EcoGenetics v1.2.1-4

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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.

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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")

Functions in EcoGenetics

Name Description
aue.access EcoGenetics slot standard notation. Returns an accessor to the slot <ecoslot> of the object <X>
aue.ad2wg Transforming an adyacency matrix into a local weight matrix for a point with coordinates (x0,y0)
aue.dataAngle Angles for an XY coordinates matrix
aue.df2image Transforming a data frame into a raster
aue.circle Circle perimeter
aue.circle.w Radial distance to a point.
EcoGenetics accessors Generic accessors for EcoGenetics objects
EcoGenetics-package Management and Exploratory Analysis of Spatial Data in Landscape Genetics
aue.aggregated_df Generate aggregated dataframe
aue.check_class Obtain the classes for each column of a data frame
aue.fqal Allelic frequencies
aue.genlab Generation of generic labels of constant length
aue.rm.nonpoly Remotion of non polymorphic loci
aue.rmspaces Remove spaces and tabs at the begining and the end of each element of charvec
aue.point Solid circle
aue.rescale Scaling a data frame or matrix to [0, 1] or [-1, 1] ranges
check_ecopop check_ecopop
aue.ellipse Solid ellipse
aue.formatLine Remove spaces in a line of text
aue.sort Ordering the content of cells in a matrix. Ordering alleles in a genetic matrix.
aue.split_categorical Split categorical variable into levels, using a second factor (hierarchy) to aggregate the data
eco.alfreq Allelic frequency histograms for an ecogen genetic data frame
eco.association Chi-square and Fisher's exact test for association of loci and alleles with a factor
eco.cbind Combining ecogen objects by column
eco.clear Clearing the working environment, maintaining only the specified objects
aue.is.poly Identification of polymorphic loci
aue.phenosimil Phenotypic similarity for vector, matrix or data frame acoording to Ritland (1996)
aue.square Solid square
check_ecogen check_ecogen
coordinates Coordinates
show,eco.lsa-method show eco.lsa
eco.bearing Angular Spatial Weights
eco.detrend-class eco.detrend class
show,eco.detrend-method show eco.detrend
eco.plotCorrelog eco.plotCorrelog
eco.plotCorrelogB eco.plotCorrelogB
eco.slide.con Sliding a window along a connection network
eco.slide.matrix Sliding window for matrix data
eco.variogram Empirical variogram
eco.weight-class eco.weight class
plot,eco.IBD,ANY-method plot eco.IBD
eco.NDVI Generation of atmospherically corrected NDVI and MSAVI2 images for temporal series of Landsat 5 and 7
eco.correlog-class eco.correlog-class
plot,eco.correlog,ANY-method globalplot
eco.NDVI.post Postprocessing for NDVI and MSAVI2 temporal series of Landsat 5 and 7
eco Eco
show,eco.lagweight-method show eco.lagweight
eco.formula Formula construction for ecogen objects
eco.gsa-class eco.gsa class
eco.lmtree Fitting Multiple Linear Regression models by stepwise AIC selection and Multiple Classification and Regression Trees via party
eco.detrend Detrending spatial data with polynomial interpolation
eco.format Format tool for genetic data
eco.lsa-class eco.lsa class
ecogen2hierfstat Converting an ecogen genetic data frame into a hierfstat data frame
ecogen2spagedi Exporting an ecogen genetic data frame into SPAGeDi format
ecopop2genpop Conversion form ecopop to genpop and genpop to ecopop
aue.geom.dist Weight matrices based on different geometries
aue.image2df Transforming a raster into a data frame with cartesian coordinates
aue.rotate Rotation of a matrix
eco.convert Conversion utility for genetic data
eco.cormantel Mantel and partial Mantel correlograms, omnidirectional and directional
show,eco.gsa-method show eco.gsa
aue.seqlist Creation of a sequence of numbers in matrix or list format, for indexing.
eco.IBD-class eco.IBD class
show,eco.IBD-method show eco.IBD
eco.correlog Moran's I, Geary's C and bivariate Moran's I correlograms, omnidirectional and directional
eco.lagweight Obtention of a list of spatial weights for classes defined by inter-individual distances or nearest-neighbors
eco.lsa Local spatial analysis
eco.malecot Global and local kinship analysis
eco.correlogB-class eco.correlogB
eco.kin.loiselle Obtention of the multilocus Loiselle's Fij matrix
eco.lagweight-class eco.lagweight class
environment environment
genotype genotype
grf.multiplot Multiple plot function for ggplot
int.genind-class int.genind
plot,eco.lsa,ANY-method plot eco.lsa
