I would like to setup a homepage and publish several R code mixed with text, pictures and references. Obviously that's what a lot of people do:
https://feliperego.github.io/blog/2015/10/23/Interpreting-Model-Output-In-R
https://yihui.org/knitr/demo/wordpress/
http://3.14a.ch/archives/2015/03/08/how-to-publish-with-r-markdown-in-wordpress/
RWordPress does not seem to support graphical outputs from the script. Instead of discussing the multitude of errors I received and options I tried, my simple question is: How did the above listed examples manage to put R code and graphs on their websites? (I haven't tried to contact those homepage owners, but this will be the next step, if no explanation can be found.)
You have several options. It depends if you want to build your website from scratch or not. In the first case, I recommend you to have a look at:
bookdown: very nice for documentation. You can find many examples on the web, for instance the bookdown documentation
blogdown: more general than bookdown. This gives very nice websites (mine is built using blogdown for instance). blogdown is based on hugo: you can find many themes.
In both cases, you write standard Rmarkdown and build your site by executing the markdowns. You can build the site locally for preview or deploy them on the web (manually or by a continuous integration system as gitlab pages). The point of using these packages is reducing the burden of handling formatting and links between pages.
The short answer is a mixture of manual and automatic generation. If you look at my website (www.jamescurran.co.nz), you'll find articles like the ones you want to write.
I achieve this in a variety of ways. Sometimes I get knitr to produce the HTML, and then I hack it into shape on the website. Other times, I use a mixture of short-tags like
[code language = "R"]
data(cars)
[/code]
and/or HTML like
<pre><code>
data(cars)
</code><pre>
The images I upload and then use Wordpress' editor to insert the correct links. It's not very satisfactory, but unless you have a hosting platform that allows you to have static content, then most of the automated solutions that go straight from R Markdown won't work.
Related
I want to create a product/project documentation in R that is going to be reviewed and discussed by a group of reviews. There are plenty of examples of how to create book-like documents using Rmarkdown (e.g. https://bookdown.org/) or interactive data visualizations using R-shiny. However, I could not find any solution for user comments similar to LibreOffice Writer, MS Word, or Google Docs. I could also imagine having a split-pane where one side is dedicated to the content presentation (e.g. text, graphs, code), while the other side is left for comments.
I am aware that such a solution requires a server-side solution for storing comments.
Any hints on existing solutions, workarounds, and implementations are welcome.
If I correctly understood, your question isn't very R specific. R is just code, R files are just text and they don't allow comments (beside the raw hashtag comments) and reviews. Your question is more about version control environments, that allow reviews on code stuff. The most used version control system is git, and git has an integrated panel in RStudio.
Git allows you to split your developpements in branches, which are the different ideas you and your coworkers can work on independentely. Once an idea is finalised, after some consecutive modifications known as commits, it is to be asked for merge in the "main branch". It is a "pull request".
That is where the different platform using git, like GitHub or GitLab, allow some review systems. Basically, when a branch is done, you ask "is that ok ?". Your reviewer can see the changes, can try you things, and tell if that is actually ok.
The other advantage of these is the continuous integration, that is : elaborating tests (in R with testthat) that will be tested on some events merge, like "on each merge to master". It is meant to ensure that the software is going forward : if a merge breaks some earlier test, you'll know it.
For beginners, in order to avoid being lost in bash commands, GitHub Desktop is a fine GUI above Git.
Note : You can also rely on the package usethis which has a few helper functions like use_git, use_gitlab_ci, use_github_action... It's not specific to reviews and comments but to the gitlab and github integration
I'm producing plenty of analyses in R and utilizing the .html Markdown format to present and communicate work. Often, my manager will need to correct/add to the text which accompanies the code blocks, and has practically no interaction with the code blocks. The analyses are typically produced by myself alone, so code collaboration is a low priority.
In an ideal world, he could open up the .html and edit the text in a browser, which I understand is not possible.
Are there any simple solutions for this? I am sure this is a common problem so there must be an easy solution I am overlooking. Here are the current solutions being considered:
Use Git (but my manager wouldn't like to learn Git)
Use Jupyter Notebooks (but I would prefer to stick with R Markdown for integration with RStudio and for the reproducible templates)
Knit the Markdown as a word document with manual version control on a shared network, allow tracking of changes in the word document, and copy-and-paste over changes made to the .Rmd file
The latter is least elegant but most likely to be used at the moment. If you have any suggestions, please let me know!
Here's a solution that is tailor-made your exact situation.
Use jupytext for bi-directional lossless interoperability between jupyter notebooks and R Markdown documents!
Maybe redoc is an option for you. Haven't tried it myself and it's still experimental but it would allow you to collaborate via Word. Basically the Word document can be edited and passed back to RMarkdown with all changes. See here.
I suggest you try trackdown https://claudiozandonella.github.io/trackdown/
trackdown offers a simple answer to collaborative writing and editing of R Markdown (or Sweave) documents. Using trackdown, the local .Rmd (or .Rnw) file is uploaded as plain-text in Google Drive where, thanks to the easily readable Markdown (or LaTeX) syntax and the well-known online interface offered by Google Docs, collaborators can easily contribute to the writing and editing of the narrative part of the document. After integrating all authors’ contributions, the final document can be downloaded and rendered locally.
Moreover, you can hide code chunks setting hide_code = TRUE (they will be automatically restored when downloaded). This prevents collaborators from inadvertently making changes to the code that might corrupt the file and it allows collaborators to focus only on the narrative text ignoring code jargon.
You can also upload the actual Output (i.e., the resulting complied document) in Google Drive together with the .Rmd (or .Rnw) document. This helps collaborators to evaluate the overall layout, figures and tables and it allows them to use comments on the pdf to propose and discuss suggestions.
