Notes

nonparametric-bayes

  • nonparametric-bayes sensitivity-trends runs.
  • nonparametric-bayes sensitivity.R runs: explore facets to see what setting causes the below-perfect performance cluster.

knitcitations

  • updates to knitcitations (paste fron NEWS)
  • Looking at adapting CSL for inline text formatting csl/issues/33
  • Implemented pandoc rendering

ropensci

  • Use of .Renviron vs .Rprofile for API keys

Seems the difference between .Rprofile and .Renviron is that (a) the latter is just a named character vector, and (b) the latter is accessed by Sys.getenv(). This keeps the working space clean (so does our use of options, instead of just writing the API key into the .Rprofile directly). Sys.getenv automatically seems to load the environmental variables of the shell (for instance, Sys.getenv(“USER”) returns the username of the computer/active shell, even if no .Renviron file exists). This is kinda convenient, e.g. with travis, if you were encrypting your API keys you could load them with Sys.getenv() without any further step. I guess it makes sense to think of security credentials as environmental variables. In principle (e.g. in the travis case) a user might do this when accessing the same keys across different software, rather than storing different files for R vs python etc.

Note that a user could have a different .Renviron file in each working directory which is loaded first, which could allow separate projects in separate working directories to only load their own keys.

I was wondering if we should provide helper functions that would write the keys to .Rprofile or .Renviron or wherever they should go from R, rather than asking the user to locate these hidden files?

rmarkdown exploration

  • Yes, you need to write a custom template to have multiple pdf templates. rmarkdown/issues/113

  • Whoops, for RStudio 0.98b (preview) I do need to apt-get install texlive-fonts-recommended even though my command-line pandoc/latex has no trouble finding some other copy of these fonts on my system.

  • Who knew? rmarkdown sets dev=png for html and dev=pdf for pdf automatically. rmarkdown/issues/111