eco.multilsa-class eco.multilsa class
plot,eco.multilsa,ANY-method plot eco.multilsa
eco.order Functions deprecated in EcoGenetics version 1.2.0-2
eco.pairtest Kruskall - Wallis + Wilcoxon (Mann-Whitney U) and aov + Tukey-HSD tests for an ecogen object
eco.gsa Global spatial analysis
eco.listw2ew Conversion from listw to ecoweight
show,eco.mlm-method show eco.mlm
eco.plotGlobal GSA plot methods
eco.plotLocal eco.plotLocal
eco2 Eco2
summary,eco.mlm-method Summary for eco.lmtree output
eco3 Eco3
ecogen2genind Conversion form ecogen to genind and genind to ecogen
ecogen2gstudio Conversion from ecogen to gstudio and gstudio to ecogen
names,ecopop-method names
ecopop Creating a new ecopop object
eco.mantel Mantel and partial Mantel tests, with truncation option
eco.mctree-class eco.mctree-class
eco.plotWeight Plot for a connection network
eco.post.geneland Log posterior probability plot for Geneland repetitions with fixed K
eco.split Splitting an ecogen object by group
eco.subset Subsetting an ecogen object by group
ecogen-class ecogen class
int.genind constructor
int.multiplot-class int.multiplot class
int.multiplot int.multiplot method. Graphical processing of multiple correlograms
eco.theilsen Theil-sen regression for a raster time series
eco.variogram-class eco.variogram class
ecogenetics_devel EcoGenetic devel site
names,ecogen-method names
eco.forestplot Forestplot graphs
genepop2ecogen Importing a Genepop file
eco.listlsa-class eco.listlsa
plot,eco.listlsa,ANY-method listplot
eco.merge Merging two ecogen objects. Ordering the rows of an ecogen object according to the rows of another
eco.mlm-class eco.mlm-class
int.check.numeric Check numeric format in a data frame
int.check.rownames Check row names
int.gendata-class int.gendata
meta2char Metachacter to character
misc.2symmetric Conversion of a non symmetric binary matrix into symmetric.
eco.rankplot Rankplot graphs
int.gendata2genind int.gendata2genind
is.meta Detection of metacharacters
is.wholenumber test whole number
spagedi2ecogen Importing a SPAGeDi file, via conversion to ecogen
ecogenetics_tutorial EcoGenetic tutorial site
int.check.colnames Check column names
int.check.con Check a connection network
int.df2genind importer
int.geary Geary internal.
int.genind2df export
[[<-,ecogen,numeric,missing-method [[<-
tab tab
eco.rbind Combining ecogen objects by row
eco.remove Creating an updated ecogen object by removing results of the slot OUT
ecogen2geneland Creating input data for Geneland with an ecogen object
ecogen2genepop Exporting an ecogen genetic data frame into Genepop format
int.check.group Check factor name consistency in a data frame and returns the corresponding column
int.check.ncod Check ploidy and number of digits per allele
int.corvarToDeg eco.correlog output to degrees list
int.crosscor Cross correlation. Internal.
eco.rasterplot,eco.multilsa-method rasterplot graph for eco.lsa results
eco.rasterplot Rasterplot graphs
show,eco.weight-method show eco.weight
int.mantel Mantel and partial Mantel tests, internal.
int.moran Moran internal.
int.popdata-class int.popdata class
int.random.test random test
plot,eco.gsa,ANY-method Plot for eco.gsa objects
plot,eco.weight,ANY-method Plot for a connection network
int.check.to_numeric check if elements are numbers and if not convert the matrix using eco.format
int.check.vnames Check a vector of names
int.jackknife d-Jackknife estimation.
int.joincount Join-count statistic, internal.
int.multitable Table construction for multiple test result.
int.order Ordering the rows of the data frames contained in an ecogen or ecopop object
structure structure
[[,ecogen,numeric,missing-method [[
eco.weight Spatial weights
ecogen Creating a new ecogen object
ecogen2ecopop Conversion form ecogen to ecopop
ecolist-class ecolist class
ecopop-class ecopop class
grf.seqmultiplot Plot a ggplot sequence in layers of n plots arranged in k rows
int.genind2gendata int.genind2gendata
misc.dlatlon2distm Computing a distance matrix in meters among points in decimal degrees under a spherical Earth model
misc.parse.filter Filter a raster using a conditional expression and values in a conditional vector
phenotype phenotype
%>% Pipe operator
int.break breaks obtention
int.kin.loiselle obtetion of multilocus Loiselle's Fij matrix
int.loc2al INTERNAL CONVERSION TOOLS FOR GENETIC DATA
misc.undimmattg Creates a matrix without diagonal, in row order
my_ecopop my_ecopop
table.sokal table.sokal
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Details

