Chronological Thread 

< Chronological >      < Thread >

---

address@hidden wrote:

I recently encountered the following problem: old TeXmacs files, that I created with a previous version of TeXmacs do not open correctly with the current version. I think the problem is inline images. The file can be downloaded from http://email.eva.mpg.de/~lachmann/R-course/Rcourse1.tm
(you can see what it is supposed to look like by looking at
http://email.eva.mpg.de/~lachmann/R-course/Rcourse1.pdf)
I tried it on old versions, and it seems to load fine under 1.0.3.XX, and has
problems starting 1.0.4
I was using the static linked versions downloaded from the texmacs.org site.
Is there a way to make the files work with the new versions of TeXmacs, or
convert them? They contain a lecture on R that I would like to give again.
The current solution is to retype it...

The images don't work, but when editing the markup, one can
see that the main bug (which turns the height of your pages
to a ridiculous size) is in :
[[
<\initial>
<\collection>
...
</collection>
</initial>
]]

(I just tried to remove doubtful parts out of the markup
till I obtained something that approximately works ; and
yes, even for TeXmacs users, emacs is still useful ;-).

Best, Henri

P.S : The hacked version of your file is
joined as an attachment to this email.
<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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bÝ+VÊêØÃÃ\|ÊÎ\\ëX\\iUŠV¨ÒKlá,¨ÑÈBE\>¢µMüXˆ%n›kӆG/¤†õp¥Í\t7

[[@O(•êqLãS`u¶®IeMnŸr\t½w¹.¼-sŸ»ÍäBwº¨t.u¯Gàaw»C¤n¹^½á-¼ä՟wˋ^ï7½ìõ\>Û_đ6¾ôEÛ{ë‹_™Í7¿üíØ}ûàxíC¹
.p˜¬kà×jÀ\nnp¬ìàû‰Á®ðÆ,Œa28öM@\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|GIF87aö
\0÷\0\0\0\0\0\0\0ÿ
%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ0‘2•–3/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XY–—Y–˜Zk\\Z—™[[[_
 ‡`N8`¢¤aŸŸb…
‚daOe[6g®¯hhghhhhlhiiij´µlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{ÐÒ\|ÐÒ\|ÑÓ}hP~xaƒjLƒkLƒlNˆŒˆˆ¸´Šx\\‘Ä¿‘Å¿’­”–ËƗƒ^˜œ˜™™™™™ÿ™·›
…fŸ8SŸu …
`¡Œm¨¬¨©Šd«—`¬è⮪®®Ï²¯j±›\|´Ö¸·–n·šv¸¼¸¹¦Œ½œs¾©ŽÀ¡zžtíjŦÇhIÇ©~ɬ…
Ì®ˆÌ±Ð¬ÐÐÐÓ°…
Ó°†Ó¸–Ô¹˜Ôº™Ö¸’×·Ù½šÜ¹ŽÝ¾•ÞŦßÁ›àÄ¡ãÇ¥äË«å̬æÑ·èÒ¶èÓ¹éÒ}êÒ~îրÿ\0\0ÿÿÿtt\0\0\0\0

€\0±N\0\0XÔð\|îÿÿ¿¿³(ì¬=Š@\0
PP\0tt\0ö¸
ïî\0ÿÿ\0¿¿(\|\0=D\0\0@@\0PP
tt¼(Èðïî¿¿¿ÀN\|ðGDÿ¿@@ÄPðt\0ÿ\0¿\0
P’±t-@XLØð{îóÔ\|¬`D!@@`Pà
t\|ö\0@
\0î\0\0¿\0’\0\0-\0\0@\0Tt0\0X\0ï\0\0ÿ\0\0¿\0\0P\0qt\0!\0@
(øñ=îÿÿ¿@¿®`\|™D`Í\0\0\0\0\0\0ñPzt
\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0ö
\0\0þ\0‹`H°
 Áƒ*\\È°¡Ã‡#JœH±¢Å‹3jÜȱ£Ç


D²¤É“(Sª\\ɲ¥Ë—0cʜI³¦Í›8sêÜɳ§ÏŸ@ƒž$"´¨Ñ£H“*]Ê´©Ó§PSJ•$LU
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«tkU³dÓª]˶­Ê±;
ȝà’\\—tóÀ«w®K´&/\t\<X(`·ˆ+^Œ.É\0#Kvù¥²åÁ_([Þ\\Y3g˱ž$LZ°JÓ6g@¢ukbG0€
 
