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.
Related
I'm kinda lost on that one:
I have set up an R project, let's call it "Test Project.Rproj". The beauty of R projects is the possibility to use relative paths (relative to the .Rproj file). My project consists of a "main.R" script, which is saved on the same level as the .Rproj file.
Additionally I have a directory called 'Output', where I want my plots and exported data to be saved. My "main.R" file looks like the following:
my_df <- data.frame(A = 1:10, B = 11:20)
my_df |>
writexl::write_xlsx(here::here("Output",
paste0("my_df_",
stringr::str_replace_all(as.character(Sys.time()), ":", ""),
".xlsx")))
My final goal is to automate the execution of the 'main.R' file using the Windows Task Scheduler. But in order to do so, I have to be able to run the script from the terminal. The problem here is the working directory. When opening an R project, all the paths are relative to .Rproj file. But in the terminal the current working directory is <C:\Users\my_name>. Of course I could manually set the working directory via cd "path\to\my\project. But I would like to avoid that.
My current call for the execution of the main.R file in the terminal is the following:
"C:\Program Files\R\R-4.1.0\bin\Rscript" -e "source('C:/Users/my_name/path/to/my/project/main.R')"
My two ideas for a solution are the following, but I am happy for other suggestions as well.
In order to replicate the usual use of a project: Is there a way to execute the .Rproj
file from the terminal? In order to create a similar environment as in RStudio, where all the relative paths are working, when executing scripts from the project afterwards?
There are two packages adressing the problem of relative paths: rprojroot and here, where the former is the basis for the latter. I am pretty sure that here does not provide the needed functionality. I tried adding here::i_am("main.R) to my main.R file, but the project root directory still is not found when executing in the terminal from a working directory outside the project.
For rprojroot to work, I think it is also necessary to have your current working directory somewhere within the project. But this package offers a lot of functionality, so I am not sure wheter I am overlooking something.
So I would be happy about any help. Maybe it is impossible and I have to change the working directory manually - then I would be glad to know that as well.
Some links I used in my research:
https://www.tidyverse.org/blog/2017/12/workflow-vs-script/
https://malco.io/2018/11/05/why-should-i-use-the-here-package-when-i-m-already-using-projects/
http://jenrichmond.rbind.io/post/how-to-use-the-here-package/
Thanks a lot!
Edit: My current implementation is an additional R script, where I manually set the working directory via setwd() and source the main.R file. However it is always suggested to avoid setwd, which is why this whole question exists.
I am working on a project where I was hoping we'd be able to set file paths using the .Rprofile. I wrote a script that defines paths for specific users and since we're using renv and that puts an activate script into the profile anyways, I just added my paths.R script after that in the .Rprofile.
When I asked a colleague to open the .Rproj file to open the project, I thought it would run renv/activate.R and my paths.R script, but they're not seeing their defined paths, only mine. Am I missing something?
# contents of my .Rprofile
source("renv/activate.R")
source("paths.R")
# contents of path.R
if (Sys.info()["user"] == "francisco"){
data_dir <-
'path/to/data'
}
# etc
Any advice on workflow is welcome. Thanks!
I am new to R and I just figured out why my history did not contain all my previous commands. R create a .Rhistory file in each working directory.
I often change working directory and I would like to have the history of all my past sessions in the same file. Is there a simple way to do that ?
Thanks.
(I am on Mac OS 10.6 and I use Rstudio)
An easy way would be to manually save your history like this:
savehistory(file = "~/.Rhistory")
and then load it when you open an R command session:
loadhistory(file = "~/.Rhistory")
Otherwise you can edit your 'Rprofile.site' and add savehistory() and loadhistory() to the functions .Last and .First respectively.
More info about Rprofile.site: here
At startup, R will source the Rprofile.site file. It will then look for a .Rprofile file to source in the current working directory. If it doesn't find it, it will look for one in the user's home directory. There are two special functions you can place in these files. .First( ) will be run at the start of the R session and .Last( ) will be run at the end of the session.
I am working with a "factory fresh" version of RStudio on Windows 7. R is installed under C:/Program Files which means the default libraries are stored here, and the two locations contained in .libPaths() on startup are both within this folder.
I want to work with another R library (igraph). Since the C:\Program Files folder is write-protected, I have set up another area to work in: C:\Users\nick\R and installed the igraph library in C:\Users\nick\R\library. I can manually add this location to the .libPaths() variable and use the library with no problems.
However, my problem is getting RStudio to automatically add this location to the .libPaths() variable on startup. I read that I could add the relevant command to my .Rprofile file - but I couldn't find any such file (presumably they are not automatically created when RStudio is installed). I then created a file called .Rprofile containing only this command. This only seemed to work when the .Rprofile file was saved in C:\Users\nick\Documents (which is the path stored in both the R_USER and HOME environmental variables). What I would like is to have the .Rprofile file stored in C:\Users\nick\R.
I have read all the information in ?Startup and it talks about where to store commands that run on startup. But I just can't make this work. For example there seems to be no way to change the location of the home directory without reading a file stored in the home directory. I don't seem to have any .Renviron files and creating these myself doesn't seem to work either.
I would really appreciate an answer in simple terms that explains how I could go about changing where the .Rprofile file is read from.
In Windows, you set the R_USER profile by opening up a command line and running:
SETX R_PROFILE_USER "C:/.../.Rprofile"
Where (obviously) the path is the path to your desired .Rpofile. In R, you can check that it worked:
Sys.getenv("R_PROFILE_USER")
Should return the path you specified. Note that you likely need to have all R sessions closed before setting the R_USER variable.
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.