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.
Related
I'd like to set the default distribution of Python for my Reticulate package to use. I use,
Sys.setenv(RETICULATE_PYTHON = "/usr/local/bin/python3")
however, I have to re-enter this line of code every time I start R. How can I set this permanently, so I don't need to specify which Python distribution I need every time?
On Windows, use Sys.getenv('R_USER') as #Brian Davis suggested in the comments to know the location of your home folder. On Linux, Sys.getenv('HOME') should be your normal home folder which you should use.
Now open up a terminal (if you're using recent versions of Rstudio there is one next to the console), go to your home folder and add a .Renviron file. You can do this without using the terminal too, but you'll probably have to confirm creation of a file starting with a dot.
cd path_to_my_home_Folder
touch .Renviron
Add RETICULATE_PYTHON = /usr/local/bin/python3 to it, and add also a new line at the end. Your file should look like this (if it's new):
> RETICULATE_PYTHON = /usr/local/bin/python3
Now you should be able to access your environment variable with Sys.getenv('RETICULATE_PYTHON') at each R session, since R looks for any .Renviron file defining environment variables in R home folder at startup (see documentation for startup?Startup).
UPDATE 29/10/2018
As it turnouts the variables defined with .Renviron are available only within Rstudio, which is not so much of a surprise since the .Renviron file is read at Rstudio startup. If you want the environment variable to be available for Rscript (for instance), you can :
Windows Add it to your user environment variables, using the Modify environment variables utility (available in the Start menu search bar)
Mac You can do the exact same procedure as above but do that on your .bash_profile instead of .Rstudio. Open up a terminal and place yourself to your user root folder (default location of the terminal usually). Add the following line (without blanks around the equal sign):
export RETICULATE_PYTHON=/usr/local/bin/python3
Save and close, restart terminal. The terminal reads your .bash_profile at start up, thus defining the environment variables. Your RETICULATE_PYTHON should now be available even in non-interactive R sessions.
The packge usethis has a function that opens the file .Renviron of your home folder.
usethis::edit_r_environ()
Once the file is opened, you just need add your pair key=value, save and close it.
RETICULATE_PYTHON=/usr/local/bin/python3
I want to change the prompt in R from > to R> and I know I should use the options command options(prompt="...") and it works, but then when I restart R the prompt is back to >.
Is there anyway to save the change so that it sticks?
Use .Rprofile file:
You can customize the R environment through a site initialization file or a directory initialization file. R will always source the Rprofile.site file first. On Windows, the file is in the C:\Program Files\R\R-n.n.n\etc directory. You can also place a .Rprofile file in any directory that you are going to run R from or in the user home directory.
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.
More details are here
I use R from the GUI app (R.app). When I open the app, it loads some data (e.g. .Rapp.history or .RData) from the working directory. However, is it possible to execute some commands or functions automatically upon launch?
I just want to load some libraries such as ggplot2 or plyr, which I always use on my session.
You can edit your Rprofile.site and add the desired commands 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.
That said, you can edit the function .First() to load the desired libraries.
.First <- function() {
library("dplyr")
library("ggplot2")
}
You can edit the same file and this command, which is used specifically for this purpose:
options(defaultPackages=c(getOption("defaultPackages"),
"dplyr","ggplot2"))
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.