I am a new user of blogdown using Hugo. I would like to create a new post that includes R code to read a data file.
The data file is in my static folder, local path C:\mydir\myblogdown\static\data\savedrecs.txt. Since I was successful in referring to an image using a relative path like this, , I tried reading the data using something similar for the data file, read.csv("/data\savedrecs.txt"), but that didn't work.
I started playing around with the list.files() function to see if I could find a relative path that worked in my local version of the post, list.files("../../static/data") worked, showing me ## [1] "savedrecs.txt".
I tried searching around other folks' blogdown repos on Github to see how they might have referred to a data file, but the only example I found referred to a data file using a URL.
I suspect that this may be due to the location of your data file. In my working example, the Rmd form of my blog post is in the directory, called p0bs/content/post. I also add my data file (a CSV in my case) to this directory.
I then treat the rest of the post as I would in a standard Rmarkdown website, with Rmd chunks (that are named without spaces). In your case, that code would include:
read.csv("savedrecs.txt")
I hope that helps you.
Related
I often have to work with shared data/code from Dropbox, and all of the files are usually loaded in as df <- import("../data/branch/file_name.csv")
However, this never loads on my computer, so I always have to type in my full directory as df <- import("C:/Users/Name/Dropbox/Folder1/Folder2/data/branch/file_name.csv")
Which makes it difficult for others to reproduce the code. Is there any way to fix this so that R can read the "../" part properly? I always get this error: Error: path does not exist: ../data/branch/file_name.csv
(I used the import function as an example but this problem occurs with other packages or loading functions as well)
I've also tried using "~/" but the problem persists. The shared code I work with always uses "../" though so I'd prefer a solution that gets that to work instead so that I don't have to change the original script each time I need to use it.
Thank you very much.
Edit: Despite the conversation below, I am still having trouble with this. I tried setting the working directory and then using "../" and it sometimes works for read_xls() (it was working a few hours ago, not anymore, depsite doing the exact same thing and setting the same working directory) but not for rio::import() or other reading functions. I've even tried setting my working directory to the exact same folder and using "./" but no luck. Errors now say "Cannot open the connection" or "No such file"
You can try setting your working directory(wd) to the current folder first, then use read.csv to import the data.
To set the working directory, first obtain the current directory using rstudioapi::getActiveDocumentContext()$path then use setwd() to set the wd to this path.
Then use whatever function to import your data.
For example, let's say your R code is saved in the "branch" folder, then the following code should work just fine:
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
mydata <- read.csv("./file_name.csv")
head(mydata)
Otherwise, if your R code was saved in a subfolder under Folder2 called code such that your R script's directory is: "C:/Users/Name/Dropbox/Folder1/Folder2/code/mycode.R", then the following should work:
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
mydata <- read.csv("../data/branch/file_name.csv")
head(mydata)
It looks like the person you are collaborating with has their working directory set to a separate folder within Folder2 (perhaps a folder with all the .R code?). The .. means that the relative path is referencing the next folder up from the working directory (the next folder up is presumably Folder2).
To solve your problem, every time you start working you need to set your working directory to the same folder that your collaborator is using for their working directory. For example, this may be something like setwd("C:/Users/Name/Dropbox/Folder1/Folder2/RCode"). Unfortunately you will have to do that every time you open up the script, but if you do it at the very beginning, then the rest of the code should work.
Working directories can be hard to manage, especially when collaborating. A better solution to the working directory problem is to create a project in R Studio and collaborate on that project using GitHub. If you don't have experience with GitHub, these videos are an approachable resource for helping you get started.
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 putting together an R package. I would like to show example code in the vignette, where example data files (included in the package) are used to generate an (example) output file.
I read about using example data in Hadley Wickham's post (http://r-pkgs.had.co.nz/data.html), and believe I should keep my example data as raw data, as it must be parsed to generate the output.
So, I created a directory in my package structure
/Users/userName/myPackage/inst/extdata/
with subdirectories InputFiles and OutputFiles.
