Rstudio Markdown

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A lot of its ideas are inspired by Markdown Preview Plus and RStudio Markdown. Visual Studio CodeのMarkdownプレビューにCSSを適用する ハチアンアーカイブズ. Learning RStudio for R Statistical Computing Mark P.J. Van der Loo, Edwin de Jonge download Z-Library. Download books for free.

Rstudio markdown preview

I'm attempting to generate an HTML document using R Markdown that includes charts and email it to a defined distribution group. I've had success doing this with just a knitr::kable, but as soon as I attempt to include an embedded plot, the email process fails.

I'm open to any suggestions on alternative ways to embed images in emails and have found a few threads on how to approach this issue here, but thus far I haven't been able to run a successful end to end test. For this use case, I'm using rmarkdown::render and the mailR package (I have to send to and from an Office 365 Outlook host).

here is my example.Rmd script

Unemployment Charts

And here's a sample email script:

Here's the error I'm getting:

org.apache.commons.mail.EmailException: Building the MimeMessage failed
at org.apache.commons.mail.ImageHtmlEmail.buildMimeMessage(ImageHtmlEmail.java:112)
at org.apache.commons.mail.Email.send(Email.java:1436)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at RJavaTools.invokeMethod(RJavaTools.java:386)
Caused by: java.io.IOException: Cant resolve the following file resource :example_fileshtmlwidgets-1.0htmlwidgets.js
at org.apache.commons.mail.resolver.DataSourceFileResolver.resolve(DataSourceFileResolver.java:105)
at org.apache.commons.mail.resolver.DataSourceFileResolver.resolve(DataSourceFileResolver.java:79)
at org.apache.commons.mail.ImageHtmlEmail.replacePattern(ImageHtmlEmail.java:151)
at org.apache.commons.mail.ImageHtmlEmail.buildMimeMessage(ImageHtmlEmail.java:106)

It’s possible to create well-designed websites for free using RStudio’s R Markdown and hosting them on Github. This is very new and incredibly cool. It is a really powerful way to communicate science using the same reproducible workflow you use for your analyses and collaborations.

Creating websites with R Markdown can be done without knowing R or HTML, CSS, etc, and that’s where we’ll start. However, R Markdown integrates with these tools so the more you know the more complex and beautiful your website can be. This tutorial borrows heavily from a lot of great tutorials and resources you should check out too – there are links throughout.

The best way to learn is to follow along with your own laptop, but all are welcome. We’ll spend half the time with the tutorial and half the time for you to work on your own website and get help. If you bring your laptop please do this beforehand:

  1. install RStudio
  2. create a GitHub account (advice)
  3. set up your computer to talk to GitHub
    • have RStudio linked directly (preferred) (instructions sections 8-14)
    • or install the Desktop App
    • or be familiar with git commands for the command line (tutorial)
Pdf

Examples:

Rstudio Markdown Tutorial

We have been using R Markdown for the Ocean Health Index: ohi-science.org/ohi-global.
And R Markdown is much more than just websites – here’s a one-minute video about R Markdown to get you excited.