EcoGenetics: Spatial Analysis of Phenotypic, Genotypic and Environmental Data

Geostatistical tools for analyzing spatial patterns in population biology. Easy integration of information from multiple sources with "ecogen" objects.

Author
Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Date of publication
2016-07-15 20:02:10
Maintainer
Leandro Roser <learoser@gmail.com>
License
GPL (>= 2)
Version
1.2.0-3
URLs

View on CRAN

Man pages

aue.access
EcoGenetics slot standard notation. Returns an accessor to...
aue.ad2wg
Transforming an adyacency matrix into a local weight matrix...
aue.circle
Circle perimeter
aue.circle.w
Radial distance to a point.
aue.df2image
Transforming a data frame into a raster
aue.ellipse
Solid ellipse
aue.filter
Functions deprecated in EcoGenetics version 1.2.0-2
aue.fqal
Allelic frequencies
aue.genlab
Generation of generic labels of constant length
aue.geom.dist
Weight matrices based on different geometries
aue.image2df
Transforming a raster into a data frame with cartesian...
aue.is.poly
Identification of polymorphic loci
aue.phenosimil
Phenotypic similarity for vector, matrix or data frame...
aue.point
Solid circle
aue.rescale
Scaling a data frame or matrix to [0, 1] or [-1, 1] ranges
aue.rm.nonpoly
Remotion of non polymorphic loci
aue.rmspaces
Remove spaces and tabs at the begining and the end of each...
aue.rotate
Rotation of a matrix
aue.seqlist
Creation of a sequence of numbers in matrix or list format,...
aue.sort
Ordering the content of cells in a matrix. Ordering alleles...
aue.square
Solid square
coordinates
Coordinates
eco
Eco
eco2
Eco2
eco.2geneland
Creating input data for Geneland with an ecogen object
eco.2genepop
Exporting an ecogen genetic data frame into Genepop format
eco.2gstudio
Converting a diploid ecogen genetic data frame into a gstudio...
eco.2hierfstat
Converting an ecogen genetic data frame into a hierfstat data...
eco.2spagedi
Exporting an ecogen genetic data frame into SPAGeDI format
eco3
Eco3
eco.alfreq
Allelic frequency histograms for an ecogen genetic data frame
eco.association
Chi-square and Fisher's exact test for association of loci...
eco.autol-methods
show eco.lsa
eco.cbind
Combining the columns of ecogen object
eco.clear
Clearing the working environment, maintaining only the...
eco.convert
Conversion utility for genetic data
eco.cormantel
Mantel and partial Mantel correlograms
eco.correlog
Moran's I, Geary's C and bivariate Moran's I correlograms
eco.correlog-class
eco.correlog-class
eco.correlog-methods
globalplot
eco.detrend
Detrending spatial data with polynomial interpolation
eco.detrend-class
eco.detrend class
eco.detrend-methods
show eco.detrend
eco.format
Format tool for genetic data
ecogen
Creating a new ecogen object
ecogen-class
ecogen class
eco.genepop2df
Importing a Genepop file
EcoGenetics-accessors
Generic accessors for EcoGenetics objects
EcoGenetics-package
Spatial Analysis of Phenotypic, Genotypic and Environmental...
ecogen-methods
names
eco.gsa
Global spatial analysis
eco.gsa-class
eco.gsa class
eco.gsa-methods
show eco.gsa
eco.IBD
plot eco.IBD
eco.IBD-class
eco.IBD class
eco.IBD-methods
show eco.IBD
eco.kin.loiselle
Obtention of the multilocus Loiselle's Fij matrix
eco.lagweight
Obtention of a list of spatial weights for classes defined by...
eco.lagweight-class
eco.lagweight class
eco.lagweight-methods
show eco.lagweight
eco.listlsa-class
eco.listlsa
eco.listlsa-method
listplot