¶mƸsë†\t¥äß
f’N{¸´ñ•—V®Y³RõÑ3V¼ÈQ\t`Œuënh¿‚wïvþ‹/¾7Pºvõ²ì›w={¿(
“68ütʹÌS:t@î
&)]З\0œ¡’
Ì%@÷]‡ÝvÜ}yVˆ˜y÷½w×J›]òYf~¸K"ŽŸh€ÌwP})%gÒ^$
ßIû
"À
-ÉeIrxÀt(5
ÀŽgÄ\0Bƒf·]\<ð]xF)åW¢T"h+¡×^L.–Ô%uï5‡"a\n†Òr)š´†ŒËɨŠ'
@
9°#r
x’\0蹞ƒc(©]”à€wL©è¢PUy’†2}Ép
™¥?¡5˜†u¡ö¢Œ_nù¦JLØY着ðÙ'Jr2˜£kþ¯ÉÁb¼P@m0ªë®G9š¥À¦Æ°Ä+ǂ‘阂
0³ÐB[X†—07cKû\td–¦’\0lkRAˆ‹\0z¤›.
o´»…h Ã
PlÀë½øò$„oÀ×R¿ÀEêiJ•\|‰ÁJÒ¦Ðb­\\Ӟ&#Œ¡©$@\|5pÁý\t``JgôÀ
®ž«îºí²!…
\<ø°ÂOtïÌ4Ï´ïI\0×$©K¿Yj©¿=i*˜ÃDG;PÄ-²&›Ë¡y"ÈsòÅÄgx
ÂÈ£$‡
µÉ'³ûF}P¡ƒ
58sÍl·­ÒÍ\<õ•\|,›,²—(ë“þÐé=×ÑŸ¹a^זä\\©¨r›x‚·¤-ØêÒFn´QÌà2»í¹ÛpŸËiJzh"L’î#§?½ð`e"­&Ä%­™Ÿ›4ÂYÒ㧚ômë*yÑí‹K_¼s‡Qà@)¸ðÁçÔ×úIWv&ú†i¾Ä:÷Øg¢Â)’¹¢™¢{YäÜÅÞˆ€h5
V\0àŹ–ôo\t%dðÃ
øp#ŒÀ,Ȃ\\P½âëzŸ‚TKX"ñ
E\>æ#YÒ%ºåŽU_ë]ªJ€’•Äˆ¼p€Æ=Ê–ÀC"ÁˆEäAG`€¸
 
†8ð‡þº‚`I,È­NÍ̓\>aù^gô¡î%‡¹€×RÈ
õ¥
~2‰bà5¹4à~ëƒa1‰G$qÀBBp5¤\0ˆpœ’WÇÏ\|ÁtœqUBÄŽ¦‰{I
ý¸/D'Kþ«D$áE4ât¨v 5` Ž˜¬Ð£ÒÇÑŠºcbi
ʪ\0Àx=Ø$aˆ;”a\nP€Tàdò–âÙ$¯j´^âò—À¤ÉÜæˤ3˜ÈLfJ†Ù¶cřʌ&2™)ÍjZóš?¡&6·ÉÍnºäH§8ÇIÎršóœèL§:×ÉÎvºóðŒ§\<çIÏzÚóžø2̧\>÷ÉÏ~ú“œ6¸JHJЂô
 M¨BÊІ:Ô

