EcoGenetics v1.2.1-5

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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 1.2.1-5

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Tutorial


Online documentation



Installation of devel version

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

Functions in EcoGenetics

Name Description
P P
aue.seqlist Creation of a sequence of numbers in matrix or list format, for indexing.
eco.cormantel Mantel and partial Mantel correlograms, omnidirectional and directional
show,eco.IBD-method show eco.IBD
aue.sort Ordering the content of cells in a matrix. Ordering alleles in a genetic matrix.
eco.correlog-class eco.correlog-class
EcoGenetics accessors Generic accessors for EcoGenetics objects
plot,eco.IBD,ANY-method plot eco.IBD
aue.dataAngle Angles for an XY coordinates matrix
aue.geom.dist Weight matrices based on different geometries
aue.circle.w Radial distance to a point.
plot,eco.listlsa,ANY-method listplot
eco eco
eco.alfreq Allelic frequency histograms for an ecogen genetic data frame
plot,eco.correlog,ANY-method globalplot
eco.correlog Moran's I, Geary's C and bivariate Moran's I correlograms, omnidirectional and directional
eco.listw2ew Conversion from listw to ecoweight
eco.old2new,ecopop-method Update an old ecogen or ecopop object to a version compatible with EcoGenetics >= 1.5.0-1
XY XY
aue.access EcoGenetics slot standard notation. Returns an accessor to the slot <ecoslot> of the object <X>
aue.get_os Detect operative system
eco.lagweight Obtention of a list of spatial weights for classes defined by inter-individual distances or nearest-neighbors
eco.formula Formula construction for ecogen objects
eco.gsa-class eco.gsa class
eco.listlsa-class eco.listlsa
aue.fqal Allelic frequencies
aue.genlab Generation of generic labels of constant length
aue.phenosimil Phenotypic similarity for vector, matrix or data frame acoording to Ritland (1996)
aue.split_categorical Split categorical variable into levels, using a second factor (hierarchy) to aggregate the data
eco.IBD-class eco.IBD class
coordinates coordinates
aue.point Solid circle
eco.old2new eco.old2new
aue.ad2wg Transforming an adyacency matrix into a local weight matrix for a point with coordinates (x0,y0)
aue.square Solid square
eco.subset Subsetting an ecogen object by group
eco.lsa Local spatial analysis
eco.split Splitting an ecogen object by group
aue.aggregated_df Generate aggregated dataframe
eco.bearing Angular Spatial Weights
eco.variogram-class eco.variogram class
eco.NDVI Generation of atmospherically corrected NDVI and MSAVI2 images for temporal series of Landsat 5 and 7
eco.cbind Combining ecogen objects by column
eco.fill_ecogen_with_ecopop Importation of ecopop to ecogen
eco.malecot Global and local kinship analysis
aue.rmspaces Remove spaces and tabs at the begining and the end of each element of charvec
eco.format Format tool for genetic data
eco.variogram Empirical variogram
summary,eco.mlm-method Summary for eco.lmtree output
eco.NDVI.post Postprocessing for NDVI and MSAVI2 temporal series of Landsat 5 and 7
eco.lock,ecogen-method Lock rows in an ecogen object
eco.lsa-class eco.lsa class
eco.unlock,ecopop-method Unlock rows in an ecogen object
aue.rotate Rotation of a matrix
ecogen2genepop Exporting an ecogen genetic data frame into Genepop format
eco.detrend-class eco.detrend class
eco.correlogB-class eco.correlogB
ecogen2genind Conversion form ecogen to genind and genind to ecogen
eco.kin.hardy Kinship and relationship estimation for dominant markers
eco.kin.loiselle Obtention of the multilocus Loiselle's Fij matrix
names,ecogen-method names
ecogen Creating a new ecogen object
ecopop-class ecopop class
eco.unlock eco.unlock
check_ecogen check_ecogen
plot,eco.lsa,ANY-method plot eco.lsa
check_ecopop check_ecopop
eco.nei_dist Estimate Nei distance matrix
names,ecopop-method names
eco.clear Clearing the working environment, maintaining only the specified objects
genepop2ecogen Importing a Genepop file
eco.lock,ecopop-method Lock rows in an ecogen object
eco.forestplot Forestplot graphs
EcoGenetics-package Management and Exploratory Analysis of Spatial Data in Landscape Genetics
int.check.rownames Check row names
eco.merge Merging two ecogen objects. Ordering the rows of an ecogen object according to the rows of another
eco.lock eco.lock
G G
aue.df2image Transforming a data frame into a raster
eco.convert Conversion utility for genetic data
eco.mlm-class eco.mlm-class
int.check.to_numeric check if elements are numbers and if not convert the matrix using eco.format
int.check.con Check a connection network
int.geary Geary internal.
show,eco.detrend-method show eco.detrend
aue.dummy2af Converion from dummy allele matrix to frequencies
eco.plotCorrelog eco.plotCorrelog
eco.old2new,ecogen-method Update an old ecogen or ecopop object to version >= 1.5.0-1
eco.rbind Combining ecogen objects by row
int.check.group Check factor name consistency in a data frame and returns the corresponding column
eco.lagweight-class eco.lagweight class
show,eco.lagweight-method show eco.lagweight
eco.detrend Detrending spatial data with polynomial interpolation
eco.plotCorrelogB eco.plotCorrelogB
eco.rasterplot,eco.multilsa-method rasterplot graph for eco.lsa results
eco.rasterplot Rasterplot graphs
ecogen2ecopop Conversion form ecogen to ecopop