eco.lmtree
Fitting Multiple Linear Regression models by stepwise AIC...
eco.lmtree.mctree-summary
Summary for eco.lmtree output
eco.lmtree-methods
show eco.mlm
eco.lsa
Local spatial analysis
eco.lsa-class
eco.lsa class
eco.lsa-methods
plot eco.lsa
eco.malecot
Global and local kinship analyses
eco.mantel
Mantel and partial Mantel tests
eco.mctree-class
eco.mctree-class
eco.merge
Merging two ecogen objects. Ordering the rows of an ecogen...
eco.mlm-class
eco.mlm-class
eco.multilsa-class
eco.multilsa class
eco.multilsa-method
rasterplot graph for eco.lsa results
eco.NDVI
Generating atmospherically corrected NDVI and MSAVI2 images...
eco.NDVI.post
Postprocessing for NDVI and MSAVI 2 temporal series of...
eco.order
Ordering the rows of the data frames contained in an ecogen...
eco.pairtest
Kruskall - Wallis + Wilcoxon (Mann-Whitney U) and aov +...
eco.post.geneland
Log posterior probability plot for Geneland repetitions with...
eco.rasterplot
rasterplot graphs
eco.rbind
Combining the rows of two ecogen objects
eco.remove
Creating an updated ecogen object by removing results of the...
eco.slide.con
Sliding window along a network
eco.slide.matrix
Sliding window for matrix data
eco.subset
Subsetting an ecogen object by group
eco.theilsen
Theil-sen regression for a raster time series
eco.variogram
Empirical variogram
eco.variogram-class
eco.variogram class
eco.weight
Spatial weights
eco.weight-class
eco.weight class
eco.weight-methods
show eco.weight
environment
environment
forestplot-methods
Forestplot graphs
genotype
genotype
grf.multiplot
Multiple plot function for ggplot
grf.seqmultiplot
Plot a ggplot sequence in layers of n plots arranged in k...
int.break
breaks obtention
int.check.colnames
Check column names
int.check.con
Check a connection network
int.check.group
Check factor name consistency in a data frame and returns the...
int.check.ncod
Check ploidy and number of digits per allele
int.check.numeric
Check numeric format in a data frame
int.check.rownames
Check row names
int.check.vnames
Check a vector of names
int.crosscor
Cross correlation. Internal.
int.df2genind
importer
int.geary
Geary internal.
int.gendata2genind
int.gendata2genind
int.gendata-class
int.gendata
int.genind
constructor
int.genind2df
export
int.genind2gendata
int.genind2gendata
int.genind-class
int.genind
int.jackknife
d-Jackknife estimation.
int.joincount
Join-count statistic, internal.
int.kin.loiselle
obtetion of multilocus Loiselle's Fij matrix
int.loc2al
INTERNAL CONVERSION TOOLS FOR GENETIC DATA
int.mantel
Mantel and partial Mantel tests, internal.
int.moran
Moran internal.
int.multiplot
int.multiplot method. Graphical processing of multiple...
int.multiplot-class
int.multiplot class
int.multitable
Table construction for multiple test result.
int.random.test
random test
is.meta
Detection of metacharacters
meta2char
Metachacter to character
misc.2symmetric
Conversion of a non symmetric binary matrix into symmetric.
misc.dlatlon2distm
Computing a distance matrix in meters among points in decimal...
misc.parse.filter
Filter a raster using a conditional expression and values in...
misc.undimmattg
Creates a matrix without diagonal, in row order
phenotype
phenotype
plot-eco.weight-ANY-method
Plot for a connection network
rankplot-methods
Rankplot graphs
structure
structure
sub-sub-ecogen-numeric-missing-method
[[
sub-subset-ecogen-numeric-missing-method
[[<-
tab
tab
table.sokal
table.sokal

