </input>

    <\output>
      [1] 1 4 5 6 7 8 9 2
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(1:3,1:3,1:3)
    </input>

    <\output>
      [1] 1 2 3 1 2 3 1 2 3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a=1:4
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(a,a,a)
    </input>

    <\output>
      \ [1] 1 2 3 4 1 2 3 4 1 2 3 4
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(a,ls())
    </input>

    <\output>
      [1] "1" "2" "3" "4" "a" "b"
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  In the last example you see that when you put a vector of numbers together
  with a vector of strings, the result is a vector of strings.

  With rep() you can repeat something several times, to create a long vector:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      rep(3,4)
    </input>

    <\output>
      [1] 3 3 3 3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      rep("R",5)
    </input>

    <\output>
      [1] "R" "R" "R" "R" "R"
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      rep(1:4,10)
    </input>

    <\output>
      \ [1] 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1
      2 3 4 1 2

      [39] 3 4
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <paragraph|Subsetting vectors, and operation on vectors>

  It is easy to get elements of a vector:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b
    </input>

    <\output>
      \ [1] \ \ 5 \ \ 6 \ \ 7 \ \ 8 \ \ 9 \ 10 \ 11 \ 12 \ 13 \ 14 \ 15 \ 16
      \ 17 \ 18 \ 19 \ 20 \ 21 \ 22 \ 23

      [20] \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34 \ 35 \ 36
      \ 37 \ 38 \ 39 \ 40 \ 41 \ 42

      [39] \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50 \ 51 \ 52 \ 53 \ 54 \ 55
      \ 56 \ 57 \ 58 \ 59 \ 60 \ 61

      [58] \ 62 \ 63 \ 64 \ 65 \ 66 \ 67 \ 68 \ 69 \ 70 \ 71 \ 72 \ 73 \ 74
      \ 75 \ 76 \ 77 \ 78 \ 79 \ 80

      [77] \ 81 \ 82 \ 83 \ 84 \ 85 \ 86 \ 87 \ 88 \ 89 \ 90 \ 91 \ 92 \ 93
      \ 94 \ 95 \ 96 \ 97 \ 98 \ 99

      [96] 100
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[2]
    </input>

    <\output>
      [1] 6
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[2]=13
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[2]
    </input>

    <\output>
      [1] 13
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b
    </input>

    <\output>
      \ [1] \ \ 5 \ <with|color|red|13> \ \ 7 \ \ 8 \ \ 9 \ 10 \ 11 \ 12 \ 13
      \ 14 \ 15 \ 16 \ 17 \ 18 \ 19 \ 20 \ 21 \ 22 \ 23

      [20] \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34 \ 35 \ 36
      \ 37 \ 38 \ 39 \ 40 \ 41 \ 42

      [39] \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50 \ 51 \ 52 \ 53 \ 54 \ 55
      \ 56 \ 57 \ 58 \ 59 \ 60 \ 61

      [58] \ 62 \ 63 \ 64 \ 65 \ 66 \ 67 \ 68 \ 69 \ 70 \ 71 \ 72 \ 73 \ 74
      \ 75 \ 76 \ 77 \ 78 \ 79 \ 80

      [77] \ 81 \ 82 \ 83 \ 84 \ 85 \ 86 \ 87 \ 88 \ 89 \ 90 \ 91 \ 92 \ 93
      \ 94 \ 95 \ 96 \ 97 \ 98 \ 99

      [96] 100
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  But it is also easy to address subvectors of vectors:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[1:4]
    </input>

    <\output>
      [1] \ 5 13 \ 7 \ 8
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[3:7]
    </input>

    <\output>
      [1] \ 7 \ 8 \ 9 10 11
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[c(1,3,5)]
    </input>

    <\output>
      [1] 5 7 9
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  You just list inside the square brackets <verbatim|[]> the vector of the
  elements you are addressing. You can also set them:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[2:6]
    </input>

    <\output>
      [1] 13 \ 7 \ 8 \ 9 10
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[2:6]=rep(1,5)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[2:6]
    </input>

    <\output>
      [1] 1 1 1 1 1
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b
    </input>

    <\output>
      \ [1] \ \ 5 \ \ 1 \ \ 1 \ \ 1 \ \ 1 \ \ 1 \ 11 \ 12 \ 13 \ 14 \ 15 \ 16
      \ 17 \ 18 \ 19 \ 20 \ 21 \ 22 \ 23

