Hoping for some help - I have been banging my head for a few hours and I can't find a solution. I am trying to optimise a workflow which involves sourcing a script from a Quarto file (I imagine this would be the same for an R markdown file). If I run the actual script using here() to load csv files, it works perfectly and sets the root directory as:
here() starts at /Users/Jobs/2023/project_x
Which is where the R project file is located.
But if I source that same script from within a Quarto file it sets the root directory to one up from the folder containing the .qmd file, and prevents the csv files from being able to be read:
here() starts at /Users/Jobs/2023/project_x/Analysis/code
The .qmd file is located at:
here() starts at /Users/Jobs/2023/project_x/Analysis/code/rmd
Is this expected behaviour and can I get around it?
Using:
here::set_here("/Users/Jobs/2023/project_x")
in a .qmd code chunk seems to work and keep all paths using here() intact in the source script, but I don't think it's ideal as I still need to specify an absolute path in the first instance.
Open to other suggestions...
Related
I am trying to use the load() function to load an .RData file into my current R session. I open my code base by double clicking on the R project file in my directory and then attempt to load the .RData file by running load('./Data/mydata.rdata'). However, this returns a 'No such file or directory' error. I verified that the working directory is correct by using getwd().
I figure I must be using incorrect syntax because I have no issues loading the file when I type in the full file path.
Working directory for R Project file: "/Users/Me/Library/OneDrive/RStuff"
Directory containing .RData file: "/Users/Me/Library/OneDrive/RStuff/Data"
Code that works: load("/Users/Me/Library/OneDrive/RStuff/Data/mydata.rdata")
Code that fails: load('./Data/mydata.rdata')
Do relative paths not work with load() or is my syntax wrong?
Do relative paths not work with load() or is my syntax wrong?
It looks like there is an error with your paths. You said the working directory is "/Users/Me/Library/OneDrive/RStuff"
But according to the code that works:
load("/Users/Me/Library/OneDrive/RStuff/Data/mydata.rdata")
...the data file is in "/Users/Me/Library/OneDrive/RStuff/Data"
Therefore to use relative paths, you would use:
load("./Data/mydata.rdata")
I'm new in R and Rstudio and I'm making a little project. The fact is that i have on one hand an .R file with the code I want to execute. And on the other hand I've an .Rmd file that I should use to report my work, including the results of the execution of my code in the other file.
How can I access the results and/or functions from de .Rmd file to the .R file?
Thank you,
By default, your .Rmd file will have its working directory as wherever the .Rmd file is saved. You can use all of R's standard functions inside the .Rmd file, including source() to run a .R file. So if your files are in the same directory, you can include source("your_r_file.R") to run the .R file. If they are in different directories, you can use relative or absolute file paths (though you should try to avoid absolute file paths in case the .Rmd file is ever run on a different computer).
If you are using RStudio, I would strongly recommend using the "Projects" feature and the here package. The readme for the here package is quite good for explaining its benefits.
Source the R file in at the top of your .Rmd file like
```{r}
source("file-name.R")
```
and the functions/objects in that R file will be avilable
I have two projects in R. I've moved an .Rmd document from project 1 to project 2.
When I used the .Rmd file which I had moved to project 2 to try and read in some data I get the following error message:
cannot open file '"mydata.csv"': No such file or directoryError in file(file, "rt") : cannot open the connection.
This kind of error usually suggests to me it's a working directory issue, however when I run getwd() in the command line it's the correct working directory that is listed and points to where the csv is stored. I've also run getwd() within the rmd doc and again the wd is correct.
Does anyone else have this experience of moving one .Rmd file to another project and then it not working in the new project?
The code in the .Rmd file that I am trying to run is:
Data <- read.csv("mydata.csv", stringsAsFactors = T) and the data is definitely within the project and has the correct title, is a csv etc.
Has anyone else seen this issue when moving an RMarkdown document into another project before?
Thanks
This may not be the answer, but rmarkdown and knitr intentionally don't respect setwd(): the code in each block is run from the directory holding the .rmd file. So, if you've moved your .rmd file but are then using setwd() to change to the directory holding the data, that does not persist across code chunks.
If this is the issue, then one solution is to use the knitr options to set the root.dir to the data location:
opts_knit$set(root.dir = '/path/to/the/data')
See here.
Maybe not relevant but it seems to be the most likely explanation for what's happening here:
The project shouldn't really interfere with your code here. When opening the project it will set your working directory to the root location of the project. However, this shouldn't matter in this case since RMarkdown files automatically set the working directory to the location where the RMarkdown file is saved. You can see this when running getwd() once in the Console and once from the RMarkdown file via run current chunk.
The behavior is the same when the file is knitted. So except in the case when "mydata.csv" is in the same directory as the RMarkdown file, the code above won't work.
There are two workarounds: you can use relative or absolute paths to navigate to your data file. In a project I prefer relative paths. Let's say the rmd file is in a folder called "scripts" and your data file is in a folder called "data" and both are in the same project folder. Then this should work:
Data <- read.csv("../data/mydata.csv", stringsAsFactors = TRUE)
The other option, which I do not recommend, is to set the working diretory in the rmd file via:
opts_knit$set(root.dir = '../data/')
The reason why I wouldn't do that is because the working direcotry is only changed when knitting the document but using the rmd file interactivly, you have a different working directory (the location of the rmd file)
This is a great application of the here package for dealing with these types of issues.
here https://github.com/jennybc/here_here looks around the Rmd file (and all R files) for the .Rproj file and then uses that as an "anchor" to search for other files using relative references. If for instance you had the following project structure:
-data
|--mydata.csv
-src
|-00-import.R
|-01-make-graphs.R
|-02-do-analysis.R
-report
|--report.Rmd
-yourproject.Rproj
And you wanted to use mydata.csv in your report.Rmd you could do the following:
library(here)
dat <- read.csv(here("data", "mydata.csv"))
here will then convert this path to "~/Users/../data/mydata.csv" for you. Note that you have to be in the Rproject for this use case.
Here is such a great package and solves a lot of issues.
My R scripts perfectly work when running when in scripts file in R studio, but when I use the same scripts in R markdown get an error; file "does not exist in current working directory"
Both are in the same wd.
What may be the reason?.
Note: All my work do in google drive offline.
This is probably because R looks for files relative to the current working directory - by default Sys.getenv("HOME"), whereas knitr looks in the same directory as the Rmarkdown file.
The solution is to specify the correct full or relative path to files in the RMarkdown code.
This is what the new here R package was designed for. It always looks at the root of the R project directory (which is what "here" refers to). It doesn't matter if your Rmarkdown file is in a subdirectory.
library(here)
here("file_i_want.csv")
This will work the same regardless of if you use R scripts or Rmarkdown
More details here (pun intended):
https://github.com/jennybc/here_here
Newbie R question: I have been trying to test the R script posted in FlowingData, but the script spit out the following error:
Error: XML content does not seem to be XML: 'NA'
I am running R on my windows box, with the .gpx files in the same directory as the script. Any help is appreciated.
Not sure if you ever found the answer to this or not, but the XML error relates to the fact that R does not know where your .gpx files are. While the FlowingData script indicates that the script will work if the .gpx files are in the same folder as your saved R script copy/pasted from FlowingData, that is not true. You must also set your working directory to this path as well, then R will see your .gpx files. If you FlowingData R script file and .gpx files are in: C:\Users\leon\Documents\R then add this line under the library(plotKML) line to set your working directory: setwd("C:\\Users\\leon\\Documents\\R")
Another word of note, make sure you only use the RunKeeper gpx files for a fairly small geographic area or the plotted data will be insanely small.