I am running some R code on a Windows computer using RStudio and my code generates Excel files and netCDF files periodically (dozens of them eventually). I don't want them to clutter my working directory. Is there a way to save the files to a directory called "Output" (ex: C:/.../original file path/Output) in the parent directory? I would like a way to change my current working directory to a different directory. I understand there is getwd() and setwd() but how do I set the path to the output directory without typing out the entire windows path (for example: setwd(current source file path for windows or Mac/output). My collaborator uses a Mac and he would have his output stored there as well.
You have a file argument in your write* function. If your Output directory is in your working directory, it works like this:
write.xlsx(df, file = "Output/table.xlsx")
write.csv(df, file = "Output/table.csv")
You can specify an argument in your write.csv function and other similar write functions which specifies your path.
#Output path
OutPath<- "C:/blah/blahblah/op/"
#Table to dump as output
OutTbl <- iris
write.csv(OutTbl, file = OutPath)
Source: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html
Related
I have a series of pieces of R code which have been designed to be run on other computers. That is, all code is relative to a root directory, which contains a Rstudio project file, .Rproj. There are no absolute file paths. This works fine when I actually open Rstudio, load the .Rproj file and then run the code.
However some of my code takes hours to run, and I need to set multiple scripts to run one after the other. This means creating a .sh file, and running the R script in turn from the command line. However non of my programs run successfully from the command line, as the root directory is no longer set to that of the .Rproj file. I have read about the here package can be used, which will automatically set the root directory to where ever a .here file is located. This is not the case for me.
The working directory it automatically uses is the home directory I have on the computational cluster I am using. The area where all my files, including the .Rproj and .here files is located in a different directory in which I have a lot more space allocated. Both are accessible from a common parent directory, so I assumed there here() function would be able to locate the directory I want to actually use to run my work. But this is not the case.
Effectively, I would like to set the root directory to a location which is not the default root directory on the system I am using. I have put a .here file there, but this is not located by there here() function, which I believe is its primary objective. Any ideas on how to proceed?
EDIT: I am working on a UNIX system. R version 3.4.2.
My problem was similar, but not exactly the same as yours. Perhaps my solution will work for you. When I opened an RStudio project, I found that if I called "library(here)", the root directory is set where the .Rproj file is located and that "set_here" would not change that directory, despite the 'here' package documentation. Perhaps I was doing something wrong, but I decided to solve the problem with a simple R function that moves up the directory tree until it finds a ".here" file. It then loads the "here" package and that sets the root directory where I want it.
I use "touch .here" in a Terminal outside of R to set my root directory, and then call "init_here()" from my newly opened R project:
init_here <- function() {
`%!in%` = Negate(`%in%`)
files <- dir( all.files = T )
while ( ".here" %!in% files & getwd()!="/" ) {
setwd("..")
files <- dir( all.files = T )
}
library(here)
}
Use Case -
In Unix:
cd( '~/myRoot' )
touch( '.here' )
In RStudio, when I open a project, the calls look like:
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
< R information removed for clarity >
[Workspace loaded from ~/myRoot/myProject/.RData]
> getwd()
[1] "/Users/me/myRoot/myProject"
> init_here()
here() starts at /Users/me/myRoot
> here()
[1] "/Users/me/myRoot"
>
I can now put a ".here" file at the root of each of my RStudio projects and set the expected root directory independently for each project. If you want to get fancy, you could put the function in each project's .Rprofile so that it runs whenever the project is opened. All of my projects have the .Rproj file in the directory above my "R" directory, so my .Rprofile looks like:
source("./R/init_here.R")
init_here()
Hope that helps.
Did you try simply adding a cd /the/path/where/you/put/the/files command in your shell script?
According to this documentation, here() "uses a reasonable heuristics to find your project's files, based on the current working directory at the time when the package is loaded". The "cd" (change directory) command in a shell script changes the current working directory.