      [20] \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34 \ 35 \ 36
      \ 37 \ 38 \ 39 \ 40 \ 41 \ 42

      [39] \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50 \ 51 \ 52 \ 53 \ 54 \ 55
      \ 56 \ 57 \ 58 \ 59 \ 60 \ 61

      [58] \ 62 \ 63 \ 64 \ 65 \ 66 \ 67 \ 68 \ 69 \ 70 \ 71 \ 72 \ 73 \ 74
      \ 75 \ 76 \ 77 \ 78 \ 79 \ 80

      [77] \ 81 \ 82 \ 83 \ 84 \ 85 \ 86 \ 87 \ 88 \ 89 \ 90 \ 91 \ 92 \ 93
      \ 94 \ 95 \ 96 \ 97 \ 98 \ 99

      [96] 100
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>

    \;
  </session>>

  Mathematical operations will usually work on a whole vector:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a=1:4; print(a)
    </input>

    <\output>
      [1] 1 2 3 4
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a+2
    </input>

    <\output>
      [1] 3 4 5 6
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a * 3
    </input>

    <\output>
      [1] \ 3 \ 6 \ 9 12
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a ^ 7
    </input>

    <\output>
      [1] \ \ \ \ 1 \ \ 128 \ 2187 16384
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      sin(a)
    </input>

    <\output>
      [1] \ 0.8414710 \ 0.9092974 \ 0.1411200 -0.7568025
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  Other than strings and numbers, there are also vectors of boolean values
  (i.e. TRUE and FALSE)

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a = 1:4 ; print(a)
    </input>

    <\output>
      [1] 1 2 3 4
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a\<less\>2
    </input>

    <\output>
      [1] \ TRUE FALSE FALSE FALSE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a\<gtr\>2
    </input>

    <\output>
      [1] FALSE FALSE \ TRUE \ TRUE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a==2
    </input>

    <\output>
      [1] FALSE \ TRUE FALSE FALSE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(T,T,F)
    </input>

    <\output>
      [1] \ TRUE \ TRUE FALSE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  You see that one can use T and F as an abbreviation for TRUE and FALSE.
  Also notice that to test for equality, we used two equal signs: '=='.

  Boolean vectors give an alternative way to get at elements of a vector:
  instead of listing the elements that we want to address, we can give a
  boolean vector saying if we want or don't want certain elements:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a
    </input>

    <\output>
      [1] 1 2 3 4
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a[c(F,T,T,F)]
    </input>

    <\output>
      [1] 2 3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  This gives us very convenient access to elements:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b
    </input>

    <\output>
      \ [1] \ \ 5 \ \ 1 \ \ 1 \ \ 1 \ \ 1 \ \ 1 \ 11 \ 12 \ 13 \ 14 \ 15 \ 16
      \ 17 \ 18 \ 19 \ 20 \ 21 \ 22 \ 23

      [20] \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34 \ 35 \ 36
      \ 37 \ 38 \ 39 \ 40 \ 41 \ 42

      [39] \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50 \ 51 \ 52 \ 53 \ 54 \ 55
      \ 56 \ 57 \ 58 \ 59 \ 60 \ 61

      [58] \ 62 \ 63 \ 64 \ 65 \ 66 \ 67 \ 68 \ 69 \ 70 \ 71 \ 72 \ 73 \ 74
      \ 75 \ 76 \ 77 \ 78 \ 79 \ 80

      [77] \ 81 \ 82 \ 83 \ 84 \ 85 \ 86 \ 87 \ 88 \ 89 \ 90 \ 91 \ 92 \ 93
      \ 94 \ 95 \ 96 \ 97 \ 98 \ 99

      [96] 100
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[b\<less\>12]
    </input>

    <\output>
      [1] \ 5 \ 1 \ 1 \ 1 \ 1 \ 1 11
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b[b\<gtr\>90] = b[b\<gtr\>90] + 4
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b
    </input>

    <\output>
      \ [1] \ \ 5 \ \ 1 \ \ 1 \ \ 1 \ \ 1 \ \ 1 \ 11 \ 12 \ 13 \ 14 \ 15 \ 16
      \ 17 \ 18 \ 19 \ 20 \ 21 \ 22 \ 23

