rNotebook | A browser based R Notebook | Version Control System library

For every code chunk that you want to produce svg output, you simply set the dev = 'svg' chunk option. Or you can set this option globally with knitr::opts_chunk$set(dev = 'svg') at the beginning of your markdown document.

Save the following as a .Rmd file, knit, and see what you get.

knitr::all_labels() returns NULL if it is not called in the full knitting process. When you run a single code chunk in the R Markdown Notebook, the document is not fully knitted.

To make knitr::all_labels() return all chunk labels, you should not use the notebook mode or preview the notebook, but knit the document instead (e.g., to the html_document output format).

I recommend you include those models as targets in the plan, but what you describe is possible. R Markdown and knitr automatically run code chunks in the calling environment, so the variable assignments you make in the report are available.

Within R studio, you can choose R markdown . Navigate to File Option -> New File -> R Markdown

There are no changes in coding. All codes that you write in R would be as-is. Just with a flexibility that you can add comments and explain your code. Make sure in .Rmd file, there are {} clauses. don't make any changes to it while writing code.

You will observe below chunk in .Rmd file. Make sure you should not delete {} but you may write any heading within these brackets.Followed by these brackets, you can write your code.

Try this:

Try to pipe the result to kable_styling. It will apply a print method so the table will be rendered.

Here is a solution to part of your problem of generating a table in pdf form. You will need to tweak the styling of your table in xtable in order to get the zebra stripe you want and merged columns. Generally speaking conversion from html to pdf is not so straightforward, so a better solution is to use LaTeX to generate your table in the first place (I know you didn't want LaTeX, but at least this is compiled to pdf with R and xtable does the hard work):

This error occurs on Windows systems when directories are nested too many levels in. The Windows API has a maximum path length of 260 characters.

Maximum Path Length Limitation In the Windows API (with some exceptions discussed in the following paragraphs), the maximum length for a path is MAX_PATH, which is defined as 260 characters. A local path is structured in the following order: drive letter, colon, backslash, name components separated by backslashes, and a terminating null character. For example, the maximum path on drive D is "D:\some 256-character path string" where "" represents the invisible terminating null character for the current system codepage. (The characters < > are used here for visual clarity and cannot be part of a valid path string.)

This is pretty easy to avoid. Just adjust your working directory, or the structure where you're saving your tempfile. Either your file name is too long, or your directory is nested too deeply so the path is exceeding Windows' path limits.

As an aside, on Unix systems this the max path significantly longer but there is a max file name length of 255 chars.

The first RMarkdown chunk calls rats <- rstan::stan_model(model_code=the_text) behind the scenes, so in order to sample from that posterior distribution you need to ultimately do rats_fit <- sampling(rats, data = list()), whose remaining arguments are pretty much the same as for stan. But you do have to call library(rstan) before all that.