Spatial Analysis of Phenotypic, Genotypic and Environmental Data

Management and exploratory analysis of spatial data in population biology. Easy integration of information from multiple sources with 'ecogen' objects.


News

EcoGenetics 1.2.0-2 (Release date: 2015-07-11)

Changes:
  • Change in package structure: the ecogen class was adapted to the update of Adegenet to version 2.0.0. A new slot ("A", including a data frame with allelic frequencies), replaces the GENIND slot of previous EcoGenetics versions. The program uses now an internal (modified) version of the "genind" class, adapted for internal use (temporal objects in internal processes).
  • New functions:
    • eco.format, replacing the deprecated functions "aue.idig" and "aue.char2num".
    • eco.convert, allowing conversion among genetic data (loci matrix, alleles matrix, loci list and alleles list). eco.2columns was deprecated and included as a conversion case in eco.convert.
  • New functionalities:
    • A generic system of accesors is implemented for all the objects included in the package.
    • In this version, the G data frame can be optionally stored in a pre-processed format. Default option generates, for codominant data, a matrix with removed separators and missing data conversion to NA and remotion of non informative alleles. An option for ordering the alleles is also available. For dominant data, the pre-process consists of the remotion of non informative alleles and monomorphic loci (in default option, loci with polymorphism level < 5%).
    • The function eco.append has been deprecated. An improved version of the function has been developed with accessors (accessor ecoslot.OUT(object)) and square brackets (object[["OUT"]])
    • Most of the functions included were adapted for genetic data of any ploidy levels.
  • Bugs correction: eco.2genepop - problem in the "POP" argument of the output file corrected.
  • Minor changes in dependences.
  • Updated examples. Improved help files and overview of the package -help("EcoGenetics").

EcoGenetics 1.2.0-1 (Release date: 2015-06-16)

Changes:
  • New functions: eco.malecot (beta version), eco.kin.loiselle, eco.genepop2df, aue.idig.
  • New plot method for correlogram analysis of multiple variables.
  • Corrections in examples.
  • Bug correction in ecogen subsetting for presence-ausence molecular markers, "DNAbin" and "alignment" objects.
  • Minor changes in dependences.

EcoGenetics 1.2.0 (Release date: 2015-05-11)

Changes:
  • This version has improvements in the modular design of the package. Many functions of the version 1.1.0 were adapted to an improved S4 structure. Three main functions for autocorrelation analysis were generated: eco.gsa, eco.lsa and eco.correlog, replacing the deprecated eco.moran, eco.geary, eco.joincount, eco.localmoran, eco.getisord and eco.autocor.
  • New functions: eco.detrend, eco.2spagedi, aux.image2df, aux.filter. New functionalities: partial Mantel test, partial Mantel correlograms, cross-correlation, cross-correlograms and local-Geary's C.
  • Incorporation of new and improved examples.
  • Bugs in the Getis-Ord (internal) function and in eco.mantel were corrected.
  • Minor changes in dependences.

EcoGenetics 1.1.0 (Release date: 2015-02-18)

Changes:
  • Included the new functions: eco.cormantel, eco.forestplot, eco.geary, eco.getisord, eco.joincount, eco.laglistw, eco.localmoran, latlon2distm, eco.mantel, eco.moran, eco.rankplot.
  • Adaptation of eco.autocor to the new functions of this version. Now also able to create a correlogram for local Getis-Ord's G and local Moran's I statistics.
  • Actualization of the function eco.variogram.
  • Minor changes in dependences.

Reference manual

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install.packages("EcoGenetics")

1.2.1 by Leandro Roser, 7 months ago


https://github.com/cran/EcoGenetics, https://github.com/leandroroser/EcoGenetics-devel, https://leandroroser.github.io/EcoGenetics-Tutorial


Browse source code at https://github.com/cran/EcoGenetics


Authors: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra


Documentation:   PDF Manual  


GPL (>= 2) license


Imports d3heatmap, edgebundleR, ggplot2, grid, htmlwidgets, igraph, jsonlite, magrittr, networkD3, party, pheatmap, plotly, raster, reshape2, rgdal, rkt, SoDA, sp

Depends on methods

Suggests adegenet


See at CRAN