EcoGenetics: 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.

Install the latest version of this package by entering the following in R:
AuthorLeandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Date of publication2017-03-03 18:01:46
MaintainerLeandro Roser <>
LicenseGPL (>= 2)

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... Circle perimeter Radial distance to a point.

aue.dataAngle: Angles for an XY coordinates matrix

aue.df2image: Transforming a data frame into a raster

aue.ellipse: Solid ellipse

aue.formatLine: Remove spaces in a line of text

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... 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

check_ecogen: check_ecogen

coordinates: Coordinates

eco: Eco

eco2: Eco2

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.bearing: Angular Spatial Weights

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, omnidirectional and...

eco.correlog: Moran's I, Geary's C and bivariate Moran's I correlograms,...

eco.correlogB-class: eco.correlogB

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

eco.formula: Conversion of a formula for an ecogen objects into an explict...

ecogen: Creating a new ecogen object

ecogen2geneland: Creating input data for Geneland with an ecogen object

ecogen2genepop: Exporting an ecogen genetic data frame into Genepop format

ecogen2genind: Conversion form ecogen to genind and genind to ecogen

ecogen2gstudio: Conversion from ecogen to gstudio and gstudio to ecogen

ecogen2hierfstat: Converting an ecogen genetic data frame into a hierfstat data...

ecogen2spagedi: Exporting an ecogen genetic data frame into SPAGeDi format

ecogen-class: ecogen class

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

ecolist-class: ecolist class

eco.listlsa-class: eco.listlsa

eco.listlsa-method: listplot

eco.listw2ew: Conversion from listw to ecoweight

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, with truncation option

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: plot eco.multilsa

eco.NDVI: Generating atmospherically corrected NDVI and MSAVI2 images... Postprocessing for NDVI and MSAVI 2 temporal series of...

eco.order: Functions deprecated in EcoGenetics version 1.2.0-2

eco.pairtest: Kruskall - Wallis + Wilcoxon (Mann-Whitney U) and aov +...

eco.plotCorrelog: eco.plotCorrelog

eco.plotCorrelogB: eco.plotCorrelogB

eco.plotGlobal: GSA plot methods

eco.plotLocal: eco.plotLocal

eco.plotWeight: Plot for a connection network Log posterior probability plot for Geneland repetitions with...

eco.rasterplot: rasterplot graphs

eco.rasterplot-eco.multilsa-method: rasterplot graph for eco.lsa results

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.split: Splitting an ecogen object by groups

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

genepop2ecogen: Importing a Genepop file

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 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.corvarToDeg: eco.correlog output to degrees list

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.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.order: Ordering the rows of the data frames contained in an ecogen...

