Anytime I try to check on a dataframe on a .Rmd file, RStudio won't run it. I can read the csv file, but when I call it, nothing happens. I can tell it's a problem with Dataframes because I can run mathematical equations and even plot some graphic.
When I open the .html file, saved using Knitr, it's all ok:
Related
I have a .Rmd file called f1.Rmd (containing a mix of text and R chunks) and an R script called f2.R.
I would like to insert a set of R instructions in f2.R that would execute all the R chunks contained in f1.Rmd, in such a way that all variables created in f1.Rmd would be created in my current R session if I source f2.R
(similarly to what happens when clicking on "Run" -> "Run all chunks below from the Rstudio menu").
If you render the f1.Rmd file from your current environment, this should happen.
You can use rmarkdown::render() from the console or a .R script. This will create all the variables in your current environment. It will also have the side effect of making the document.
When you use the knit button in RStudio, this launches the render in a new r session as a background process.
See also the envir option for render.
See also this answer for other options. knitr: run all chunks in an Rmarkdown document
It also depends what your .Rmd is doing.
I'm currently doing an R Markdown File of an analysis I recently finished using R. With that, whenever I add details, I click Knit to ensure everything I added goes well on the HTML knit file.
I noticed that when I used ggplot on my R Markdown file, the file doesn't knit anymore and it says:
Error while opening file - No Such File or directory.
But when I deleted the ggplot command, it gets knitted again.
But this time, without the visualization, it gets knitted again.
UPDATE: I see this error message on the console tab everytime I use ggplot on my .rmd file.
So with that, I call on install.packages("ggplot2") & library("ggplot2") on my .rmd file. However, I get this error instead.
How will I be able to retain the ggplot command and at the same time be able to knit the file? As an added reference, the ggplot command executes on the .rmd file, it just doesn't knit. Can someone help me please?
I have a large Markdown file (*.Rmd) and want to execute only the R commands in that file (not the text) in RStudio. How can this be done?
If I mark the whole document and try to execute it, R tries to execute also the text in the Markdown file, which, of course, results in errors.
Click on the arrows at the top right of the chunks:
I have a sweave code that is producing a pdf. The code works fine.
I run it from the command line using:"
R CMD Sweave --pdf filename.Rnw
The resulting pdf that is produced is save in the working directory as
filename.pdf
Instead I would like 2 things:
Have the resulting output .pdf saved in another directory say wrk\random\dir
Change the name on a daily basis by adding the date at the end of it so I can maintain a history - such as filename.05032017.pdf
I tried using suggestions from here: Attach date to PDF generated with Sweave
but that didn't work. Needless to say it could be because I am absolutely new to R/SWEAVE and suck?
I don't think that can be done on the command line, but you can do it if you run Sweave within R:
filename <- paste0("wrk/random/dir/filename", format(Sys.Date(), "%d%m%Y"), ".tex")
Sweave("filename.Rnw", output=filename)
tools::texi2pdf(filename)
You could put this in a *.R file and run it with Rscript if you don't want to start R.
I'm trying to write a Bash script in Ubuntu 10.04 that opens a Python file which exports a CSV, and then runs the following Rscript with the goal of exporting a HTML with plots from Dashboard.Rmd:
require(knitr)
setwd('/home/sensors/Desktop/')
knit2html('Dashboard.Rmd')
browseURL('Dashboard.html')
Dashboard.Rmd is an R markdown that calls read.csv on the csv from the first step, makes a data frame and creates plots, but that part's working fine. According to this, I figure that Rscript should replicate the action of pressing "Knit HTML" in R Studio. However, the html it creates is identical to the last time Knit HTML was pressed; i.e. even if the CSV is different, the html doesn't reflect the change.
I also tried using a separate line for knit and markdownToHTML with the same effect. It seems like it doesn't source the code from the Rmd when performing knit. It does update the html properly when I enter the commands from that Rscript into the console of R Studio with Dashboard.Rmd open. However I'm not sure how to translate that into a Bash script. I also tried knit2html with envir=new.env(), envir=R_GlobalEnv, and envir=parent.frame() with no luck. Any help would be appreciated!
So it turns out that this was an artifact of cache=TRUE -- the HTML file was not changed because everything was cached.