Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Management and exploratory analysis of spatial data in landscape genetics. Easy integration of information from multiple sources with "ecogen" objects.


EcoGenetics 1.2.1-3 Build Status AppVeyor Build Status R CRAN Status Badge CRAN Downloads


Tutorial


Online documentation



Installation of devel version:

library(devtools)
'install_github("leandroroser/EcoGenetics-devel")

News

EcoGenetics 1.2.1-4 (Release date: 2018-01-13)

Changes:

  • Corrections in DESCRIPTION file

EcoGenetics 1.2.1-3 (Release date: 2018-01-12)

Changes:

  • New object: ecopop, for analysis of aggregated data (populations)
  • Correction of bugs
  • Testing of the package via testthat

EcoGenetics 1.2.1-2 (Release date: 2017-11-21)

Changes:

  • Correction of bugs in conversion functions
  • Improvements in eco.format and conversion functions

EcoGenetics 1.2.1-1 (Release date: 2017-11-13)

Changes:

  • Improvement of the function eco.theilsen
  • Correction of bugs and documentation

EcoGenetics 1.2.1 (Release date: 2017-03-02)

Changes:

  • ecogen objects code now the slot A as integer (0,1 or 2) in the case of codominant markers
  • Validation defined for ecogen objects.
  • New ecogen methods: nrow, ncol, dim, logical subsetting for "["
  • new export and import methods for ecogen objects
  • Improved graphical display using ggplotly, networkD3, edgebundleR, igraph and pheatmap in addition to ggplot2
  • Algorithm used to compute Join-count statistic has been improved, and now is faster
  • New functions: eco.plotCorrelog, eco.plotCorrelogB, eco.plotLocal, eco.plotGlobal, eco.bearing, eco.formula, eco.split, eco.plotWeight
  • New option to compute a Mantel test with a truncated or an angular weights object
  • Definition of new functions for the conversion to/from other formats, and standardization of the nomenclature used for the names of conversion functions
  • eco.order has been converted in an internal function of the ecogen constructor

EcoGenetics 1.2.0-3 (Release date: 2015-07-15)

Changes:
  • eco.lsa function is able now to perform a multivariate analysis over single variables. The output is an S4 object, who contains matrices of individuals x variables. The multivariate capabilities incorporated in the packace (a multivariate support was added also for eco.correlog in EcoGenetics 1.2.0-1), provide a gereralized framework for the analysis of spatial autocorrelation in R.
  • A new multivariate plot method is available ("eco.rasterplot"). This is a generalized method which allows to plot by group and using conditional filters. The method is applicated in the package for multivariate local spatial analysis.
  • correction in eco.lsa for supporting NAs presence.
  • Enhanced examples for eco.lsa showing the multivariate functionality.
  • Minor corrections in package style and code.
  • The slot A of ecogen object was removed for dominant (presence- absence) markers, to avoid redundant data storage. The "show" and other methods were adapted to this marker type case.
  • Plot method available for connection networks.
  • Deprected aue.filter and included as a case in eco.slidewindow.

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

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("EcoGenetics")

1.2.1-4 by Leandro Roser, 4 months ago


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


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


Authors: Leandro Roser [aut, cre], Juan Vilardi [aut], Beatriz Saidman [aut], Laura Ferreyra [aut], Thibaut Jombart [ctb] (author of included adegenet code), Winston Chang [ctb] (author of the multiplot function included under the name grf.multiplot)


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, testthat, covr


See at CRAN