Files in this package

EcoGenetics
EcoGenetics/inst
EcoGenetics/inst/extdata
EcoGenetics/inst/extdata/ingpop
EcoGenetics/NAMESPACE
EcoGenetics/data
EcoGenetics/data/eco.test.RData
EcoGenetics/data/eco2.RData
EcoGenetics/data/tab.RData
EcoGenetics/data/eco3.RData
EcoGenetics/data/sokal1986.RData
EcoGenetics/R
EcoGenetics/R/show_summary.methods.R
EcoGenetics/R/classes.R
EcoGenetics/R/ecogen.4OF5.brackets.R
EcoGenetics/R/int.crosscor.R
EcoGenetics/R/int.geary.R
EcoGenetics/R/eco.rankplot.R
EcoGenetics/R/eco.variogram.R
EcoGenetics/R/eco.convert.R
EcoGenetics/R/eco.lsa.R
EcoGenetics/R/eco.2genepop.R
EcoGenetics/R/eco.detrend.R
EcoGenetics/R/eco.2spagedi.R
EcoGenetics/R/plot.methods.R
EcoGenetics/R/ecogen.2OF5.constructor.R
EcoGenetics/R/eco.lagweight.R
EcoGenetics/R/int.genind.R
EcoGenetics/R/eco.NDVI.R
EcoGenetics/R/eco.weight.R
EcoGenetics/R/control.R
EcoGenetics/R/eco.lmtree.R
EcoGenetics/R/eco.kin.loiselle.R
EcoGenetics/R/eco.pairtest.R
EcoGenetics/R/miscellaneous.R
EcoGenetics/R/eco.correlog.R
EcoGenetics/R/eco.theilsen.R
EcoGenetics/R/eco.subset.R
EcoGenetics/R/eco.cbind.R
EcoGenetics/R/eco.rbind.R
EcoGenetics/R/eco.clear.R
EcoGenetics/R/eco.2geneland.R
EcoGenetics/R/accesors.R
EcoGenetics/R/eco.genepop2df.R
EcoGenetics/R/int.kin.loiselle.R
EcoGenetics/R/deprecated.R
EcoGenetics/R/int.jackknife.R
EcoGenetics/R/int.multitable.R
EcoGenetics/R/eco.malecot.R
EcoGenetics/R/int.mantel.R
EcoGenetics/R/eco.slide.con.R
EcoGenetics/R/eco.format.R
EcoGenetics/R/int.random.test.R
EcoGenetics/R/eco.2gstudio.R
EcoGenetics/R/ZZZ.R
EcoGenetics/R/int.moran.R
EcoGenetics/R/plot.generic.R
EcoGenetics/R/ecogen.1OF5.definition.R
EcoGenetics/R/auxiliar.R
EcoGenetics/R/eco.gsa.R
EcoGenetics/R/eco.NDVI.post.R
EcoGenetics/R/eco.alfreq.R
EcoGenetics/R/eco.association.R
EcoGenetics/R/eco.slide.matrix.R
EcoGenetics/R/ecogen.5OF5.get&set.R
EcoGenetics/R/eco.merge.R
EcoGenetics/R/eco.forestplot.R
EcoGenetics/R/eco.mantel.R
EcoGenetics/R/roxygen.auxiliar.R
EcoGenetics/R/ecogen.3OF5.basic.methods.R
EcoGenetics/R/eco.remove.R
EcoGenetics/R/eco.rasterplot.R
EcoGenetics/R/eco.2hierfstat.R
EcoGenetics/R/eco.cormantel.R
EcoGenetics/R/int.convert.R
EcoGenetics/R/eco.post.geneland.R
EcoGenetics/R/int.break.R
EcoGenetics/R/eco.order.R
EcoGenetics/R/int.joincount.R
EcoGenetics/MD5
EcoGenetics/DESCRIPTION
EcoGenetics/man
EcoGenetics/man/eco.order.Rd
EcoGenetics/man/eco.clear.Rd
EcoGenetics/man/int.genind2df.Rd
EcoGenetics/man/eco.post.geneland.Rd
EcoGenetics/man/eco.lagweight-methods.Rd
EcoGenetics/man/grf.multiplot.Rd
EcoGenetics/man/eco.pairtest.Rd
EcoGenetics/man/eco.mantel.Rd
EcoGenetics/man/eco.lsa.Rd
EcoGenetics/man/eco.variogram.Rd
EcoGenetics/man/eco.IBD-class.Rd
EcoGenetics/man/eco.alfreq.Rd
EcoGenetics/man/int.jackknife.Rd
EcoGenetics/man/aue.ellipse.Rd
EcoGenetics/man/int.random.test.Rd
EcoGenetics/man/int.gendata2genind.Rd
EcoGenetics/man/int.genind2gendata.Rd
EcoGenetics/man/int.break.Rd
EcoGenetics/man/aue.rotate.Rd
EcoGenetics/man/plot-eco.weight-ANY-method.Rd
EcoGenetics/man/misc.2symmetric.Rd
EcoGenetics/man/int.loc2al.Rd
EcoGenetics/man/aue.phenosimil.Rd
EcoGenetics/man/eco.weight-methods.Rd
EcoGenetics/man/int.gendata-class.Rd
EcoGenetics/man/aue.rescale.Rd
EcoGenetics/man/int.mantel.Rd
EcoGenetics/man/eco.listlsa-method.Rd
EcoGenetics/man/misc.undimmattg.Rd
EcoGenetics/man/eco.merge.Rd
EcoGenetics/man/aue.square.Rd
EcoGenetics/man/eco.weight-class.Rd
EcoGenetics/man/structure.Rd
EcoGenetics/man/eco.mlm-class.Rd