}¨D'JъZô¢ͨ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\0ÿ
%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ0‘2•–3/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XY–—Y–˜Zk\\Z—™[[[_
 ‡`N8`¢¤aŸŸb…
‚daOe[6g®¯hhghhhhlhiiij´µlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{ÐÒ\|ÐÒ\|ÑÓ}hP~xaƒjLƒkLƒlNˆŒˆˆ¸´Šx\\‘Ä¿‘Å¿’­”–ËƗƒ^˜œ˜™™™™™ÿ™·›
…fŸ8SŸu …
`¡Œm¨¬¨©Šd«—`¬è⮪®®Ï²¯j±›\|´Ö¸·–n·šv¸¼¸¹¦Œ½œs¾©ŽÀ¡zžtíjŦÇhIÇ©~ɬ…
Ì®ˆÌ±Ð¬ÐÐÐÓ°…
Ó°†Ó¸–Ô¹˜Ôº™Ö¸’×·Ù½šÜ¹ŽÝ¾•ÞŦßÁ›àÄ¡ãÇ¥äË«å̬æÑ·èÒ¶èÓ¹éÒ}êÒ~îրÿ\0\0ÿÿÿ\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0\0
\tH°
 Á˜*T˜p¡C„/Iœ8ñ`C‚3J4xQ 
Ə;fÄD’dF‚G–,yR`ʉ+cR„èQ"€›8s¨èràD\0$\nÊÐËK71\tUŠ³èQ¥P‡šÜس&Ò¥9§^¢\tˆb̕3«võúµ¥QŒdY†kõcQ¶mA†ŒèÖâûïÚÕË·/Á€\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\0ÿ
%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ0‘2•–3/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XY–—Y–˜Zk\\Z—™[[[_
 ‡`N8`¢¤aŸŸb…
‚daOe[6g®¯hhghhhhlhiiij´µlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{ÐÒ\|ÐÒ\|ÑÓ}hP~xaƒjLƒkLƒlNˆŒˆˆ¸´Šx\\‘Ä¿‘Å¿’­”–ËƗƒ^˜œ˜™™™™™ÿ™·›
…fŸ8SŸu …
`¡Œm¨¬¨©Šd«—`¬è⮪®®Ï²¯j±›\|´Ö¸·–n·šv¸¼¸¹¦Œ½œs¾©ŽÀ¡zžtíjŦÇhIÇ©~ɬ…
Ì®ˆÌ±Ð¬ÐÐÐÓ°…
Ó°†Ó¸–Ô¹˜Ôº™Ö¸’×·Ù½šÜ¹ŽÝ¾•ÞŦßÁ›àÄ¡ãÇ¥äË«å̬æÑ·èÒ¶èÓ¹éÒ}êÒ~îրÿ\0\0ÿÿÿ\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0n\0
\tH°
 Áƒ*\\È°!ÁK—&Œˆp͆ØxqaF\0èhÐ" 
kFZ‰ãǍ0n¼t‘¤Ä“#CÞ1¥J‹&ú\t“eBŸSv4jpãÀŒF™zéôæǝ\<¯bÝʵ«W¬

