I'm using a .yaml file as my config file for some R code. When I was the only R developer this didn't pose a problem, but now we're trying to bring multiple people on board. We don't want to keep rewriting the config file because that's slow, and we don't want to create individual config files because we keep adding new elements to them so we'll likely end up running different code.
To access the .yaml file, I typically run the code below in R
config = yaml::read_yaml('base/config.yaml')
and the text in config.yaml starts with
experiments:
# Config paths
first: 'C:/Users/BNye/OneDrive/Science/experiments/first'
second: 'C:/Users/BNye/OneDrive/Science/experiments/second'
third: ...
and so on. What I'd like to do is swap that out for something like
'C:/Users/{username}/OneDrive/Science/experiments/first'
and have it spit back 'C:/Users/BNye/OneDrive/Science/experiments/first' when I run config$experiments$first in R, but that just returns the same line of text ('C:/Users/{username}/OneDrive/Science/experiments/first') right back to me. Using setwd(paste0("C:/Users/",Sys.info()[6], "/OneDrive/Science/experiments"))
in R worked fine, so the real hang up is config. How should I code this?
Using this query as a reference, I found a way to get R to parse the config file as an R expression. My config files now read:
experiments:
# Config paths
first: !expr 'paste0("C:/Users/",Sys.info()[6], "/OneDrive/Science/experiments/first")'
second: !expr 'paste0("C:/Users/",Sys.info()[6], "/OneDrive/Science/experiments/second")'
third: ...
Then, when I read it in R, I use config = yaml::read_yaml('base/config.yaml', eval.expr=TRUE) and it works perfectly. It feels like a fragile solution, but so far it's holding up.
Related
I do not know how to create a reproducible example of this issue since it would require access to a folder on my computer(if anyone has a suggestion I am fine to follow up). However, what I would like to do is upload a file in a folder without actually referencing the name but only referencing the order it appears in the file, and I would like to do it in R if possible(although python would be fine as well). I want to do this because the folder has 40 or so files and I need to format them all the same, but they all have different names.
In other words I want a code that would look something like this:
setwd(folder)
for(i in 1:number of files in folder){
upload file i
process file i
rbind(master file,file i)
}
Obviously this is not an actual code, but merely a framework, so I did not put it in the code framework on the site. The line I do not know how to do is the first line in the loop(download file i). Is it possible to do this, or do I need to download every file individually with their specified name?
I think you're looking for list.fles()
ff <- list.files()
for(i in seq_along(ff)){
print(ff[i])
read.csv(ff[i], ...) # etc
...
}
I used to work with R on my mac and never had any problems.
Now I would like to use it on my work computer (windows). The problem is I can't import any files to start working with them. I tried several options:
mydata<-read.table("c:/temp/myfile.csv",header=TRUE)
mydata<-read.csv("myfile.csv",header=TRUE)
mydata<-read.table("c:/myfile.csv",header=TRUE)
mydata<-read.table("Desktop/myfile.csv",header=TRUE)
I also tried to change / into \ in all variants above.
Nothing seems to work. R displays the command in red, sometimes with a comment "connection can't be opened" or "no such file or directory" (my translation from German).
I tried copying the file I want to open to a different location (desktop, c:, temp), but alas, nothing helps.
Do you have any ideas why I have this problem and how I can solve it? Thanks in advance.
There is a safer way to work with paths; just using file.path().
So, if you're trying to get a file in C:/temp/turtles.csv, then you'd use:
targetFile <- file.path('C:/', 'temp', 'turtles.csv')
read.csv( targetFile, header=TRUE )
Minor point since it showed up on Twitter; DO NOT USE PATHS THAT EXIST ONLY IN YOUR ENVIRONMENT.
Try to keep the data in a path either in or directly under where the script is.
You have three ways to do this with read.csv() function
To avoid inserting actual path you can do it simply nesting function
read.csv(file.choose(),header=TRUE)
it will open pop up for selecting your file just select file from directory
where you have saved it.
Now if you have to insert a path then just get actual location of your file
by
read.csv("C:\path\to\your\file\filename.csv",header=TRUE)
for Example
read.csv("C:\Users\Amway\Desktop\resources.csv",header=TRUE)
Best way is to have your own work space directory
so create a directory by your preferred name and just set that directory as a
R session work space by
setwd("C:\path\to\your\workspace directory\")
check your current directory by
getwd()
now if you want to read a file into R session just copy your file to work
space and just write
read.csv("resources.csv",header=TRUE)
So, it should be like this.
setwd("c:/mydir") # note / instead of \ in windows
Also.
MyData <- read.csv(file="c:/mydir/TheDataIWantToReadIn.csv", header=TRUE, sep=",")
Windows uses the other backslash.
https://www.howtogeek.com/181774/why-windows-uses-backslashes-and-everything-else-uses-forward-slashes/
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'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.
Situation
I wrote an R program which I split up into multiple R-files for the sake of keeping a good code structure.
There is a Main.R file which references all the other R-files with the 'source()' command, like this:
source(paste(getwd(), dirname1, 'otherfile1.R', sep="/"))
source(paste(getwd(), dirname3, 'otherfile2.R', sep="/"))
...
As you can see, the working directory needs to be set correctly in advance, otherwise, this could go wrong.
Now, if I want to share this R program with someone else, I have to pass all the R files and folders in relative order of each other for things to work. Hence my next question.
Question
Is there a way to replace all the 'source' commands with the actual R script code which it refers to? That way, I have a SINGLE R script file, which I can simply pass along without having to worry about setting the working directory.
I'm not looking for a solution which is an 'R package' (which by the way is one single directory, so I would lose my own directory structure). I simply wondering if there is an easy way to combine these self-referencing R files into one single file.
Thanks,
Ok I think you could use something like scaning all the files and then writting them again in the same new one. This can be done using readLines and sink:
sink("mynewRfile.R")
for(i in Nfiles){
current_file = readLines(filedir[i])
cat("\n\n#### Current file:",filedir[i],"\n\n")
cat(current_file, sep ="\n")
}
sink()
Here I have supposed all your file directories are in a vector filedir with length Nfiles, I guess you can adapt that