[R] Automate running files in R

[Jim Lemon]

Hi Serena,
I think the directory structure you have described is something like this:

mov_study___________________________
                 |                                                     |
             mov1                      ...                    mov9
             /       \                                            /         \
mov1_csv  mov1_graphs                 mov9_csv  mov9_graphs

If so, you can put your R scripts in the mov_study directory and
change directories like this:

for(movdir in paste0("mov",1:9,) {
 setwd(movdir)
 source("R1")
 source("R2")
 setwd("..")
}

In R1 and R2 add a "movdir" argument set the target directories for
your output like this:
 R1<-function(...,movdir=movdir)
 R2<-function(...,movdir=movdir)

 path_to_csv<-paste(movdir,"csv",sep="_")
 path_to_graph<-paste(movdir,"graphs",sep="_")

and when you write an output file:
# for CSV files
filename<-paste(path_to_csv,csvfilename,sep="/")
# for graph files
filename<-paste(path_to_graph,graphfilename,sep="/")

Obviously I can't test this on your directory structure, but I think
it will do what you want.

Jim

On Mon, Jul 23, 2018 at 6:26 AM, Serena De Stefani
<serenadestefani using gmail.com> wrote:
> I need to automate a process in R. Basically I have a an R script (I will
> call it R1) that needs three separate files to run. These three files are
> the results output of one trial in my study.
>
> So from each run in R I obtain the summary results for one trial, in a csv
> file, plus 32 graphs for each decision point in the trial.
>
> One subject goes through of nine trials. I was thinking about putting all
> the files generated by one subject in one big folder, so I will have 27
> files (three files times nine trials). This way I won't have to change
> working directory multiple times (I wonder if there is a way to have R open
> a folder with a certain name as directory, run a scripts, move the
> directory to the next folder, run the script again...)
>
> The trials are specified by the labels: AA AB AM BA BB BM MA MB MM. So for
> subject 1, trial 1, I will have three files with the ending
> …mov1_AA
>
> For subject one, trial 2, R should choose the three files with the ending …
> mov1_AB and so on.
>
> At each run, R should save the csv summary output in a folder called
> “summary_mov1” and name the files summary_mov1_AA, summary_mov1_AB etc. R
> should save the 32 graphs in a different folder, named mov1_graphs,
> graph1_mov1_AA, graph1_mov1_AB and so on (ideally, at this point another R
> script (R2) should take these nine csv files and build some graphs out of
> them).
>
> Once R has run R1 script nine times, I would proceed to a new subject.
>
> So basically: use R1 with three mov1 files, get a summary csv file in a
> summary folder (plus 32 graphs in a different folder).
>
> Do this nine times. Once one get the nine csv summary files in the same
> folder, use R2 to average them and build a graph.
>
> Then do this for each subject (right now I have 7).
>
> I have never done this type of automation so I am a bit lost. Any
> suggestions? Any examples you can point me to? Which would be the best
> workflow? At which level should I automate and which things should I rather
> do by hand?
>
> Thank you,
> Serena DeStefani
>
>         [[alternative HTML version deleted]]
>
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