<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>RstatisTik/RstatisTikPortal/RcourSe/FinalFunction</title><revhistory><revision><revnumber>16</revnumber><date>2015-03-16 17:23:05</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>15</revnumber><date>2015-03-15 15:12:19</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>14</revnumber><date>2015-03-15 15:07:19</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>13</revnumber><date>2015-03-15 15:07:01</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>12</revnumber><date>2015-03-15 15:06:43</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>11</revnumber><date>2015-03-15 15:05:21</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>10</revnumber><date>2015-03-15 15:04:05</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>9</revnumber><date>2015-03-15 15:03:30</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>8</revnumber><date>2015-03-15 14:59:46</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>7</revnumber><date>2015-03-15 14:51:46</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>6</revnumber><date>2015-03-15 14:51:00</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>5</revnumber><date>2015-03-15 14:39:56</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>4</revnumber><date>2015-03-15 09:40:54</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>3</revnumber><date>2015-03-15 08:39:38</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>2</revnumber><date>2015-03-15 08:36:34</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision><revision><revnumber>1</revnumber><date>2015-03-15 08:06:07</date><authorinitials>mandy.vogel@googlemail.com</authorinitials></revision></revhistory></articleinfo><section><title>Final Functions</title><section><title>Reading File() - going through the function line by line</title><para>Here is the function as whole, below we go through it line by line. </para><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><methodname><![CDATA[read.file]]></methodname><![CDATA[ <- ]]><methodname><![CDATA[function]]></methodname><![CDATA[(]]><methodname><![CDATA[file]]></methodname><![CDATA[,]]><methodname><![CDATA[skip]]></methodname><![CDATA[,]]><methodname><![CDATA[verbose]]></methodname><![CDATA[=]]><token><![CDATA[T]]></token><![CDATA[){]]>
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</programlisting><section><title>line 1</title><itemizedlist><listitem><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_1">line 1</link> gives the function its name including arguments and their default values </para></listitem><listitem><para>the file argument will take the file name and is without a default </para></listitem><listitem><para>skip takes a number which indicates how many lines will be skipped at the beginning of the file </para></listitem><listitem><para>verbose indicates if the file name will be printed out while reading </para></listitem></itemizedlist><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><![CDATA[ ]]><methodname><![CDATA[read.file]]></methodname><![CDATA[ <- ]]><methodname><![CDATA[function]]></methodname><![CDATA[(]]><methodname><![CDATA[file]]></methodname><![CDATA[,]]><methodname><![CDATA[skip]]></methodname><![CDATA[=3,]]><methodname><![CDATA[verbose]]></methodname><![CDATA[=]]><token><![CDATA[T]]></token><![CDATA[){]]>
</programlisting></section><section><title>line 2</title><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><![CDATA[ ]]><methodname><![CDATA[if]]></methodname><![CDATA[(]]><methodname><![CDATA[verbose]]></methodname><![CDATA[) ]]><methodname><![CDATA[print]]></methodname><![CDATA[(]]><methodname><![CDATA[paste]]></methodname><![CDATA[(]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[read"]]></phrase><![CDATA[, ]]><methodname><![CDATA[file]]></methodname><![CDATA[))]]>
</programlisting><itemizedlist><listitem><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_2">this line</link> just prints out the name of the file while reading it unless verbose is set to wrong </para></listitem></itemizedlist></section><section><title>Line 3-5</title><itemizedlist><listitem><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_3">here</link> we have the command to read in the text file </para></listitem><listitem><para>it takes the skip argument from above </para></listitem><listitem><para>we are setting sep which indicates the field separator to tab </para></listitem><listitem><para>set header to T because the file contains the columns names </para></listitem><listitem><para>with setting na.strings to the empty string or any string containing only spaces to we indicate to code this fields as missings </para></listitem><listitem><para><ulink url="https://wiki.init.mpg.de/IT4Science/RstatisTik/RstatisTikPortal/RcourSe/FinalFunction/IT4Science/RstatisTik/RstatisTikPortal/RcourSe/FinalFunction/ReadingFiles#">more on reading files</ulink>  </para></listitem></itemizedlist><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><![CDATA[ ]]><methodname><![CDATA[tmp]]></methodname><![CDATA[ <- ]]><methodname><![CDATA[read.table]]></methodname><![CDATA[(]]><methodname><![CDATA[file]]></methodname><![CDATA[,]]><methodname><![CDATA[skip]]></methodname><![CDATA[ = ]]><methodname><![CDATA[skip]]></methodname><![CDATA[,]]><methodname><![CDATA[sep]]></methodname><![CDATA[ = ]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[\t"]]></phrase><![CDATA[,]]>
<![CDATA[                          ]]><methodname><![CDATA[header]]></methodname><![CDATA[=]]><token><![CDATA[T]]></token><![CDATA[,]]><methodname><![CDATA[na.strings]]></methodname><![CDATA[ = ]]><methodname><![CDATA[c]]></methodname><![CDATA[(]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[ +"]]></phrase><![CDATA[,]]><phrase><![CDATA["]]></phrase><phrase><![CDATA["]]></phrase><![CDATA[),]]>
