I usually switch between Windows and Mac while accessing my R codes from Google Drive. One of the repetitive tasks I need to do whenever I switch between my desktop and laptop is to (un-)comment the file path to the respective directories where my google drive is located. Can anyone share an automation code on how to do this? I am already doing this in Stata.
Usually, for each project or analysis that I start I use a "config-like" R file which looks more or less like this:
.job <- list ()
## rootDir in my laptop
.job$base_data_dir <- file.path ("", "home", "dmontaner", "datos")
## rootDir in my server
##.job$base_data_dir <- file.path ("", "scratch", "datos")
In this "config" file I set the root directory where I am keeping the data in each machine. I keep a different "config" file in each machine and do not synchronize them via dropbox.
Then I start my R scripts with this line:
try (source (".job.r"))
and when I have to address any file or folder I do:
setwd (file.path (.job$base_data_dir, "raw_data"))
...
setwd (file.path (.job$base_data_dir, "results"))
Like this, if you keep the internal structure of the data directory in both machines, you are able to set the base or root dir where it is allocated and reach the data in both machines.
Also the file.path function takes care of the changes in operative system.
In the R session I call the config variable starting with a dot for it to be a hidden variable so I do not see it when I do a ls () or similar things.
That's my solution:
setwd(ifelse(.Platform$OS.type=="unix", "/Users/.../Google Drive", "C:/Users/.../Google Drive/"))
Related
I would like to write a csv file to a remote folder in a computer identified by user#ip-address, running a different OS (e.g. my current OS is iOS and remote OS is Ubuntu-19).
Below, the straightforward code saves a file in local folder
write.csv(1:10, 'Save.csv')
But I want to have something like
write.csv(1:10, "root#xx.xxx.x.x:/folder/Save.csv")
Any pointer will be highly appreciated.
This seems to be possible with the cp.remote function of the ssh-utils package
https://cran.r-project.org/web/packages/ssh.utils/ssh.utils.pdf
A wrapper around the scp shell command that handles local/remote files and allows copying between remote hosts via the local machine.
cp.remote(remote.src, path.src, remote.dest, path.dest, verbose = FALSE,
via.local = FALSE, local.temp.dir = tempdir())
Could you separate it into two steps?
Save it locally with write.csv()
Call iOS's equivalent of scp (wrapped in R's system()) to copy the file to the remote machine.
It would look like
write.csv(1:10, 'Save.csv')
system("scp Save.csv root#xx.xxx.x.x:/folder/Save.csv")
I'm having issues on windows with R failing when changing the working directory to a mapped network drive (e.g. \Share\Folder mapped to Z:) in batch mode. If I run the same script in an interactive console I don't have any issues. I am accomplishing this by running R.exe with the script specified inside of a windows batch (.bat) file. The .bat file contains the following.
"C:\RRO\R-3.2.1\bin\R.exe" CMD BATCH "C:/Scripts/Rscript.R"
The error is simply...
> setwd( 'Z:/' )
Error in setwd("Z:/") : cannot change working directory
I'd be open to a different approach entirely for scheduling these scripts via the windows task scheduler if that helps avoid the issue. The reason for mapping the drive is that I need to supply some credentials in order to access it, which is done automatically when it is mapped, but can test to see if that's not the case in R if anyone knows how.
I hope this can help with your question.
I duplicated the problem with no errors by using Rscript command instead of a CMD BATCH
my R code which I saved as a script (test1.R)
library(openxlsx)
setwd("P:/Records/Indexing Operations/Indexing Data Analysis/Daily Reports")
my.data = read.xlsx("FSI Daily Project Status Report - 18 Mar 2016.xlsx", sheet = 1)
setwd("C:/Users/golieth/Documents/")
png(filename = "test.png", width = 500, height = 350 )
plot(my.data$Total.Images, my.data$Completed.Images.A,
main = Sys.time())
dev.off()
Note I change the directory 2 times in this file. Once to access data on a mapped network drive and a 2nd to save the image to the computer. I put a timestamp of the current time as the main plot title so you can run the batch file repeatedly and verify it works
my batch file
cd C:\Program Files\R\R-3.2.3\bin\i386
Rscript C:\Users\golieth\Documents\test1.R
Note: On the batch file if your code relies on 32 bit you need to change the directory of your R program (cd) to the R 32bit program. Same with R64. Next the Rscript should reference where you have saved your .R file
Finally, and this might be stating the obvious but make sure you are connected to your VPN before running the batch file.
Imagine a batch file with
cd Z:\<Destination>
Z:
RScript "C:/Scripts/Rscript.R"
This will enable Windows to change to the directory with all credentials and then start R within that directory. So the working dir. is the location from where R is started. Doing so requires that "C:\RRO\R-3.2.1\bin\" is part of your PATH variable.
Good luck!
When writing a .bat file, remember that cd is not used to change drive letters. To change drive letters you simply enter the name of the drive letter, which should be done prior to issuing the final cd to the working directory.