int.random.test: random test

is.meta: Detection of metacharacters

is.wholenumber: test whole number

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

pipe: Pipe operator

plot-eco.gsa-ANY-method: Plot for eco.gsa objects

plot-eco.weight-ANY-method: Plot for a connection network

rankplot-methods: Rankplot graphs

spagedi2ecogen: Importing a SPAGeDi file, via conversion to ecogen

structure: structure

sub-sub-ecogen-numeric-missing-method: [[

sub-subset-ecogen-numeric-missing-method: [[<-

tab: tab

table.sokal: table.sokal


\%>\% Man page Man page
as.list,ecogen-method Man page
aue.access Man page
aue.ad2wg Man page Man page Man page
aue.dataAngle Man page
aue.df2image Man page
aue.ellipse Man page
aue.formatLine Man page
aue.fqal Man page
aue.genlab Man page
aue.geom.dist Man page
aue.image2df Man page Man page
aue.phenosimil Man page
aue.point Man page
aue.rescale Man page
aue.rm.nonpoly Man page
aue.rmspaces Man page
aue.rotate Man page
aue.seqlist Man page
aue.sort Man page
aue.square Man page
check_ecogen Man page
coordinates Man page
dim,ecogen-method Man page
eco Man page
eco2 Man page
eco3 Man page
eco.alfreq Man page
eco.association Man page
eco.bearing Man page
eco.cbind Man page
eco.clear Man page
eco.convert Man page
eco.cormantel Man page
eco.correlog Man page
eco.correlogB-class Man page
eco.correlog-class Man page
eco.detrend Man page
eco.detrend-class Man page
eco.forestplot Man page
eco.forestplot,dataframeORmatrix-method Man page
eco.forestplot,eco.lsa-method Man page
eco.forestplot,generic-method Man page
eco.format Man page
eco.formula Man page
ecogen Man page
ecogen2geneland Man page
ecogen2genepop Man page
ecogen2genind Man page
ecogen2gstudio Man page
ecogen2hierfstat Man page
ecogen2spagedi Man page
$<-,ecogen,character,ANY-method Man page
$,ecogen,character-method Man page
[,ecogen,character,missing-method Man page
[[<-,ecogen,character,missing-method Man page
[[,ecogen,character,missing-method Man page
ecogen-class Man page
EcoGenetics Man page
EcoGenetics accessors Man page
EcoGenetics-package Man page
[,ecogen,logical,missing,ANY-method Man page
[,ecogen,logicalORmissing,missing,ANY-method Man page
$<-,ecogen-method Man page
$,ecogen-method Man page
[,ecogen,numeric,missing,ANY-method Man page
[[<-,ecogen,numeric,missing-method Man page
[[,ecogen,numeric,missing-method Man page
[,ecogen,numericORmissing,missing,ANY-method Man page
eco.gsa Man page
eco.gsa-class Man page
eco.IBD-class Man page
eco.kin.loiselle Man page
eco.lagweight Man page
eco.lagweight-class Man page
ecolist-class Man page
eco.listlsa-class Man page
eco.listsa-class Man page
eco.listw2ew Man page
eco.lmtree Man page
eco.lsa Man page
eco.lsa-class Man page
eco.malecot Man page
eco.mantel Man page
eco.mctree-class Man page
eco.merge Man page
eco.mlm-class Man page
eco.multilsa-class Man page
eco.NDVI Man page Man page
eco.order Man page
eco.pairtest Man page
eco.plotCorrelog Man page
eco.plotCorrelogB Man page
eco.plotGlobal Man page
eco.plotLocal Man page
eco.plotWeight Man page Man page
eco.rankplot Man page
eco.rankplot,eco.lsa-method Man page
eco.rankplot,eco.lsa,missing,missing-method Man page
eco.rankplot,factor,dataframeORmatrix,missing-method Man page
eco.rankplot,factor-method Man page
eco.rankplot,numeric,dataframeORmatrix,missing-method Man page
eco.rankplot,numeric-method Man page
eco.rasterplot Man page
eco.rasterplot,eco.multilsa-method Man page
eco.rbind Man page
eco.remove Man page
eco.slide.con Man page
eco.slide.matrix Man page
ecoslot.A Man page
ecoslot.A<-,ecogen-method Man page
ecoslot.A,ecogen-method Man page
ecoslot.ALTER Man page
ecoslot.ANALYSIS Man page
ecoslot.ANOVA.MLM Man page
ecoslot.AVERAGE Man page
ecoslot.BREAKS Man page
ecoslot.C Man page
ecoslot.C<- Man page
ecoslot.CARDINAL Man page
ecoslot.C<-,ecogen-method Man page
ecoslot.C,ecogen-method Man page
ecoslot.COND Man page
ecoslot.CONNECTED Man page
