Many R packages/tools have come out recently for doing ecology and evolution. All of the below were described in Methods in Ecology and Evolution, except for spider, which came out in Molecular Ecology Resources. Here are some highlights.

• mvabund paper – get R pkg
  • Model-based analysis of multivariate abundance data. Visualising data, fitting predictive models, checking assumptions, hypothesis testing.
• popdemo paper – get R pkg
  • Population demography using projection matrix analysis.
• motmot paper – get R pkg
  • Models of trait macroevolution on trees
• spider paper – get R pkg
  • Analysis of species identity and evolution, with particular reference to DNA barcoding
• BaSTA paper – get R pkg
  • Bayesian estimation of age-specific survival from incomplete mark–recapture/recovery data with covariates
• abc paper – get R pkg
  • Approximate Bayesian Computation (ABC)
• RNetLogo paper – get R pkg
  • Running and exploring individual-based models implemented in NetLogo
• phytools paper – get R pkg
  • Tools for phylogenetic comparative biology
• smatr paper – get R pkg
  • Estimation and inference about allometric lines
• RBrownie paper – get R pkg ?
  • Testing hypotheses about rates of evolutionary change
• polytomy resolver paper – get R pkg
  • Resolve polytomies on dated phylogenies with their R scripts [here][].

And a cool tool came out for the Python programming language.

• NichePy paper – get python
  • Modular tools for estimating the similarity of ecological niche and species distribution models