I am creating a question in r-exams that contains a graph made in TikZ, more specifically https://texample.net/tikz/examples/the-3dplot-package/. For its correct operation it is required that the 3dplot.sty file be in a certain R folder. In which folder should I include this file?
Error message in RStudio: "!LaTeX Error: File`3dplot.sty'not found".
If you only need it for one project, simply place the .sty file in the same folder as your .rmd file. The current working folder is the normally the first place latex searches for packages, before looking in your personal texmf folder or your tex distribution.
I would strongly recommend to install this in the texmf tree of your LaTeX installation. Then it is always found, no matter where you compile a LaTeX file.
Alternatively, you can also specify it using the header argument in include_tikz() with the full absolute file path:
include_tikz(..., header = "\\usepackage{/full/path/to/3dplot}")
Note that the .sty suffix is not to be included, even when using the full file path.
Related
In the documentation, R suggests that raw data files (not Rdata nor Rda) should be placed in inst/extdata/
From the first paragraph in: http://cran.r-project.org/doc/manuals/R-exts.html#Data-in-packages
The data subdirectory is for data files, either to be made available
via lazy-loading or for loading using data(). (The choice is made by
the ‘LazyData’ field in the DESCRIPTION file: the default is not to do
so.) It should not be used for other data files needed by the package,
and the convention has grown up to use directory inst/extdata for such
files.
So, I have moved all of my raw data into this folder, but when I build and reload the package and then try to access the data in a function with (for example):
read.csv(file=paste(path.package("my_package"),"/inst/extdata/my_raw_data.csv",sep=""))
# .path.package is now path.package in R 3.0+
I get the "cannot open file" error.
However, it does look like there is a folder called /extdata in the package directory with the files in it (post-build and install). What's happening to the /inst folder?
Does everything in the /inst folder get pushed into the / of the package?
More useful than using file.path would be to use system.file. Once your package is installed, you can grab your file like so:
fpath <- system.file("extdata", "my_raw_data.csv", package="my_package")
fpath will now have the absolute path on your HD to the file.
You were both very close and essentially had this. A formal reference from 'Writing R Extensions' is:
1.1.3 Package subdirectories
[...]
The contents of the inst subdirectory will be copied recursively
to the installation directory. Subdirectories of inst should not
interfere with those used by R (currently, R, data, demo,
exec, libs, man, help, html and Meta, and earlier versions
used latex, R-ex). The copying of the inst happens after src
is built so its Makefile can create files to be installed. Prior to
R 2.12.2, the files were installed on POSIX platforms with the permissions in the package sources, so care should be taken to ensure
these are not too restrictive: R CMD build will make suitable
adjustments. To exclude files from being installed, one can specify a
list of exclude patterns in file .Rinstignore in the top-level
source directory. These patterns should be Perl-like regular
expressions (see the help for regexp in R for the precise details),
one per line, to be matched(10) against the file and directory paths,
e.g. doc/.*[.]png$ will exclude all PNG files in inst/doc based on
the (lower-case) extension.
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.
In the documentation, R suggests that raw data files (not Rdata nor Rda) should be placed in inst/extdata/
From the first paragraph in: http://cran.r-project.org/doc/manuals/R-exts.html#Data-in-packages
The data subdirectory is for data files, either to be made available
via lazy-loading or for loading using data(). (The choice is made by
the ‘LazyData’ field in the DESCRIPTION file: the default is not to do
so.) It should not be used for other data files needed by the package,
and the convention has grown up to use directory inst/extdata for such
files.
So, I have moved all of my raw data into this folder, but when I build and reload the package and then try to access the data in a function with (for example):
read.csv(file=paste(path.package("my_package"),"/inst/extdata/my_raw_data.csv",sep=""))
# .path.package is now path.package in R 3.0+
I get the "cannot open file" error.
However, it does look like there is a folder called /extdata in the package directory with the files in it (post-build and install). What's happening to the /inst folder?
Does everything in the /inst folder get pushed into the / of the package?
More useful than using file.path would be to use system.file. Once your package is installed, you can grab your file like so:
fpath <- system.file("extdata", "my_raw_data.csv", package="my_package")
fpath will now have the absolute path on your HD to the file.
You were both very close and essentially had this. A formal reference from 'Writing R Extensions' is:
1.1.3 Package subdirectories
[...]
The contents of the inst subdirectory will be copied recursively
to the installation directory. Subdirectories of inst should not
interfere with those used by R (currently, R, data, demo,
exec, libs, man, help, html and Meta, and earlier versions
used latex, R-ex). The copying of the inst happens after src
is built so its Makefile can create files to be installed. Prior to
R 2.12.2, the files were installed on POSIX platforms with the permissions in the package sources, so care should be taken to ensure
these are not too restrictive: R CMD build will make suitable
adjustments. To exclude files from being installed, one can specify a
list of exclude patterns in file .Rinstignore in the top-level
source directory. These patterns should be Perl-like regular
expressions (see the help for regexp in R for the precise details),
one per line, to be matched(10) against the file and directory paths,
e.g. doc/.*[.]png$ will exclude all PNG files in inst/doc based on
the (lower-case) extension.
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")))