      [20] \ 24 \ 25 \ 26 \ 27 \ 28 \ 29 \ 30 \ 31 \ 32 \ 33 \ 34 \ 35 \ 36
      \ 37 \ 38 \ 39 \ 40 \ 41 \ 42

      [39] \ 43 \ 44 \ 45 \ 46 \ 47 \ 48 \ 49 \ 50 \ 51 \ 52 \ 53 \ 54 \ 55
      \ 56 \ 57 \ 58 \ 59 \ 60 \ 61

      [58] \ 62 \ 63 \ 64 \ 65 \ 66 \ 67 \ 68 \ 69 \ 70 \ 71 \ 72 \ 73 \ 74
      \ 75 \ 76 \ 77 \ 78 \ 79 \ 80

      [77] \ 81 \ 82 \ 83 \ 84 \ 85 \ 86 \ 87 \ 88 \ 89
      \ <with|color|red|<with|color|black|90> \ 95 \ 96 \ 97 \ 98 \ 99 100
      101 102 103>

      [96] <with|color|red|104>
    </output>

    \;
  </session>>

  When you join a boolean vector to a numeric vector, TRUE becomes 1, and
  FALSE becomes 0:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      c(T,F,3)
    </input>

    <\output>
      [1] 1 0 3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a\<less\>10
    </input>

    <\output>
      \ [1] \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE
      FALSE FALSE FALSE

      [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
      FALSE

      [25] FALSE FALSE FALSE FALSE FALSE FALSE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      (a\<less\>10)+2
    </input>

    <\output>
      \ [1] 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  The paratheses above are necessary, and one often needs them in R. Compare:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a\<less\>10
    </input>

    <\output>
      \ [1] \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE
      FALSE FALSE FALSE

      [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
      FALSE

      [25] FALSE FALSE FALSE FALSE FALSE FALSE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a\<less\>10+2
    </input>

    <\output>
      \ [1] \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE \ TRUE
      \ TRUE \ TRUE FALSE

      [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
      FALSE

      [25] FALSE FALSE FALSE FALSE FALSE FALSE
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      1:10
    </input>

    <\output>
      \ [1] \ 1 \ 2 \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      1:10+2
    </input>

    <\output>
      \ [1] \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10 11 12
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      1:(10+2)
    </input>

    <\output>
      \ [1] \ 1 \ 2 \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10 11 12
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      length(a)
    </input>

    <\output>
      [1] 30
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      1:length(a)-1
    </input>

    <\output>
      \ [1] \ 0 \ 1 \ 2 \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10 11 12 13 14 15 16 17
      18 19 20 21 22 23 24

      [26] 25 26 27 28 29
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      1:(length(a)-1)
    </input>

    <\output>
      \ [1] \ 1 \ 2 \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10 11 12 13 14 15 16 17 18 19
      20 21 22 23 24 25

      [26] 26 27 28 29
    </output>

    \;
  </session>>

  I often make the above mistake.

  If you want to address all elements but some, you use negative indexes:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a
    </input>

    <\output>
      \ [1] \ 1 \ 2 \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10 11 12 13 14 15 16 17 18 19
      20 21 22 23 24 25

      [26] 26 27 28 29 30
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a[-1]
    </input>

    <\output>
      \ [1] \ 2 \ 3 \ 4 \ 5 \ 6 \ 7 \ 8 \ 9 10 11 12 13 14 15 16 17 18 19 20
      21 22 23 24 25 26

      [26] 27 28 29 30
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      a[-(1:10)]
    </input>

    <\output>
      \ [1] 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <subsection|What is statistics?>

  ``Statistics is the science of learning from experience'' (Brad Efron)

  Statistics can do various things, here we will deal with the following:

  <\itemize-minus>
    <item>Given an experiment we would like to estimate a parameter (in the
    world).

    <item>Given an experiment, we would like to test whether a certain
    hypothesis is can be said to be unlikely.
  </itemize-minus>

  These are essencially the same thing. If we knew the world exactly, we
  would be able to say for sure if a hypothesis is true or false, and we
  would know the parameter exactly.

  Two factors prevent us from gaining certainty:

  <\enumerate-numeric>
    <item>Sampling

    <item>Measurement error
  </enumerate-numeric>

  Let us look at an example:

  Let us say that in a school there are 3000 students, and that we wish to
  know the average height.