When I write an R markdown file in RStudio and Knit HTML, my formulas (inline using $..$ or display using $$..$$) can be displayed properly. However, when I push my .md file to GitHub, these formulas cannot be displayed. They only show $..$ and $$..$$. Is there a way to let GitHub know how to parse latex formulas? Thanks!
Is there a way to let GitHub know how to parse latex formulas?
Some sites provide users with a service that would fit your need without any javascript involved: on-the-fly generation of images from url encoded latex formulas.
codecogs.com
iTex2Img.
given the following markdown syntax
it will display the following image
Note: In order for the image to be properly displayed, you'll have to ensure the querystring part of the url is percent encoded. You can easily find online tools to help you with that task, such as www.url-encode-decode.com
I also looked for how to render math on GitHub pages, and after a long time of research I found a nice solution.
I used KateX to render formulas server side: it is really faster than MathJaX.
Please note that same solution could be arranged to work also client side, but, I prefer server side rendering, cause
you know your server environment, but you don't know the client environment of your visitors
it is also faster client side, if the formulas are rendered on the server, only once.
I wrote an article showing the steps, I hope it can help math divulgation: see Math on GitHub Pages.
I'm not sure if this is possible, but this is what I'd like to do:
I'd like to create a literate program, hosted on github, and have the resulting human-friendly literature automatically published on my github's project page. By "automatically published," I mean that I can run a script on my local machine that ends with "git push origin master," and ends up with a published human-friendly, math-containing document on github. I'm open to compromises on the procedure to get there, but the simpler, the better.
Many people don't know what literate programming is, so I'll summarize that. It's a system where you write a single document that can be translated into either source code or a human-friendly document. The purpose is to very clearly explain the algorithm, in English (or other natural language), and it is considered useful when users may be as interested in reading about your algorithm as they are in using it directly. Some folks (like Donald Knuth) consider literate programming as a critical tool in building any complex piece of software.
One idea to do this would be to generate something like a README.md file as the output of the literate program, but I don't know of any math support in github's markdown formatting. It looks like github's wikis might support some math, but I don't know how to make the wiki be generated from the code -- as in, I'd like to be able to do a git push origin master from my machine, and have the github wiki automatically updated.
(Also, to understand why math support is important: I'm coming from a world of always using TeX or LaTeX to write papers, and I'm interested in a general system that other authors used to LaTeX could also use.)
Any ideas how to achieve this?
The wikis are backed by their own git repo, so you can push to it and have it automatically update. That's a different repo than the main one though. As far as I know that stuff is only supported in the wikis, not in the main repo markdown processor.
I'm currently looking at different solutions getting 2 dimensional mathematical formulas into webpages. I think that the wikipedia solution (generating png images from LaTeX sourcecode) is good enough until we get support for MathML in webbrowsers.
I suddenly realized that it might be possible to create a Google Charts API equivalent for mathformulas. Has this already been done? Is it even possible due to the strange characters involved in LaTeX-code?
I would like to hit an url like latex2png.org/api/?eq="E = mc^2" and get the following response:
edit:
Thanks for the answers sofar. However, I am already aware of several tools to generate png images from latex source code (both online and from my commandline), but what I was looking for was a simple way to get the image via an Http GET request. Perhaps such a service does not exist.
Update
As #hughes (and others) pointed out, the previous Google Chart API has been deprecated.
The example I wrote still works as of Sept 2015, but a new one shall be used now (documentation):
Old answer
Google Chart can do it (Documentation):
http://chart.apis.google.com/chart?cht=tx&chl=%5CLaTeX
I'm using this with Google Docs, because it doesn't support math yet.
chart.apis.google with background color changed
https://chart.apis.google.com/chart?cht=tx&chf=bg,s,FFFF00&chl=%0D%0A4x_0%5CDelta%28x%29%2B3%5CDelta%28x%29%2B2%5CDelta%28x%5E2%29%3E0%0D%0A
or chart.apis.google with background color transparent and resized
For better readability URL needs to be decoded.
https://chart.apis.google.com/chart?cht=tx&chs=428x35&chf=bg,s,FFFFFF00&chl=
4x_0\Delta(x)+3\Delta(x)+2\Delta(x^2)>0
Data structure looks like this
{
"cht":"tx",
"chs":"428x35",
"chf":"bg,s,FFFFFF00",
"chl":"n4x_0\Delta(x) 3\Delta(x) 2\Delta(x^2)>0"
}
https://chart.apis.google.com/chart?cht=tx&chs=428x35&chf=bg,s,FFFFFF00&chl=%0D%0A4x_0%5CDelta%28x%29%2B3%5CDelta%28x%29%2B2%5CDelta%28x%5E2%29%3E0%0D%0A
You could try the Online image generator for mathematical formulas for a start.
mathurl is a mathematical version of TinyURL.com. It allows you to reference LaTeXed mathematical expressions using a short url. For example, http://mathurl.com/?5v4pjw will show [LaTeX output Image] which you can then edit. More details on mathurl’s help page
I just ran across MathJax on Ajaxian [via Wayback Machine]:
MathJax seems to have a chance at being a practical solution that offers a high quality display of LaTeX and MathML math notation in HTML pages.
The output is remarkably beautiful, and it's all pure HTML and CSS, which makes it scalable and selectable. Performance is currently a bit sluggish, but this is recognized.
As everyone has said, there are many services that do this already. Here is another easy one that I've used a number of times (and you can install it locally on your server if necessary):
http://www.codecogs.com/components/equationeditor/equationeditor.php
I'd take a good look at how the MediaWiki LaTeX support does it and borrow from there.
Please check out this site for a way to create TeX documents without any software installed. You can then snippet the result image with any screen capture method and embed the resulting image into a any website.
Go to http://sharelatex.com
The software is free to use, but you need to register to create documents.