I am a new user to R Markdown and was wondering if there was a way to "incrementally" compile an html markdown page as I am writing the code. Say I add 20 lines of code to an existing markdown file today. Is there a way to have the program "remember" the past compilations so that only the 20 new lines are added to the html file preserving the past rendering. I have a lot of memory heavy steps in my code (loading unloading files), and I find that when I add new bits of code I am having to compile everything from the beginning.
I tried looking into the "cache" option but it does not seem to be working.
I am assuming that all the variables I will be needing are present in my environment. In other words, i want to incrementally build an html markdown file without having to compile everything the moment I add an extra line to an existing document. Thanks for your help!
You should look into using the excellent editR package. It does exactly what you're looking for:
https://github.com/swarm-lab/editR
Related
To preface this, I think my question is related to this, but it's not exactly the same: How to source R Markdown file like `source('myfile.r')`?
Basically, I perform most of my data cleaning and analysis in Rmarkdown files because the visual separation between chunks of code and my own comments on what should be done for the analysis/cleaning is very helpful to me. It also helps that within Rstudio if you run a table, df, then it'll display an interactive snippet of it in the document. This is all very helpful in complicated cleaning/analyses. So in other words, I'd like to develop in one R-Markdown file and write in another R-Markdown file. Splitting/writing the code into a source.R file is not ideal, unless there was a very automated and reproducible way to do it.
The issue is that for reports, I'd sometimes like to take specific objects that were generated from these lengthy data-cleaning and analyses files in Rmarkdown. For example, let's say that during my data-cleaning in Rmarkdown-file-1, there was a particular table that was giving me trouble problematic.df and that I'd like to call in my report or possibly perform further manipulations in my report (Rmarkdown-file-2).
So ultimately I think this is the question:
How can I call any arbitrary object generated at any arbitrary point of one Rmarkdown file in another Rmarkdown file?
Obviously, the above would be the ideal, but it sounds unreasonable, so perhaps this is a better question/request:
How can I call any arbitrary objects generated by the end of one Rmarkdown file in another Rmarkdown file?
Upon further reflection, my question might already be answered in the post I linked, but it's been a while since that question was posted and perhaps there are new solutions or perspectives on this issue.
So I recently helped write a code for my lab which takes our processed data and makes a merged data frame of it. For purpose of keeping the lab updated, we keep our data tables updated on a secure wiki and thus I need an HTML made so I can basically upload the dataframe onto the wiki easily. It's worked before - all I did was basically copy what was already written and working and edited it to work for a different time point in our data collection. I have no errors given back to me and the data looks how I want it to look. As far as I know this script should be written logically and working well and so far it does except for one issue: R will make a file for the HTML, but there is no HTML written in the text document.
I have HTML's written from the other data time points which are written the exact same as this one, so I don't think it is a script construction thing.
Any ideas as to why this could be happening? I just need to know where to triage.
The package used for HTML is R2HTML, included in my packages list up at the top of the script. For HTML(, file=paste()), you will need to use your own directory to see if the HTML is written as a text file.
If I am not wrong , You are trying to get the dataframe in html format .
In this case you need to use xtable package in R
Just the below code in bottom of the script
## install the xtable package before importing it
library("xtable")
print(xtable(ChildSRPtotsFU_wiki), type="html", file="check_stack_overflow.html")
I love knitr & rmarkdown, but I often find myself in situations where I have a lengthy report that takes some nontrivial amount of time to run. After it's generated, I notice my inevitable typos in text. However, re-knitting everything to just fix a couple typos (just in text, not code) takes a long time and seems avoidable. I was about to start taking a hack at developing my own solution to this, but I'm thinking it's the kind of thing that could already have a mature solution which would likely be more robust than the one I'd build.
I'm wondering if there is solution out there within knitr or third party that would allow me to edit just the text of my reports without rerunning code, generating plots and outputs etc. I know, I can simply edit the generated html text, but then those changes must be replicated in the R/Rmd code that generated it, or they get out of sync. I'm envisioning a function like this:
argument 1: the R/Rmd script with text edits (no code changes)... perhaps a warning is generated when code chunks change
argument 2: the html output file from the last time the R script in argument was knitted without the text edits.
return: the html report (argument 2) updated with the comments in the R/Rmd script (argument 1).
I use the cache option sometimes for large datasets. I toggle eval and echo on and off when developing if I'm just working on the text of my report. However, I'm looking for a function that would take care of all this for me, so one doesn't have to mess with the code and chunk options to make small edits to text.
Here's an interim solution that lets you retain the speed of making changes directly to the rendered text, but you have to do a little work after you're done making changes.
Assuming the following files:
input.knitr is the original Knitr file with text and code integrated.
output.html is the resulting HTML code that has been rendered by Knitr.
Consider making direct text edits to output.html and then running something like Meld visual merge tool:
meld output.html input.knitr
Then manually select the edits in output.html that are new and should be fixed in the original source input.knitr. Tools such as Meld do a pretty good job of aligning the texts so that the chunks and knitted output will appear as large "changes" that, in practice, you would ignore. You would focus on the small changes in the non-chunk sections.
I have a .Rnw document in which I include childs. The childs produce tables via the 'latex' command of the Hmisc library in R.