And I put the example file (exampleData.csv) inside of the InputFiles subdirectory (/Users/userName/myPackage/inst/extdata/InputFiles).
My vignette is located in:
/Users/userName/myPackage/vignettes/myPackage.Rnw
It contains the following syntax:
<<eval=FALSE>>=
fileString = "/Users/userName/myPackage/inst/extdata/InputFiles/exampleData.csv"
doFunction1(fileString)
doFunction2(fileString)
doFunction3(fileString, output ="Users/userName/myPackage/inst/extdata/OutputFiles")
#
I am having two problems with developing this vignette and its example datasets:
1) I am unsure if my use of the extdata file is appropriate. This seemed to be the best directory name and location to place my example files, according to the aforementioned Hadley Wickham reference.
2) I am unsure how to make the pathways relative, instead of absolute, as I have them currently. This example code does not run automatically, as you can see. Instead, I have it under an R chunk of eval=FALSE so that it is simply listed there for the users to test themselves. After running the example code, the users can also check that the output file was indeed created in (/Users/userName/myPackage/inst/extdata/OutputFiles). What is the best way for me to allow the user to not have to use an absolute path when following the example? Is it possible to just follow a relative path from within the package directory myPackage?
My data files consist of .csv, .htm, and .text files. In the past, when constructing a package, I have saved a data frame as .rda file, and then the user could simply use:
data(example.rda)
to read that file. They would not have to write the entire pathway. Is there a similar function that can be used to read .csv, .html, and .text files, and then output them to an example output location - without having to use the full pathway? Would it be possible to have help functions that also read in the input files and write to the output files? Would this cause a conflict in CRAN if various example help functions in the /man folder physically save the example output file to the example output folder?
The standard way to refer to a file in a package is:
# gives root package directory
system.file(package="myPackage")
# specific file
system.file("extdata/InputFiles/exampleData.csv", package="myPackage")
# best is to use cross-platform way to write a file path:
system.file("extdata", "InputFiles", "exampleData.csv", package="myPackage")
When developing with devtools, the inst subdirectory is ignored, so you never need to worry about absolute paths. This should work in a vignette. Note that a vignette, I think, only ever uses the installed version of a package, not the one you may have loaded in your development environment (specifically, devtools::load_all() does not change the code which is used to build the vignette, you must install() it first).
Finally, using data() is a bit old fashioned. Hadley and others recommend using lazy data, so the data appears in the namespace automatically. Try the following in your DESCRIPTION.
LazyData: true
LazyDataCompression: xz
I have a number of R files with an .R extension. I've tried various ways to see what is inside these file, including Xcode, vim, etc.
What I find is utterly indecipherable. For example, it looks like this Lçæ§o‡dµ’Ò6ÇìùëfiFŒÀ±y2Â8á∫˝É, but pages of it.
Is it safe to say that these files are fundamentally corrupt? Or should I be using R to open these files to see what's actually in them?
EDIT: I've never worked with a file like this. After using load() in R, how would I read the data? I have used
> data <- load("~/filename.RData")
> data
The output is [1] "filename".
EDIT2: It appears these are gzip files saved with an .R extension. I can using load() to read the data into R. Is there any other way I can access these data files?
"filename" is now loaded and it is stored in an object of the same name. You should be able to see what it is inside by running:
filename
I am relatively new to R and am having some trouble with how to access my data. I have my test.xls file created in my MYDocuments. How to I access it from R
library(xlsReadWrite)
DF1 <- read.xls("test.xls") # read 1st sheet
Set the working directory with:
setwd("C:/Documents and Settings/yourname/My Documents")
This link may be useful as a method of making working folders per project and then placing all relevant info in that folder. It's a nice tutorial for making project files that contain everything you need. This is one approach.
http://www.dangoldstein.com/flash/Rtutorial2/Rtutorial2.html
The setwd() is another approach. I use a combination of the two in my work.