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.

AuthorLeandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Date of publication2016-07-15 20:02:10
MaintainerLeandro Roser <learoser@gmail.com>
LicenseGPL (>= 2)
Version1.2.0-3
https://github.com/cran/EcoGenetics

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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