My R Markdown script was running well until I had to access documents from another WD than my RMarkdown-file. I tried to change the WD. But it doesn't take it.
I might access documents from different folder during my R Markdown Document. How can I be more flexible without coping my files into R Markdown folders? (that would be wasting space!)
Is this the right command?
knitr::opts_knit$set(root.dir = "C:/Users/Nadine/OneDrive/ZID_Kurse/Einführung/Kursmaterial")
And do I need to put it in the beginning of the document???
It just halts at the chunk with setWD() command.
Cheers,
Nadine
You probably do not need to change the working directory; just explain where to find the files relative to the project working directory. You can use an absolute path to the files on the filesystem, e.g.
list.files("C:/projects/another_project/data/")
Or you may try to use relative paths to navigate to files through the parent directory. e.g.
list.files("../another_project/data/")
Related
I would like to import an external dataset using read.table() (or any other function for reading files) and then randomize or sample over it. The file is stored in a subfolder within the parent folder that contains the exercises *.rmd. I am working within a RStudio project. I tried placing the dataset in different levels of the folder structure. Using relative path did not work, but absolute paths did.
My folder structure is:
$home/project_name/exercises # It contains the RMD files
$home/project_name/exercises/data # It contains data files that I want to process
$home/project_name/datasets # this folder could eventually contain the dataset I want to process
To make this code more portable, I would like to know o the manage relative paths within *.Rmd for the knitting process.
The exercises are copied to a temporary directory and processed there. Hence, the easiest option is to copy these files to the temporary directory using include_supplement("file.csv"). By default this assumes that the file.csv is in the same directory that the exercise itself resides in. If it is in a subdirectory you can use include_supplement("file.csv", recursive = TRUE) and then subdirectories are searched recursively for file.csv.
After using include_supplement(), the copied file is available locally and can be processed with read.table() or also included in the exercise as a supplementary file. See http://www.R-exams.org/templates/Rlogo/ for a worked example. However, note that the Rlogo template explicitly specifies the directory from which the file should be copied. This is not necessary if that directory is the same as the exercise or a subdirectory.
I have a fully functional interactive shiny doc using knitr/r markdwon.
However, when I try to publish (deploy) it to shinyApps.io, I get an error saying the .PNG file I try to incorporate into the doc (using readPNG from the png package) is unable to open.
I know the problem is related to working directories.
In my original code I assigned a working directory to my folder (i.e., "C:/Users/NAME/documents/...." that contains both my .rmd file and my .png file. However, obviously my folder doesn't exist on the shinyapps.io.
So how exactly do I set my working directory to open the .png file via my doc on shinyapps.io?
I can't find anywhere that explicitly walks through this process. Please help explain this simply/basically for me.
Example:
Assume I have a folder in "C:/Users/NAME/documents/Shiny" that contains 2 files: "shiny.rmd" and "pic.png". I want "pic.png" to be rendered in my shiny.rmd doc.
Currently I have:
---
title: "TroubleShoot"
output: html_document
runtime: shiny
---
```{r ,echo=FALSE,eval=TRUE}
library(png)
library(grid)
direct <- "C:/Users/NAME/documents/Shiny/"
img <- readPNG(paste0(direct,"pic.PNG"))
grid.raster(img)
```
How do I rewrite my code so it works on shinyApps.io?
Do I need to create and name folders in specific ways to place my 2 files into before deploying?
When you paste the c drive to direct, and read the direct into img, you are sending the app/markdown to your local drive. You need to use a relative path to the project. I would suggest something like:
direct <- "./"
Which uses the relative path, not the absolute path.
That said you might be able to skip that step entirely if the .png is in the same folder as the shiny object. just call the file name and format and leave it as that.
Also, check you use of ". Your syntax highlighting indicates your code won't run properly as it thinks some of your functions and variables are character strings because you've misplaced your quotes around read.png(). That's probably just a copy and paste typo though.
In summary, call the image via grid.raster("./pic.PNG"), and brush up on how working directories and relative paths work.
In the absence of knowing exactly how you're 'setting' your working directory:
In rStudio to correct and easiest approach is to make a 'New Project' for every New Project. You can do this as the first step in your project, or you can add a project file to an existing directory.
When you do this it automatically sets your working directory correctly. The way you seem to be doing it is not correct, you are merely supplying a 'path'. If you were to not want to use a project for some reason (I can't think of a case where that would be right), then you can always use setwd(), however, I believe this needs to be used in every session. A true project doesn't have that requirement.