  First, let us chose the heights:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      heights=rnorm(3000,mean=170,sd=10)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      hist(heights);v()
    </input>

    <\output>
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    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  These are the heights of all the students in school. We can easily
  calculate their mean:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      mean(heights)
    </input>

    <\output>
      [1] 170.2498
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  Now let us assume that we want to estimate the mean height. we take 10
  students, measure their height with an error of around 1cm, and then round
  to the nearest cm:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      measured.heights=sample(heights,10)+rnorm(10,mean=0,sd=1)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      measured.heights=round(measured.heights)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      measured.heights
    </input>

    <\output>
      \ [1] 176 172 149 186 179 168 146 187 166 160
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  Now we can calculate the mean height in the sample

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      mean(measured.heights)
    </input>

    <\output>
      [1] 168.9
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  So, we know that this is the mean of the sample. But what does it say about
  the real mean? What are the ranges that we believe now the real mean to be?

  If we knew the sampling process, and all the various errors involved in
  measuring (and in this case we do know it), then we could estimate how far
  we are from the real mean.\ 

  But how would we know all those parameters? We would have to estimate them,
  too!

  Bootstraping (boot-straping) allows us some magic without all the
  estimation. It says that a good estimate for distribution that we measured
  are our measurements. so instead of trying to estimate heights and their
  error and sampling, we just sample from the measurements we have:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b=sample(measured.heights,10,replace=T)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      mean(b)
    </input>

    <\output>
      [1] 170.7
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b=sample(measured.heights,10,replace=T)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      mean(b)
    </input>

    <\output>
      [1] 172.2
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      b=sample(measured.heights,10,replace=T)
    </input>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      mean(b)
    </input>

    <\output>
      [1] 169.3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  \ Now we have some idea in what range the real mean could be.

  <paragraph|So?>

  This was done to show two things:

  <\enumerate-numeric>
    <item>R is really conventient for addressing such matters. We can easily
    simulate situations and then assess our statistical methods.

    <item>Bootstraping is useful, simple, and (as we'll see later),
    convenient to do with R.
  </enumerate-numeric>

  \;

  <subsection|Some simple random functions in R>

  We saw the following 2 ways of generating random data in R:

  <paragraph|<verbatim|sample>>

  Sample randomly:

  Roll a die

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      sample(1:6,1)
    </input>

    <\output>
      [1] 3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  Roll 50 die:

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      sample(1:6,50,replace=T)
    </input>

    <\output>
      \ [1] 3 5 6 1 6 5 1 3 2 2 6 5 5 4 1 1 4 6 6 3 4 2 5 5 4 3 3 2 5 5 5 2 2
      2 6 5 2 4

      [39] 5 1 6 5 6 1 6 3 5 6 4 3
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  or

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      sample(6,50,replace=T)
    </input>

    <\output>
      \ [1] 3 1 3 5 3 2 4 4 3 4 1 1 3 3 5 5 4 5 2 5 1 4 3 1 4 2 2 2 1 1 3 6 5
      6 6 1 4 5

      [39] 2 6 1 5 2 1 3 1 2 2 4 1
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      \;
    </input>
  </session>>

  <paragraph|<verbatim|rnorm>>

  Sample from a normal distibution

  <with|prog-language|r|prog-session|default|<\session>
    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      rnorm(10)
    </input>

    <\output>
      \ [1] -1.9329962 \ 1.0924528 \ 0.5751292 -0.3561676 \ 0.2812530
      -1.3551893

      \ [7] -1.4555352 \ 1.7605307 -0.6611010 \ 0.6395928
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      rnorm(10,mean=3,sd=0.1)
    </input>

    <\output>
      \ [1] 3.032633 3.123962 2.989857 3.142417 2.874144 2.855629 3.048683
      2.898982

      \ [9] 2.923673 2.987789
    </output>

    <\input|<with|color|red|\<gtr\> <with|color|black|>>>
      hist(rnorm(1000));v()
    </input>

    <\output>
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      <with|par-left|<quote|6fn>|font-size|<quote|0.84>|So?<value|toc-dots><pageref|toc-17>>

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      <with|par-left|<quote|3fn>|<value|toc-dots><pageref|toc-19>>

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