Useful knowledge

This page is intended to collate group knowledge.  For example, how to perform a specific statistical analysis.  Or links to a GIS data source.  We hope to keep this regularly updated.




  1. What:  pbapply: A lightweight package that adds progress bar to vectorized R functions (‘*apply’).
    Why:  Apply family functions (see here and here for intros) are great resources.  And incredibly efficient!  But sometimes we might use these to run a function that takes a very long time to finish.  If the function doesn’t print any intermediate output, the impatient among us are probably wondering what is going on?  How much longer until we’re at the finish?
    How:  Once you load it, all you have to do is add “pb” onto any apply function and you’re off with a nice progress bar from 0 to 100%.
  2. glmer2stan: fitting Bayesian models in STAN through R using lme4-type syntax. Great way to transition from mixed-effects models in R to hierarchical Bayes in STAN.
  3. Nice tutorial on fitting linear mixed models using JAGS and STAN.
  4. plot3D: R package for plotting 3D data in just about any way you can think of.
  5. R2G2:  R package to plot spatially explicit output directly in Google Earth.
  6. Discussion on how to do spatial joins in R (another here, and here for QGIS).
  7. Tutorial for converting shape files to rasters in R.



  1. WhatIdeone: Compiler and debugging tool for >60 programming languages.
    How:  Choose a language, paste the source into an online form with optional input data, and you’re off!

Species distributions

  1. What: Lifemapper: Creates species distribution maps from geospatial occurrence data.

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