This will then allow you to deploy your app properly as it will update the working directory to the one on the host machine at shinyapps.io when it is initialised there.
Finally, using the correct relative syntax "./path/to/my.file" to reference all your assets, images, data etc, should correct your issue as stated in the question.
I am using RStudio to knit an .Rnw file to .pdf. This .Rnw file is stored in directory that is under git version control. This directory also contains a .RProj file for the project.
I collaborate with colleagues who don't know the first thing about .Rnw files and git. These colleagues want to open a Word file and track change their hearts out. So I give the people what they want.
Everyone needs access, so storing the Word file on a cloud service like Box makes sense. In the past I created a subfolder in my repo that I shared—keeping everything within the root directory—but this time around I needed to store the file in a shared folder that someone else created. So my solution was to copy the Word file from this shared directory to my repository.
Technical Approach
I don't know how to make this a reproducible problem, but hopefully you will give me some latitude since I'm trying to make my work fully reproducible ;)
Let's say that my .Rnw file is stored in repoRoot/subfolder. Since knitr changes the working directory to subfolder where this .Rnw file is located, the first chunk sets the root.dir one level up at the project root.
<<knitr, include=FALSE>>=
library(knitr)
opts_knit$set(root.dir=normalizePath('../')) # go up 1 level
#
The next chunk copies the Word file from the shared folder to my git repo and runs the analysis file. The shared directory path is hard coded to my machine, which is the problem I'm writing for your help solving.
file.copy(from='/Users/ericpgreen/Box Sync/Project/Paper/draft.docx',
to='subfolder/draft.docx', # my repo
overwrite=TRUE)
source(scripts/analysis.R) # generates objects we reference in the .docx file
After adding \begin{document}, I include a chunk where I convert the .docx file to .txt and then rename it to .Rnw.
# convert docx to txt
system("textutil -convert txt 'subfolder/draft.docx'")
# rename txt to .Rnw
file.rename('subfolder/draft.txt',
'subfolder/draft.Rnw')
The next child chunk calls this .Rnw file that contains the text of the Word file with references to R objects included through \Sexpr{}:
<<include-draft, child='draft.Rnw', include=FALSE>>=
#
This works just fine for me. Whenever I knit the .Rnw file it grabs the latest version of the .docx file that my colleagues have edited (complete with track changes and comments) and, in a later step not shown here, returns the .pdf file to the shared folder.
Problem to Solve
This setup meets almost every need for me, except that the initial file.copy() command is hard coded to my machine. So if someone in my group clones my repo (e.g., research assistants who DO use version control), it won't run out of the box. Is there a workaround to hard coding in this type of case?
Ultimately you won’t get around hard-coding paths that are outside your control, such as paths to network shares. What you can and should avoid is hard-coding these paths in your documents.
Instead, relegate them to configuration files and/or environment variables (which, again, will be controlle by configuration files, to with .bashrc and similar). The simplest approach is then to use
network_share_path = Sys.getenv('NETWORK_SHARE_PATH',
stop('no network share path configured'))
file.copy(from = network_share_path, to = 'subfolder/draft.docx', overwrite = TRUE)
I'm making a simple line in r to automatically open my generated plots.
I output the plots to a file called "plots.pdf" in the same directory as my r file, and at the end i use this two lines to try to open it:
dir <- paste("/Applications/Skim.app/Contents/MacOS/Skim ",getwd(),"/plots.pdf",sep="")
system(dir)
Basically, dir concatenates the full path of the skim app and the full path of the generated plot.
If i run the string stored at dir in a shell it works perfect, it opens the pdf file in Skim, but when i run it with system() from inside R it doesn't work (Skim says 'The document “plots.pdf” could not be opened.').
I believe this is a very little mistake somewhere in the syntax regarding the absolute/relative paths, but haven't managed to find it... Any advice is welcome! (Or a better way to achieve the same)
I found a way to bypass that problem, i just changed the path to Skim for the 'open' command and i let the system to assign the default app for pdf viewing. So:
dir <- paste("open ",getwd(),"/plots.pdf",sep="")
And it works.
I understand that we shouldn't purl() a chunk with knitrbut instead use knit_hooks$set(purl = hook_purl). That works, but it puts the R script in the working directory. I would like to put it in an R/ directory. It's probably due to my own incompetence, but I couldn't find anything about specifying the directory for the R script (I looked in the R documentation as well as several places online). Anyone have any ideas? I'm knitting from within RStudio, by the way.
You can generate the script under the current directory, and file.rename() it to the R/ directory.