Collection of R-related Resources

R-package: pascal

This R package described contains some "convenience" functions I programmed for my own use. I make them available here mainly for my own collaborators. They are reasonably well tested but use them at your own risk. Also, I do not provide any support. In case you find a bug, however, I am happy if you report it. The functions provided cover the following topics:

  • Aggregating/re-shaping data frames
  • Analysis of variance
  • Functions supporting the work with ASReml
  • Plotting
  • Formatting of output
  • ...plus many "convenience" functions

The package is hosted on GitHub: https://github.com/pascal-niklaus/pascal

The easiest way to install it is by using the package "devtools"

library(devtools)
install_github("pascal-niklaus/pascal/pascal")

Precompiled binaries are also available from https://github.com/pascal-niklaus/pasca/tree/master/pkgs

R-package: pgeo

This package contains more "biogeo"-related functions. The topics covered so far are:

  • conversion to/from delta-permille (isotope abundances)
  • conversion of MODIS pixel coordinates to WGS-84 and Swiss Grid

This package is hosted on GitHub: https://github.com/pascal-niklaus/pgeo

The easiest way to install it is by using the package "devtools"

library(devtools)
install_github("pascal-niklaus/pgeo/pgeo")

Precompiled binaries are also available from https://github.com/pascal-niklaus/pgeo/tree/master/pkgs

R-package: pdiv

This R package contains some "biodiversity"-related functions I programmed for my own use.

  • hill.Na, hill.Ha, shannon.H, simpson.D, evenness.1overD: Biodiversity indices, including the general Hill series.
  • calcFD: Calculates Petchey \amp; Gaston's functional diversity index
  • calcPD: Calculates phylogenetic diversity, using exactly the same algorithm as calcFD
  • calcMPD: Calculates mean phylogenetic distances, with or without abundance weighing
  • communityFromMatrix, communityToMatrix:Converts community composition data between matrix and data.frame format. Useful with calcFD and calcPD
  • addpart: Calculates Loreau and Hector's additive partitioning, providing a comfortable interface using model formula.

This package is hosted on GitHub: https://github.com/pascal-niklaus/pdiv

The easiest way to install it is by using the package "devtools"

library(devtools)
install_github("pascal-niklaus/pdiv/pdiv")

Precompiled binaries are also available from https://github.com/pascal-niklaus/pdiv/tree/master/pkgs