Editing Software Plugins and Codes (section)

===Reading a spreadsheet into R===

Refer to http://cran.r-project.org/doc/manuals/R-intro.html#The-read_002etable_0028_0029-function .  There is also a whole import/export manual for R at http://cran.r-project.org/doc/manuals/R-data.html

The first step is to export your spreadsheet as a text file from your spreadsheet program.  You might want to copy only the relevant columns into a new spreadsheet.  

If you are using Excel, I believe that you can export as a text file, although I am not certain of this.

I was using Apple's Numbers.  In Numbers, select the spreadsheet or the columns that you want to Export, then start up TextEdit.  Make sure that the new blank text document is plain text (Format -> Make Plain Test), then Paste in the spreadsheet.  This resulted in a text file in exactly the right format for importing into R, like this

 cage	fnbmd10
 20	0.72
 20.1	0.74
 20.1	1.02
 20.2	0.97
 20.2	0.84
 20.4	0.69
 20.4	0.98
 20.5	
 20.6	0.82

It may happen that there are some missing data in your columns (as in the above example).  This command (from the command line) will copy all lines from file fnbmd10.data to file fnbmd10_trimmed.data that have exactly two fields, which is what we want:

 awk '(NF==2) {print $0}' fnbmd10.data > fnbmd10_trimmed.data

If you have a column for sex, and you want to split it into two files, one for each sex, you can do this:

 awk '($2==0) {print $0}' input.txt > output_w.txt
 awk '($2==1) {print $0}' input.txt > output_m.txt

In this example, the sex is the second field (hence $2).  You will need to manually add the column headings again after doing this.

Once your text file looks correct, you can load it into R with the following command (from within R obviously):

 dataframe <- read.table("fnbmd10_trimmed.data", header=TRUE)

I recommend at this point using some of R's graphical capabilities to plot and examine the data, just to make sure it seems to be reasonable.

 plot (dataframe$cage, dataframe$fnbmd10)

====Tip: Setting the Working Directory in R====

 setwd("/Users/eric/Documents/change_point")

====Tip: Converting line endings====

In case it's required, this can be done from a command prompt in OS-X or Linux:

 cat input.txt | tr '\r' '\n' > output.txt