On a mac using iCloud file optimization, large files that are seldom used are uploaded to iCloud and only a small pointer file is left. When I look for the file in Finder, I see the file name and to the left is an icon that indicates that the file is in the cloud. To access the file, I click on the icon and the file is downloaded. With the file.exist command, R returns FALSE for the existence of the file. But after some research I found that the file link is stored in a directory below ~/Library/Mobile\ Documents/com~apple~CloudDocsand the file name is changed to xxx.icloud where xxx is the original file name.
Here's an example of the path to a a directory that holds a .icloud file from a shell in my mac
/Users/gcn/Library/Mobile Documents/com~apple~CloudDocs/Documents/workspace/nutmod/data-raw/NutrientData
I can query for the existence of the file with exists(xxx.icloud). But how do I tell my mac to download the iCloud file and then read it in? Using something like read.table or read.csv doesn't work because the pointer file is not csv.
You can read a csv file directly from a iCloud folder on the Mac by using the path to that folder. Get the path by finding it in the finder. Then right click on the filename at the bottom of the finder window where it shows all the folders leading to the file and choose: Copy "YourFile" as Pathname.
That path will look something like this:
"/Users/NAME/Library/Mobile
Documents/com~apple~CloudDoc/Docs/YourFile.csv"
Use that in your read code:
iCloudDat <- read_csv("/Users/NAME/Library/Mobile Documents/com~apple~CloudDocs/Documents/YourFileName.csv")
That should work.
If the extension isn't .txt or .csv read.table and read.csv won't work.
you have to download the file and extract the tables to a readable format.
you can download the file using download.file() which is is the utils basic library.
I have a rstudio addin package located here.
One of the addins allows the user to define a directory and it will copy a file that is located in the package to that directory.
the file is located:
atProjectManageAddins/inst/Docs/RMarkdownSkeleton.Rmd
And I am trying to copy it to the user defined directory with something like this:
file.copy("inst/Docs/RMarkdownSkeleton.Rmd",
paste0(Dir, FolderName, "/Reports/", FolderName, "_report.Rmd"))
Where I am trying to copy it from where it is in the package, to where the user defines it to be (Based on two separate arguments Dir and FolderName).
But this doesn't seem to work. My assumption is that I am not referring to the package directory in the correct way. I've tried ./Inst/, ~/Inst/ and maybe a couple more. My assumption now is that there is a more systematic reason for my inability to get file.copy() to work.
Any suggestions? Is this even possible?
Note that if I run the function locally via source() and runGadget(), it works just fine. Only when the package is installed and I use the RStudio addins GUI where it references the intalled package, does it fail. Thus, I'm quite certain I am not correctly defining the file path for the installed .Rmd files.
Edit: I've changed to the following, based on Carl's suggestion (as can be seen on github), but the files are still not being copied over.
file.copy(system.file("Docs","Rmarkdownskeleton.rmd",package="atProjectManageAddins"),
paste0(Dir, FolderName, "/Reports/", FolderName, "_report.Rmd"))
system.file is the best function for getting a file from a package. I believe this should work for you:
file.copy(system.file("Docs","Rmarkdownskeleton.rmd",package="atProjectManageAddins"),
paste0(Dir, FolderName, "/Reports/", FolderName, "_report.Rmd"))
You got the right idea putting the files in inst/.
Use this code to copy the file from the package dir to the current dir :
file.copy(from = file.path(path.package("packagename"), "path/to/file"),
to = file.path("path/to/file"), overwrite = T)
file.path creates a path by concatenating the strings passed to it (OS-specific separators are automatically added).
path.package retrieves the path of a loaded package. Files presents in inst/ are copied at the root of the package dir when installed, thus "path/to/file" here should be the path relative to your inst/ dir.
overwrite can be used to overwrite the file if it already exists.
In your specific case, this should do the trick :
file.copy(file.path(path.package("atProjectManageAddins"), "Docs/RMarkdownSkeleton.Rmd",
file.path(getwd(), "Reports", paste0(reportName, "_report.Rmd")))
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
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.