eco.remove Creating an updated ecogen object by removing results of the slot OUT
ecogen2gstudio Conversion from ecogen to gstudio and gstudio to ecogen
ecogen2geneland Creating input data for Geneland with an ecogen object
aue.rescale Scaling a data frame or matrix to [0, 1] or [-1, 1] ranges
eco.mantel Mantel and partial Mantel tests, with truncation option
int.gendata2genind int.gendata2genind
eco.weight Spatial weights
aue.rm.nonpoly Remotion of non polymorphic loci
eco_dom eco_dom
eco.mctree-class eco.mctree-class
int.multiplot int.multiplot method. Graphical processing of multiple correlograms
meta2char Metachacter to character
eco2 eco2
ecogen-class ecogen class
int.gendata-class int.gendata
int.multitable Table construction for multiple test result.
eco.order Functions deprecated in EcoGenetics version 1.2.0-2
int.genind-class int.genind
eco.plotWeight Plot for a connection network
eco.post.geneland Log posterior probability plot for Geneland repetitions with fixed K
ecogen2hierfstat Converting an ecogen genetic data frame into a hierfstat data frame
eco.theilsen Theil-sen regression for a raster time series, with parallelization available
int.order Ordering the rows of the data frames contained in an ecogen or ecopop object
eco.unlock,ecogen-method Unlock rows in an ecogen object
eco.pairtest Kruskall - Wallis + Wilcoxon (Mann-Whitney U) and aov + Tukey-HSD tests for an ecogen object
misc.2symmetric Conversion of a non symmetric binary matrix into symmetric.
int.break breaks obtention
plot,eco.gsa,ANY-method Plot for eco.gsa objects
ecogenetics_tutorial EcoGenetic tutorial site
ecolist-class ecolist class
plot,eco.weight,ANY-method Plot for a connection network
int.popdata-class int.popdata class
ecogen2spagedi Exporting an ecogen genetic data frame into SPAGeDi format
int.check.colnames Check column names
ecogenetics_devel EcoGenetic devel site
genotype genotype
genotype_dom genotype_dom
eco.association Chi-square and Fisher's exact test for association of loci and alleles with a factor
int.genind2gendata int.genind2gendata
is.meta Detection of metacharacters
int.check.vnames Check a vector of names
grf.multiplot Multiple plot function for ggplot
is.wholenumber test whole number
structure structure
int.jackknife d-Jackknife estimation.
int.corvarToDeg eco.correlog output to degrees list
grf.seqmultiplot Plot a ggplot sequence in layers of n plots arranged in k rows
int.check.ncod Check ploidy and number of digits per allele
is.locked,ecopop-method Test if rows of an ecopop object are locked
is.locked,ecogen-method Test if rows of an ecogen object are locked
show,eco.lsa-method show eco.lsa
int.random.test random test
int.check.numeric Check numeric format in a data frame
[[<-,ecogen,numeric,missing-method [[<-
eco.dom_af Compute allele frequencies for dominant data using different methods
int.genind constructor
tab tab
[[,ecogen,numeric,missing-method [[
eco.fill_ecogen_with_df Importation of data frames to ecogen
is.locked is.locked
show,eco.gsa-method show eco.gsa
int.genind2df export
table.sokal table.sokal
phenotype phenotype
eco.gsa Global spatial analysis
int.moran Moran internal.
show,eco.mlm-method show eco.mlm
eco.lmtree Fitting Multiple Linear Regression models by stepwise AIC selection and Multiple Classification and Regression Trees via party
eco.multilsa-class eco.multilsa class
plot,eco.multilsa,ANY-method plot eco.multilsa
int.multiplot-class int.multiplot class
%>% Pipe operator
misc.undimmattg Creates a matrix without diagonal, in row order
eco.plotGlobal GSA plot methods
eco.plotLocal eco.plotLocal
eco.slide.con Sliding a window along a connection network
eco.slide.matrix Sliding window for matrix data
eco.weight-class eco.weight class
show,eco.weight-method show eco.weight
eco3 eco3
my_ecopop my_ecopop
spagedi2ecogen Importing a SPAGeDi file, via conversion to ecogen
eco.rankplot Rankplot graphs
eco4 eco4
ecopop Creating a new ecopop object
ecopop2genpop Conversion form ecopop to genpop and genpop to ecopop
ecopop_counts2af ecopop_counts2af
environment environment
int.crosscor Cross correlation. Internal.
int.df2genind importer
int.joincount Join-count statistic, internal.
int.kin.loiselle obtetion of multilocus Loiselle's Fij matrix
int.loc2al INTERNAL CONVERSION TOOLS FOR GENETIC DATA
misc.parse.filter Filter a raster using a conditional expression and values in a conditional vector
int.mantel Mantel and partial Mantel tests, internal.
misc.dlatlon2distm Computing a distance matrix in meters among points in decimal degrees under a spherical Earth model
S S
aue.check_class Obtain the classes for each column of a data frame
E E
aue.ellipse Solid ellipse
aue.formatLine Remove spaces in a line of text
aue.image2df Transforming a raster into a data frame with cartesian coordinates
aue.is.poly Identification of polymorphic loci
aue.circle Circle perimeter
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Details

Type Package
Date 2018-06-23
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' 'fill_ecogen_with_pop.R' 'plot.generic.R' 'plot.methods.R' 'roxygen.auxiliar.R' 'show_summary.methods.R' 'eco.dom_af.R' 'eco.kin.hardy.R' 'eco.nei_dist.R'
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2018-06-24 05:42:15 UTC; leandro
Repository CRAN
Date/Publication 2018-06-24 06:13:31 UTC

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