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R - Packages

R package "ecospat"

ecospat is an R package for the support of spatial analyses and modelling of species niches and distributions, written by current and former members and collaborators of the ecospat group of Antoine Guisan. The ecospat package includes niche quantification and overlap functions that were used in Broennimann et al. 2012 and Petitpierre et al. 2012 to quantify climatic niche shifts between the native and invaded ranges of invasive species. In addition, this package offers the possibility to perform pre-modelling analysis to species distribution models, such as spatial autocorrelation analysis, MESS (Multivariate Environmental Similarity Surfaces) analyses, phylogenetic diversity measures and biotic interactions metrics. It also provides functions to complement biomod2 in preparing the data, calibrating and evaluating (e.g. boyce index) and projecting the models. Post-modelling analyses include predictions of community composition and environmentally-constrained species co-occurrences analyses. ecospat can also be complemented with the MigClim package, developed by members of the same group.

 

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R package "MigClim"

The MigClim R package is a function library for the open source R software that enables the implementation of species-specific dispersal constraints into projections of species distribution models under environmental change and/or landscape fragmentation scenarios. The model is based on a cellular automaton and the basic modeling unit is a cell that is inhabited or not. Model parameters include dispersal distance and kernel, long distance dispersal, barriers to dispersal, propagule production potential and habitat invasibility. The MigClim R package has been designed to be highly flexible in the parameter values it accepts, and to offer good compatibility with existing species distribution modeling software. Possible applications include the projection of future species distributions under environmental change conditions and modeling the spread of invasive species.

 

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BgeeDB R package

BgeeDB is a collection of functions to import data from the Bgee database (http://bgee.org/) directly into R, and to facilitate downstream analyses, such as gene set enrichment test based on expression of genes in anatomical structures. Bgee provides annotated and processed expression data and expression calls from curated wild-type healthy samples, from humans and many other animal species.

The package retrieves the annotation of RNA-seq or Affymetrix experiments integrated into the Bgee database, and downloads into R the quantitative data and expression calls produced by the Bgee pipeline. The package also allows to run GO-like enrichment analyses based on anatomical terms, where genes are mapped to anatomical terms by expression patterns, based on the topGO package. This is the same as the TopAnat web-service available at (http://bgee.org/?page=top_anat#/), but with more flexibility in the choice of parameters and developmental stages.

In summary, the BgeeDB package allows to:

  1. List annotation of RNA-seq and microarry data available the Bgee database
  2. Download the processed gene expression data available in the Bgee database
  3. Download the gene expression calls and use them to perform TopAnat analyses

 

Link on CRAN

Link on the web page of the research group

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