EcoGenetics/man/aue.fqal.Rd
EcoGenetics/man/aue.df2image.Rd
EcoGenetics/man/eco2.Rd
EcoGenetics/man/int.multiplot.Rd
EcoGenetics/man/int.check.ncod.Rd
EcoGenetics/man/EcoGenetics-package.Rd
EcoGenetics/man/eco.association.Rd
EcoGenetics/man/eco.detrend-class.Rd
EcoGenetics/man/sub-sub-ecogen-numeric-missing-method.Rd
EcoGenetics/man/int.genind.Rd
EcoGenetics/man/aue.point.Rd
EcoGenetics/man/aue.is.poly.Rd
EcoGenetics/man/aue.geom.dist.Rd
EcoGenetics/man/genotype.Rd
EcoGenetics/man/eco.cormantel.Rd
EcoGenetics/man/eco.multilsa-method.Rd
EcoGenetics/man/int.check.vnames.Rd
EcoGenetics/man/ecogen-methods.Rd
EcoGenetics/man/eco.correlog-class.Rd
EcoGenetics/man/aue.filter.Rd
EcoGenetics/man/eco.lagweight-class.Rd
EcoGenetics/man/tab.Rd
EcoGenetics/man/environment.Rd
EcoGenetics/man/EcoGenetics-accessors.Rd
EcoGenetics/man/int.check.colnames.Rd
EcoGenetics/man/eco.kin.loiselle.Rd
EcoGenetics/man/eco.NDVI.Rd
EcoGenetics/man/int.joincount.Rd
EcoGenetics/man/aue.circle.w.Rd
EcoGenetics/man/eco.subset.Rd
EcoGenetics/man/int.check.group.Rd
EcoGenetics/man/rankplot-methods.Rd
EcoGenetics/man/int.check.numeric.Rd
EcoGenetics/man/eco.2spagedi.Rd
EcoGenetics/man/eco.genepop2df.Rd
EcoGenetics/man/eco.correlog-methods.Rd
EcoGenetics/man/eco.gsa-methods.Rd
EcoGenetics/man/eco.detrend.Rd
EcoGenetics/man/eco.lmtree-methods.Rd
EcoGenetics/man/int.kin.loiselle.Rd
EcoGenetics/man/forestplot-methods.Rd
EcoGenetics/man/int.moran.Rd
EcoGenetics/man/aue.ad2wg.Rd
EcoGenetics/man/aue.sort.Rd
EcoGenetics/man/eco.autol-methods.Rd
EcoGenetics/man/eco.lsa-methods.Rd
EcoGenetics/man/coordinates.Rd
EcoGenetics/man/eco.Rd
EcoGenetics/man/int.multiplot-class.Rd
EcoGenetics/man/eco.rasterplot.Rd
EcoGenetics/man/misc.dlatlon2distm.Rd
EcoGenetics/man/int.df2genind.Rd
EcoGenetics/man/eco.convert.Rd
EcoGenetics/man/eco.correlog.Rd
EcoGenetics/man/int.crosscor.Rd
EcoGenetics/man/eco3.Rd
EcoGenetics/man/eco.listlsa-class.Rd
EcoGenetics/man/aue.circle.Rd
EcoGenetics/man/eco.2genepop.Rd
EcoGenetics/man/eco.2gstudio.Rd
EcoGenetics/man/eco.slide.con.Rd
EcoGenetics/man/eco.rbind.Rd
EcoGenetics/man/eco.multilsa-class.Rd
EcoGenetics/man/eco.weight.Rd
EcoGenetics/man/phenotype.Rd
EcoGenetics/man/aue.rmspaces.Rd
EcoGenetics/man/eco.lsa-class.Rd
EcoGenetics/man/aue.access.Rd
EcoGenetics/man/eco.lagweight.Rd
EcoGenetics/man/meta2char.Rd
EcoGenetics/man/aue.genlab.Rd
EcoGenetics/man/int.check.rownames.Rd
EcoGenetics/man/ecogen-class.Rd
EcoGenetics/man/int.geary.Rd
EcoGenetics/man/eco.variogram-class.Rd
EcoGenetics/man/grf.seqmultiplot.Rd
EcoGenetics/man/eco.mctree-class.Rd
EcoGenetics/man/aue.rm.nonpoly.Rd
EcoGenetics/man/eco.2geneland.Rd
EcoGenetics/man/eco.gsa.Rd
EcoGenetics/man/eco.IBD-methods.Rd
EcoGenetics/man/aue.image2df.Rd
EcoGenetics/man/eco.cbind.Rd
EcoGenetics/man/sub-subset-ecogen-numeric-missing-method.Rd
EcoGenetics/man/eco.slide.matrix.Rd
EcoGenetics/man/eco.remove.Rd
EcoGenetics/man/int.multitable.Rd
EcoGenetics/man/eco.gsa-class.Rd
EcoGenetics/man/is.meta.Rd
EcoGenetics/man/eco.format.Rd
EcoGenetics/man/eco.malecot.Rd
EcoGenetics/man/aue.seqlist.Rd
EcoGenetics/man/eco.IBD.Rd
EcoGenetics/man/eco.lmtree.mctree-summary.Rd
EcoGenetics/man/eco.theilsen.Rd
EcoGenetics/man/ecogen.Rd
EcoGenetics/man/eco.2hierfstat.Rd
EcoGenetics/man/eco.lmtree.Rd
EcoGenetics/man/int.check.con.Rd
EcoGenetics/man/int.genind-class.Rd
EcoGenetics/man/table.sokal.Rd
EcoGenetics/man/eco.NDVI.post.Rd
EcoGenetics/man/misc.parse.filter.Rd
EcoGenetics/man/eco.detrend-methods.Rd