Like this:
sample.bat
z:
cd z:\your\working\directory\
C:\RRO\R-3.2.1\bin\Rscript.exe C:/Scripts/Rscript.R
You can save the files locally in your code, and use file.copy in your code to copy the files over to your network drive. Also try replacing the path in file.copy the network drive letter by the full network address name eg. \\....\.....\
In R, if I use the command
write.csv(res,"~/table1_n500.csv")
, then the result is saved in C:\Users\John Smith\Documents.
But I expected it to be saved in C:\Users\John Smith\.
Can I change this home directory (referred by ~ mark) to C:\Users\John Smith\?
From my personal experience, i usually import data from a file (for example in the directory C:\Users\John Smith\DATA)
then i will set working directory as
setwd("C:/Users/John Smith/DATA")
While i want to save the output file in other directory like "C:\Users\John Smith" but not in the data folder.
so i will set relative working directory like
setwd("../")
And when you type getwd()
you will get [1] "C:/Users/John Smith"
Wish this help.
There are two ways to deal with this problem.
1.) Use the function setwd() to set the working directory (or home directory). All save and read commands will look for files in that working directory. I use this only sparingly, and for quick tiny project.
2.) A more preferred approach is to define a variable like dataInputDir, and use function file.path(dataInputDir, <your filename>) to generate a file path. The advantage is that if you are reading (writing) data from (to) multiple directories, you can do this more efficiently:
file.path(dataInputDir1, <your file or dir name>)
file.path(dataInputDir2, <your file or dir name>)
file.path(dataOutputDir1, <your file or dir name>)
file.path(dataOutputDir2, <your file or dir name>)
This approach is really handy for large complicated projects, and is highly recommended.
This is also helpful, if your program is to be executed on multiple platform like Windows, Mac, Linux. You'll have to change the directory location only at one place, and everything else will work smoothly.
Additionally, following functions/handles will be useful for dealing with directory names:
Quick fix:
setwd("../") # setwd to parent folder of current working directory (getwd())
More robust:
setwd(dirname(dataInputDir)) # Setwd to parent folder of dataInputDir
In R and RStudio, I think I have messed around with the .Rprofile file a few times, and I currently am loading up an old version of it upon startup of R or RStudio, is there a way that I can quickly find the location of the file that is generating the default options?
Thanks
Like #Gsee suggested, ?Startup has all you need. Note that there isn't just the user profile file, but also a site profile file you could have messed with. And that both files can be found in multiple locations.
You could run the following to list existing files on your system among those listed on the page:
candidates <- c( Sys.getenv("R_PROFILE"),
file.path(Sys.getenv("R_HOME"), "etc", "Rprofile.site"),
Sys.getenv("R_PROFILE_USER"),
file.path(getwd(), ".Rprofile"),
file.path(Sys.getenv("HOME"), ".Rprofile"))
Filter(file.exists, candidates)
Note that it should be run on a fresh session, right after your started R, so that getwd() will return the current directory at startup. There is also the tricky possibility that your profile files do modify the current directory at startup, in which case you would have to start a "no-profile" session (run R --no-site-file --no-init-file) before running the code above.
How do I start a new .R file default in a new session for new objects in that session?
Workspaces are .RData files, not .R files. .R files are source files, i.e. text files containing code.
It's a bit tricky. If you saved the workspace, then R saves two files in the current working directory : an .RData file with the objects and a .RHistory file with the history of commands. In earlier versions of R, this was saved in the R directory itself. With my version 2.11.1, it uses the desktop.
If you start up your R and it says : "[Previously saved workspace restored]", then it loaded the file ".RData" and ".RHistory" from the default working directory. You find that one by the command
getwd()
If it's not a desktop or so, then you can use
dir()
to see what's inside. For me that doesn't work, as I only have the file "desktop.ini" there (thank you, bloody Windoze).
Now there are 2 options : you manually rename the workspace, or use the command:
save.image(file="filename.RData")
to save the workspaces before you exit. Alternatively, you can set those options in the file Rprofile.site. This is a text file containing the code R has to run at startup. The file resides in the subdirectory /etc of your R directory. You can add to the bottom of the file something like :
fn <- paste("Wspace",Sys.Date(),sep="")
nfiles <- length(grep(paste(fn,".*.RData",sep=""),dir()))
fn <- paste(fn,"_",nfiles+1,".RData",sep="")
options(save.image.defaults=list(file=fn))
Beware: this doesn't do a thing if you save the workspace by clicking "yes" on the message box. You have to use the command
save.image()
right before you close your R-session. If you click "yes", it will still save the workspace as ".RData", so you'll have to rename it again.
I believe that you can save your current workspace using save.image(), which will default to the name ".RData". You can load a workspace simply using load().
If you're loading a pre-existing workspace and you don't want that to happen, rename or delete the .RData file in the current working directory.
If you want to have different projects with different workspaces, the easiest thing to do is create multiple directories.
There is no connection between sessions, objects and controlling files .R. In short: no need to.
You may enjoy walking through the worked example at the end of the Introduction to R - A Sample Session.
Fire up R in your preferred environment and execute the commands one-by-one.