ecoslot.DF1 Man page
ecoslot.DF2 Man page
ecoslot.DISTMETHOD Man page
ecoslot.E Man page
ecoslot.E<- Man page
ecoslot.E<-,ecogen-method Man page
ecoslot.E,ecogen-method Man page
ecoslot.EXP Man page
ecoslot.FREQUENCIES Man page
ecoslot.G Man page
ecoslot.G<- Man page
ecoslot.G<-,ecogen-method Man page
ecoslot.G,ecogen-method Man page
ecoslot.IN Man page
ecoslot.LOGMEAN Man page
ecoslot.LWR Man page
ecoslot.MEAN Man page
ecoslot.METHOD Man page
ecoslot.MLM Man page
ecoslot.MODEL Man page
ecoslot.MULTI Man page
ecoslot.NAMES Man page
ecoslot.NONZERO Man page
ecoslot.NONZEROIND Man page
ecoslot.NSIM Man page
ecoslot.OBS Man page
ecoslot.OBS.RES Man page
ecoslot.OUT Man page
ecoslot.OUT<- Man page
ecoslot.OUT<-,ecogen-method Man page
ecoslot.OUT,ecogen-method Man page
ecoslot.P Man page
ecoslot.P<- Man page
ecoslot.PADJUST Man page
ecoslot.PAR Man page
ecoslot.PAR.VAL Man page
ecoslot.P<-,ecogen-method Man page
ecoslot.P,ecogen-method Man page
ecoslot.POLY.DEG Man page
ecoslot.POP Man page
ecoslot.PREDICTIONS Man page
ecoslot.PVAL Man page
ecoslot.RES Man page
ecoslot.ROW.SD Man page
ecoslot.S Man page
ecoslot.S<- Man page
ecoslot.S<-,ecogen-method Man page
ecoslot.S,ecogen-method Man page
ecoslot.SELF Man page
ecoslot.SP Man page
ecoslot.SUMMARY.MLM Man page
ecoslot.TEST Man page
ecoslot.TREES Man page
ecoslot.UPPR Man page
ecoslot.W Man page
ecoslot.XY Man page
ecoslot.XY<- Man page
ecoslot.XY<-,ecogen-method Man page
ecoslot.XY,ecogen-method Man page
eco.split Man page
eco.subset Man page
eco.theilsen Man page
eco.variogram Man page
eco.variogram-class Man page
eco.weight Man page
eco.weight-class Man page
environment Man page
genepop2ecogen Man page
genind2ecogen Man page
genotype Man page
grf.multiplot Man page
grf.seqmultiplot Man page
gstudio2ecogen Man page
int.break Man page
int.check.colnames Man page
int.check.con Man page Man page
int.check.ncod Man page
int.check.numeric Man page
int.check.rownames Man page
int.check.vnames Man page
int.corvarToDeg Man page
int.crosscor Man page
int.df2genind Man page
int.ecoslot.INT Man page
int.ecoslot.INT<- Man page
int.geary Man page
int.gendata2genind Man page
int.gendata-class Man page
int.genind Man page
int.genind2df Man page
int.genind2gendata Man page
int.genind-class Man page
int.jackknife Man page
int.joincount Man page
int.kin.loiselle Man page
int.loc2al Man page
int.mantel Man page
int.moran Man page
int.multiplot Man page
int.multiplot-class Man page
int.multitable Man page
int.order Man page
int.random.test Man page
is.ecogen Man page
is,ecogen-method Man page
is.meta Man page
is.wholenumber Man page
meta2char Man page
misc.2symmetric Man page
misc.dlatlon2distm Man page
misc.parse.filter Man page
misc.undimmattg Man page
names<-,ecogen,character-method Man page
names,ecogen-method Man page
ncol,ecogen-method Man page
nrow,ecogen-method Man page
phenotype Man page
plot,eco.correlog,ANY-method Man page
plot,eco.correlog-method Man page
plot,eco.gsa,ANY-method Man page
plot,eco.gsa-method Man page
plot,eco.IBD,ANY-method Man page
plot,eco.IBD-method Man page
plot,eco.listlsa,ANY-method Man page
plot,eco.listlsa-method Man page
plot,eco.lsa,ANY-method Man page
plot,eco.lsa-method Man page
plot,eco.multilsa,ANY-method Man page
plot,eco.multilsa-method Man page
plot,eco.weight,ANY-method Man page
plot,eco.weight-method Man page
show,eco.correlog-method Man page
show,eco.detrend-method Man page
show,ecogen-method Man page
show,eco.gsa-method Man page
show,eco.IBD-method Man page
show,eco.lagweight-method Man page
show,eco.listlsa-method Man page
show,eco.lsa-method Man page
show,eco.mctree-method Man page
show,eco.mlm-method Man page
show,eco.multilsa-method Man page
show,eco.weight-method Man page
spagedi2ecogen Man page
structure Man page
summary,eco.lmtree-method Man page
summary,eco.mctree-method Man page
summary,eco.mlm-method Man page
tab Man page
table.sokal Man page