<![CDATA[                          ]]><methodname><![CDATA[fill]]></methodname><![CDATA[=]]><token><![CDATA[T]]></token><![CDATA[)]]>
</programlisting></section><section><title>Line 7</title><itemizedlist><listitem><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_7">here</link> we remove all rows with a missing Subject field </para></listitem><listitem><para>therefore we need indexing </para></listitem><listitem><para>is.na(x) gives back a logical vector, containing TRUE for missings in x and FALSE for any existing value </para></listitem><listitem><para><ulink url="https://wiki.init.mpg.de/IT4Science/RstatisTik/RstatisTikPortal/RcourSe/FinalFunction/IT4Science/RstatisTik/RstatisTikPortal/RcourSe/FinalFunction/indeXing#">read more on indexing/subscripting</ulink> </para></listitem></itemizedlist><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><![CDATA[    ]]><methodname><![CDATA[tmp]]></methodname><![CDATA[ <- ]]><methodname><![CDATA[tmp]]></methodname><methodname><![CDATA[[]]></methodname><![CDATA[!]]><methodname><![CDATA[is.na]]></methodname><![CDATA[(]]><methodname><![CDATA[tmp]]></methodname><![CDATA[$]]><methodname><![CDATA[Subject]]></methodname><![CDATA[),]]><methodname><![CDATA[]]]></methodname><![CDATA[ ]]>
</programlisting></section><section><title>Line 9-10</title><itemizedlist><listitem><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_9">Line 9 and 10</link> print the content of Subject to stdout if the content is not in standard form </para></listitem><listitem><para>str_detect() is a R function and part of the stringr package it gives back a logical value dependend on if the pattern is contained in the given string </para></listitem><listitem><para>the pattern is a regular expression which is more flexible than to use absolut strings </para></listitem><listitem><para>so we check every entry of Subject, take the negation and sum the resulting logical vector - this sum is zero if no deviant Subject coding is found, otherwise the print command is executed </para></listitem><listitem><para><ulink url="https://wiki.init.mpg.de/IT4Science/RstatisTik/RstatisTikPortal/RcourSe/FinalFunction/IT4Science/RstatisTik/RstatisTikPortal/RcourSe/FinalFunction/StringOperations#">some basic information about strings and regular expression can be found here</ulink> </para></listitem></itemizedlist><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><![CDATA[    ]]><methodname><![CDATA[if]]></methodname><![CDATA[(]]><methodname><![CDATA[sum]]></methodname><![CDATA[(!]]><methodname><![CDATA[str_detect]]></methodname><![CDATA[(]]><methodname><![CDATA[tmp]]></methodname><![CDATA[$]]><methodname><![CDATA[Subject]]></methodname><![CDATA[,]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[^0[012][0-9]_[1-8]$|^0[012][0-9]_test[12]$"]]></phrase><![CDATA[)))]]>
<![CDATA[        ]]><methodname><![CDATA[print]]></methodname><![CDATA[(]]><methodname><![CDATA[paste]]></methodname><![CDATA[(]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[id"]]></phrase><![CDATA[,]]><methodname><![CDATA[tmp]]></methodname><![CDATA[$]]><methodname><![CDATA[Subject]]></methodname><methodname><![CDATA[[1]]></methodname><methodname><![CDATA[]]]></methodname><![CDATA[))]]>
</programlisting></section><section><title>Line 12</title><itemizedlist><listitem><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_12">Line 12</link> checks if there is at least one line containing the code for a correct (hit) or incorrect (incorrect) answer </para></listitem><listitem><para>if there is no such line the function gives back a NULL value </para></listitem></itemizedlist><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><![CDATA[ ]]><methodname><![CDATA[if]]></methodname><![CDATA[(]]><methodname><![CDATA[sum]]></methodname><![CDATA[(]]><methodname><![CDATA[tmp]]></methodname><![CDATA[$]]><methodname><![CDATA[Stim.Type]]></methodname><![CDATA[ %in% ]]><methodname><![CDATA[c]]></methodname><![CDATA[(]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[hit"]]></phrase><![CDATA[,]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[incorrect"]]></phrase><![CDATA[))==0) ]]><methodname><![CDATA[return]]></methodname><![CDATA[(]]><symbol><![CDATA[NULL]]></symbol><![CDATA[)]]>
</programlisting><para><link linkend="CA-a8692f97d06bd15e4a572260cf8b72ef3c9d984e_18">Line 18</link>:  </para><para><link linkend="CA-efbf8a93fbd22f17bfbdcb535a155bbb9c389093_22">Line 22</link>:  </para></section></section><section><title>Funtion: Reading All Files from a DIRECTORY</title><programlisting format="linespecific" language="highlight" linenumbering="numbered" startinglinenumber="1"><methodname><![CDATA[read.files]]></methodname><![CDATA[ <- ]]><methodname><![CDATA[function]]></methodname><![CDATA[(]]><methodname><![CDATA[filesdir]]></methodname><![CDATA[,]]><methodname><![CDATA[skip]]></methodname><![CDATA[=3,]]><symbol><![CDATA[...]]></symbol><![CDATA[){]]>
<![CDATA[    ]]><methodname><![CDATA[files]]></methodname><![CDATA[ <- ]]><methodname><![CDATA[paste]]></methodname><![CDATA[(]]><methodname><![CDATA[filedir]]></methodname><![CDATA[,]]><methodname><![CDATA[dir]]></methodname><![CDATA[(]]><methodname><![CDATA[filedir]]></methodname><![CDATA[),]]><methodname><![CDATA[sep]]></methodname><![CDATA[=]]><phrase><![CDATA["]]></phrase><phrase><![CDATA[/"]]></phrase><![CDATA[)]]>
<![CDATA[    ]]><methodname><![CDATA[Reduce]]></methodname><![CDATA[(]]><methodname><![CDATA[rbind]]></methodname><![CDATA[,]]><methodname><![CDATA[lapply]]></methodname><![CDATA[(]]><methodname><![CDATA[files]]></methodname><![CDATA[,]]><methodname><![CDATA[read.file]]></methodname><![CDATA[,]]><methodname><![CDATA[skip]]></methodname><![CDATA[=]]><methodname><![CDATA[skip]]></methodname><![CDATA[))}]]>
</programlisting></section></section></article>