Type Package
Date 2018-01-13
License GPL (>= 2)
URL https://github.com/cran/EcoGenetics, https://leandroroser.github.io/EcoGenetics-Tutorial
LazyLoad yes
Collate 'ZZZ.R' 'generics.R' 'auxiliar.R' 'int.genind.R' 'ecogen.1OF6.definition.R' 'ecogen.2OF6.constructor.R' 'ecogen.3OF6.basic.methods.R' 'ecogen.4OF6.brackets.R' 'ecogen.5OF6.get&set.R' 'ecogen.6OF6.converters.R' 'ecopop.1OF6.definition.R' 'ecopop.2OF6.constructor.R' 'ecopop.3OF6.basic.methods.R' 'ecopop.4OF6.brackets.R' 'ecopop.5OF6.get&set.R' 'ecopop.6OF6.converters.R' 'accessors.R' 'classes.R' 'control.R' 'deprecated.R' 'eco.formula.R' 'eco.NDVI.R' 'eco.NDVI.post.R' 'eco.alfreq.R' 'eco.association.R' 'eco.bearing.R' 'eco.cbind.R' 'eco.clear.R' 'eco.convert.R' 'eco.cormantel.R' 'eco.correlog.R' 'eco.detrend.R' 'eco.forestplot.R' 'eco.format.R' 'eco.gsa.R' 'eco.kin.loiselle.R' 'eco.lagweight.R' 'eco.lmtree.R' 'eco.lsa.R' 'eco.malecot.R' 'eco.mantel.R' 'eco.merge.R' 'eco.pairtest.R' 'eco.plotCorrelog.R' 'eco.plotGlobal.R' 'eco.plotLocal.R' 'eco.plotWeight.R' 'eco.post.geneland.R' 'eco.rankplot.R' 'eco.rasterplot.R' 'eco.rbind.R' 'eco.remove.R' 'eco.slide.con.R' 'eco.slide.matrix.R' 'eco.split.R' 'eco.subset.R' 'eco.theilsen.R' 'eco.variogram.R' 'eco.weight.R' 'int.break.R' 'int.convert.R' 'int.crosscor.R' 'int.geary.R' 'int.jackknife.R' 'int.joincount.R' 'int.kin.loiselle.R' 'int.mantel.R' 'int.moran.R' 'int.multitable.R' 'int.order.R' 'int.random.test.R' 'miscellaneous.R' 'plot.generic.R' 'plot.methods.R' 'roxygen.auxiliar.R' 'show_summary.methods.R'
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2018-01-13 18:27:29 UTC; leandro
Repository CRAN
Date/Publication 2018-01-13 22:29:39 UTC

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