R/show_summary.methods.R R/ecogen.2OF6.constructor.R R/classes.R R/int.crosscor.R R/eco.plotWeight.R R/int.geary.R R/eco.rankplot.R R/eco.variogram.R R/eco.convert.R R/ecogen.5OF6.get&set.R R/eco.lsa.R R/eco.detrend.R R/plot.methods.R R/eco.lagweight.R R/eco.split.R R/ecogen.6OF6.converters.R R/int.genind.R R/eco.NDVI.R R/eco.plotLocal.R R/eco.weight.R R/control.R R/eco.lmtree.R R/eco.kin.loiselle.R R/eco.pairtest.R R/ecogen.1OF6.definition.R R/eco.bearing.R R/miscellaneous.R R/eco.correlog.R R/eco.theilsen.R R/eco.subset.R R/int.order.R R/eco.cbind.R R/eco.rbind.R R/eco.clear.R R/ecogen.4OF6.brackets.R R/accesors.R R/int.kin.loiselle.R R/ecogen.3OF6.basic.methods.R R/deprecated.R R/int.jackknife.R R/int.multitable.R R/eco.malecot.R R/int.mantel.R R/eco.slide.con.R R/eco.format.R R/int.random.test.R R/eco.plotGlobal.R R/eco.plotCorrelog.R R/ZZZ.R R/int.moran.R R/plot.generic.R R/auxiliar.R R/eco.gsa.R R/ R/eco.alfreq.R R/eco.association.R R/eco.slide.matrix.R R/eco.merge.R R/eco.forestplot.R R/eco.mantel.R R/roxygen.auxiliar.R R/eco.formula.R R/eco.remove.R R/eco.rasterplot.R R/eco.cormantel.R R/int.convert.R R/ R/int.break.R R/int.joincount.R
man/eco.order.Rd man/eco.clear.Rd man/int.genind2df.Rd man/ man/eco.lagweight-methods.Rd man/grf.multiplot.Rd man/eco.pairtest.Rd man/eco.mantel.Rd man/eco.lsa.Rd man/eco.variogram.Rd man/eco.correlogB-class.Rd man/eco.IBD-class.Rd man/ecogen2spagedi.Rd man/eco.alfreq.Rd man/int.jackknife.Rd man/aue.ellipse.Rd man/pipe.Rd man/int.random.test.Rd man/int.gendata2genind.Rd man/ecogen2hierfstat.Rd man/int.genind2gendata.Rd man/int.break.Rd man/aue.rotate.Rd man/plot-eco.weight-ANY-method.Rd man/misc.2symmetric.Rd man/int.loc2al.Rd man/aue.phenosimil.Rd man/eco.weight-methods.Rd man/int.gendata-class.Rd man/aue.rescale.Rd man/ecolist-class.Rd man/int.mantel.Rd man/eco.listlsa-method.Rd man/misc.undimmattg.Rd man/plot-eco.gsa-ANY-method.Rd man/eco.merge.Rd man/aue.square.Rd man/eco.weight-class.Rd man/structure.Rd man/aue.formatLine.Rd man/genepop2ecogen.Rd man/eco.mlm-class.Rd man/aue.fqal.Rd man/aue.df2image.Rd man/eco2.Rd man/ecogen2genepop.Rd man/int.multiplot.Rd man/int.check.ncod.Rd man/eco.bearing.Rd man/EcoGenetics-package.Rd man/eco.association.Rd man/eco.detrend-class.Rd man/is.wholenumber.Rd man/sub-sub-ecogen-numeric-missing-method.Rd man/int.genind.Rd man/aue.point.Rd man/ man/eco.split.Rd man/ecogen2geneland.Rd man/aue.geom.dist.Rd man/genotype.Rd man/eco.cormantel.Rd man/eco.multilsa-method.Rd man/int.check.vnames.Rd man/ecogen-methods.Rd man/eco.correlog-class.Rd man/eco.plotCorrelog.Rd man/eco.lagweight-class.Rd man/tab.Rd man/environment.Rd man/EcoGenetics-accessors.Rd man/int.check.colnames.Rd man/eco.kin.loiselle.Rd man/eco.NDVI.Rd man/int.joincount.Rd man/ man/eco.subset.Rd man/ man/eco.formula.Rd man/rankplot-methods.Rd man/int.check.numeric.Rd man/eco.correlog-methods.Rd man/eco.gsa-methods.Rd man/eco.detrend.Rd man/eco.lmtree-methods.Rd man/int.kin.loiselle.Rd man/eco.plotCorrelogB.Rd man/forestplot-methods.Rd man/int.moran.Rd man/ecogen2gstudio.Rd man/aue.ad2wg.Rd man/aue.sort.Rd man/eco.autol-methods.Rd man/eco.lsa-methods.Rd man/coordinates.Rd man/eco.Rd man/int.multiplot-class.Rd man/eco.rasterplot.Rd man/misc.dlatlon2distm.Rd man/int.df2genind.Rd man/eco.convert.Rd man/eco.correlog.Rd man/int.crosscor.Rd man/eco3.Rd man/eco.listlsa-class.Rd man/ man/int.order.Rd man/eco.slide.con.Rd man/eco.rbind.Rd man/eco.multilsa-class.Rd man/eco.plotWeight.Rd man/eco.weight.Rd man/phenotype.Rd man/aue.rmspaces.Rd man/eco.lsa-class.Rd man/aue.access.Rd man/eco.lagweight.Rd man/meta2char.Rd man/aue.genlab.Rd man/int.check.rownames.Rd man/ecogen-class.Rd man/int.geary.Rd man/eco.variogram-class.Rd man/grf.seqmultiplot.Rd man/eco.mctree-class.Rd man/aue.rm.nonpoly.Rd man/eco.gsa.Rd man/eco.IBD-methods.Rd man/aue.image2df.Rd man/eco.cbind.Rd man/aue.dataAngle.Rd man/sub-subset-ecogen-numeric-missing-method.Rd man/ecogen2genind.Rd man/eco.slide.matrix.Rd man/eco.remove.Rd man/int.multitable.Rd man/eco.gsa-class.Rd man/eco.plotGlobal.Rd man/eco.listw2ew.Rd man/is.meta.Rd man/eco.format.Rd man/eco.malecot.Rd man/aue.seqlist.Rd man/eco.plotLocal.Rd man/eco.IBD.Rd man/eco.lmtree.mctree-summary.Rd man/eco.theilsen.Rd man/check_ecogen.Rd man/ecogen.Rd man/eco.lmtree.Rd man/int.check.con.Rd man/eco.rasterplot-eco.multilsa-method.Rd man/spagedi2ecogen.Rd man/int.genind-class.Rd man/table.sokal.Rd man/ man/misc.parse.filter.Rd man/int.corvarToDeg.Rd man/eco.detrend-methods.Rd

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.