\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\0ÿ
%%;\<(!JK!,+"0'&$(,((wx+}~/OP/PC/QQ0‘2•–3/%3VR8\<88KI8LJ;OM;de\<2$\>hiAmnG`^HLHI_ZJ?1JE8O)OPCPPCPmjProQnkTroTUtqVI6VtqWI6WVGX\\XY–—Y–˜Zk\\Z—™[[[_
 ‡`N8`¢¤aŸŸb…
‚daOe[6g®¯hhghhhhlhiiij´µlmlnnmoZ@o\\EooooxdtbJwk@x\|xxx{ÐÒ\|ÐÒ\|ÑÓ}hP~xaƒjLƒkLƒlNˆŒˆˆ¸´Šx\\‘Ä¿‘Å¿’­”–ËƗƒ^˜œ˜™™™™™ÿ™·›
…fŸ8SŸu …
`¡Œm¨¬¨©Šd«—`¬è⮪®®Ï²¯j±›\|´Ö¸·–n·šv¸¼¸¹¦Œ½œs¾©ŽÀ¡zžtíjŦÇhIÇ©~ɬ…
Ì®ˆÌ±Ð¬ÐÐÐÓ°…
Ó°†Ó¸–Ô¹˜Ôº™Ö¸’×·Ù½šÜ¹ŽÝ¾•ÞŦßÁ›àÄ¡ãÇ¥äË«å̬æÑ·èÒ¶èÓ¹éÒ}êÒ~îրÿ\0\0ÿÿÿ\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0,\0\0\0\0\0\0\0\0
\tH°
 Á˜*T˜p¡C„/Iœ8ñ`C‚3J4xQ 
Ə;fÄD’dF‚G–,yR`ʉ+cR„èQ"€›8s¨èràD\0$\nÊÐËK71\tUŠ³èQ¥P‡šÜس&Ò¥9§^¢\tˆb̕3«võúµ¥QŒdY†kõcQ¶mA†ŒèÖâûïÚÕË·/Á€\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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EPSF-3.0\n%%DocumentNeededResources: font Helvetica\n%%+ font
Helvetica-Bold\n%%+ font Helvetica-Oblique\n%%+ font
Helvetica-BoldOblique\n%%+ font Symbol\n%%Title: R Graphics
Output\n%%Creator: R Software\n%%Pages: (atend)\n%%BoundingBox: 162 252
450 540\n%%EndComments\n%%BeginProlog\n/bp \ { gs gs } def\n% begin
.ps.prolog\n/gs \ { gsave } def\n/gr \ { grestore } def\n/ep \ {
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\ { newpath } def\n/cp \ { closepath } def\n/f \ \ { fill } def\n/o
\ \ { stroke } def\n/c \ \ { newpath 0 360 arc } def\n/r \ \ { 4 2 roll
moveto 1 copy 3 -1 roll exch 0 exch rlineto 0 rlineto -1 mul 0 exch
rlineto closepath } def\n/p1 \ { stroke } def\n/p2 \ { gsave bg
setrgbcolor fill grestore newpath } def\n/p3 \ { gsave bg setrgbcolor
fill grestore stroke } def\n/t \ \ { 6 -2 roll moveto gsave rotate\n
\ \ \ \ \ \ ps mul neg 0 2 1 roll rmoveto\n \ \ \ \ \ \ 1 index
stringwidth pop\n \ \ \ \ \ \ mul neg 0 rmoveto show grestore }
def\n/cl \ { grestore gsave newpath 3 index 3 index moveto 1 index\n
\ \ \ \ \ \ 4 -1 roll lineto \ exch 1 index lineto lineto\n
\ \ \ \ \ \ closepath clip newpath } def\n/rgb { setrgbcolor } def\n/s
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.5 0 90 t\n196.80 346.69 (100) .5 0 90 t\n196.80 400.52 (300) .5 0 90
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p1\n330.36 319.78 12.36 115.19 r p1\n342.72 319.78 12.36 82.09 r
p1\n355.08 319.78 12.36 33.37 r p1\n367.44 319.78 12.36 17.22 r
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p1\n404.53 319.78 12.36 0.27 r p1\nep\n%%Trailer\n%%Pages:
2\n%%EOF\n>|ps>||||||>
</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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</output>

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

\;
</body>

<\initial>
<\collection>
</collection>
</initial>

<\references>
<\collection>
<associate|toc-20|<tuple|2.|14>>
<associate|toc-10|<tuple|<uninit>|6>>
<associate|toc-21|<tuple|2.|14>>
<associate|toc-11|<tuple|<uninit>|6>>
<associate|toc-22|<tuple|2.|14>>
<associate|toc-12|<tuple|<uninit>|7>>
<associate|toc-23|<tuple|2.|15>>
<associate|toc-13|<tuple|<uninit>|7>>
<associate|toc-24|<tuple|2.|?>>
<associate|toc-14|<tuple|<uninit>|7>>
<associate|toc-15|<tuple|<uninit>|9>>
<associate|toc-16|<tuple|<uninit>|12>>
<associate|toc-17|<tuple|2.|14>>
<associate|toc-18|<tuple|2.|14>>
<associate|toc-19|<tuple|2.|14>>
<associate|toc-1|<tuple|<uninit>|2>>
<associate|toc-2|<tuple|<uninit>|2>>
<associate|toc-3|<tuple|<uninit>|4>>
<associate|toc-4|<tuple|<uninit>|4>>
<associate|toc-5|<tuple|<uninit>|4>>
<associate|toc-6|<tuple|<uninit>|4>>
<associate|toc-7|<tuple|<uninit>|4>>
<associate|toc-8|<tuple|<uninit>|5>>
<associate|toc-9|<tuple|<uninit>|5>>
</collection>
</references>

<\auxiliary>
<\collection>
<\associate|toc>
Lecture 1<value|toc-dots><pageref|toc-1>

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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


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

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

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

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


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


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


<with|par-left|<quote|6fn>|font-size|<quote|0.84>|<with|font-family|<quote|tt>|language|<quote|verbatim>|rnorm><value|toc-dots><pageref|toc-23>>
</associate>
</collection>
</auxiliary>

---

• help: change in file format?, lachmann, 04/19/2006
  • Re: [TeXmacs] help: change in file format?, Henri Lesourd, 04/19/2006

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