When I make changes in the child documents, these changes do not anymore change the pdf document. My first guess was to use the chunk option 'eval=TRUE', but this does not change anything. Then, I saw, that the tables are actually saved to a .tex file with same name as the .Rnw document. I deleted this file and after compilation with knitr I got an error:
Error: Latexmk: Could not find file documentname.tex.
I assume, this is not the way to do it. Now I am out of ideas what to do. I appreciate some help on my problem.
Best
Simon
Allright, when trying to construct a simple example, I actually found out, that neither the packages I included nor the nesting of child documents interfere with the compilation via knitr. The reason was a simple error in the low-level .Rnw document, where a Hmisc latex table had a label, that missed a closing speech mark.
This causes then the output pdf not to change - I assume, that in this case the already constructed .tex file is included instead of letting knitr recompile the .Rnw documents and this hasn't changed since the last compilation?
What I wonder about is the different format of the landscape ctable in the document. Using a simple knitr document just with \documentclass{article} produces well placed tables. In my document using a template for the JFE, I get a table that extends over the whole page and even in footnotesize it is far away from the great appearance in the simple document. There is only a margin of less than half a cm on the right and the left. Page size is the same: both US letter... Can I probably control that via knitr or only via resizebox?
my question(s) might be less general than the title suggests. I am running R on Mac OS X with a MySQL database to store the data. I have been working with the Komodo / Sciviews-R for some time. Recently I had the need for auto-generated reports and looked into Sweave. I guess StatET / Eclipse appears to be the "standard" solution for Sweavers.
1) Is it reasonable to switch from Komodo to StatET Eclipse? I tried StatET before but chose Komodo over StatET because I liked the calltip / autosuggest and the more convenient config from Komodo so much.
2) What´s a reasonable workflow to generate Sweave files? Usually I develop my R code first and then care about the report later. I just learned today that there is one file in Sweave that contains R code and Latex code at once and that from this file the .tex document is created. While the example files look handily and can't really imagine how to enter my 250 + lines of R code to a file and mixed it up with Latex.
Is it possible to just enter the qplot() and ggplot() statements to a such a document and source the functionality like database connection and intermediate results somehow?
Or is it just a matter of being used to the mix of Latex and R code?
Thx for any suggestions, hints, links and back-to-the-roots-shout-outs…
You've asked several questions, so here's several answers;
Is StatEt/Eclipse the right way to do Sweave ?
Not nessarily (note: I'm an avid StatEt/Eclipse user, and use it for both pure R and Sweave/R and love it, I haven't used Komodo / sciviews-R). You should be able to run the sweave command from any R command line which will generate a .tex file. You can then turn the .tex file into something readable (like pdf) from any tex environment.
What's a good Sweave workflow ?
When I have wanted to turn an r script into a sweave report I generaly start with an empty sweave template and copy/paste my entire R script into a sweave R block just after the title, i.e;
<<label=myEntireRScript, echo=false, include=false>>
#Insert code here
myTable<-dataframe(...)
myPlot<-qplot(....)
#
Then I go through and find the parts I want to report. For instance, if i want to put a table into the report, I'll cut the R block and put an xtable block in, and the same for variables and plots.
<<label=myEntireRScript, echo=false, include=false>>=
#Insert code here
#
Put any text I want before my table here, maybe with a \Sexpr{print(variable)} named variable
<<label=myTable, result=Tex>>=
myTable<-dataframe(...)
print(xtable(mytable,...),...)
#
Any text I want before my figure
<label=myplot, result=figure>>=
myPlot<-qplot(....)
print(qplot)
#
You may want to look at these related SO posts. The rest of my post relates to your question 2.
When creating reports with Sweave, I usually keep most of the R code and the report text separate. If the R code is fast to run, then I prefer I will include something like the following at the start of the .Rnw file:
<<>>
source('/path/to/script.r')
#
On the other hand, if the R code takes a long time, I will often include something like the following at the end of the R script:
Sweave('/path/to/report.Rnw'); system('pdflatex report.tex')
That way, I can re-generate the report quickly, without needing to run all the R code again. Then, the only work R has to do in the Sweave file is print tables, make graphs and maybe extract a few figures.
Like nullglob, I prefer to keep the R and Sweave files separate, but I prefer to save the workspace with save.image() rather than to source() the file. This avoids running the R calculations with each .Rnw file compiling (and I always end up tinkering with the typesetting more than I'd like).
My general work flow is to do each paper/project in it's own folder with it's own R file(s). When the calculation side is "done", I save.image() to store all the workspace variables as-is.
Then, in the .Rnw file in the same directory I set the working directory with setwd() and load all variables with load(".Rdata"). Of course, you can change the name you use for your workspace, but I do one workspace per folder and keep the default name. Oh, and if you tinker with the R file, be sure save the workspace image and watch out for variables that linger in the workspace and .Rnw file, but are no longer part of the R file... this is where the save.image() approach can cause some headaches.
I am on a Mac and I suggest TextMate if you're mildly geeky and emacs/ess if you're really geeky. I use vim and command line R, but emacs/ess works best for most. If you're in this for the long haul, I doubt you'll regret learning emacs/ess for R, Sweave, and LaTeX.