Management and Exploratory Analysis of Spatial Data in Landscape Genetics

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Documentation for package ‘EcoGenetics’ version 1.2.1-5

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A C E G I M P S T X

EcoGenetics-package Management and Exploratory Analysis of Spatial Data in Landscape Genetics

-- A --

aue.aggregated_df Generate aggregated dataframe
aue.check_class Obtain the classes for each column of a data frame
aue.dataAngle Angles for an XY coordinates matrix
aue.df2image Transforming a data frame into a raster
aue.dummy2af Converion from dummy allele matrix to frequencies
aue.image2df Transforming a raster into a data frame with cartesian coordinates
aue.phenosimil Phenotypic similarity for vector, matrix or data frame acoording to Ritland (1996)
aue.rescale Scaling a data frame or matrix to [0, 1] or [-1, 1] ranges
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

-- C --

coordinates coordinates

-- E --

E E
eco eco
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.bearing Angular Spatial Weights
eco.cbind Combining ecogen objects by column
eco.clear Clearing the working environment, maintaining only the specified objects
eco.convert Conversion utility for genetic data
eco.cormantel Mantel and partial Mantel correlograms, omnidirectional and directional
eco.correlog Moran's I, Geary's C and bivariate Moran's I correlograms, omnidirectional and directional
eco.detrend Detrending spatial data with polynomial interpolation
eco.dom_af Compute allele frequencies for dominant data using different methods
eco.fill_ecogen_with_df Importation of data frames to ecogen
eco.fill_ecogen_with_ecopop Importation of ecopop to ecogen
eco.forestplot Forestplot graphs
eco.forestplot-method Forestplot graphs
eco.format Format tool for genetic data
eco.formula Formula construction for ecogen objects
eco.gsa Global spatial analysis
eco.kin.hardy Kinship and relationship estimation for dominant markers
eco.kin.loiselle Obtention of the multilocus Loiselle's Fij matrix
eco.lagweight Obtention of a list of spatial weights for classes defined by inter-individual distances or nearest-neighbors
eco.listw2ew Conversion from listw to ecoweight
eco.lmtree Fitting Multiple Linear Regression models by stepwise AIC selection and Multiple Classification and Regression Trees via party
eco.lock,ecogen Lock rows in an ecogen object
eco.lock,ecopop Lock rows in an ecogen object
eco.lock-method Lock rows in an ecogen object
eco.lock-method Lock rows in an ecogen object
eco.lsa Local spatial analysis
eco.malecot Global and local kinship analysis
eco.mantel Mantel and partial Mantel tests, with truncation option
eco.merge Merging two ecogen objects. Ordering the rows of an ecogen object according to the rows of another
eco.NDVI Generation of atmospherically corrected NDVI and MSAVI2 images for temporal series of Landsat 5 and 7
eco.NDVI.post Postprocessing for NDVI and MSAVI2 temporal series of Landsat 5 and 7
eco.nei_dist Estimate Nei distance matrix
eco.old2new,ecogen Update an old ecogen or ecopop object to version >= 1.5.0-1
eco.old2new,ecopop Update an old ecogen or ecopop object to a version compatible with EcoGenetics >= 1.5.0-1
eco.old2new-method Update an old ecogen or ecopop object to version >= 1.5.0-1
eco.old2new-method Update an old ecogen or ecopop object to a version compatible with EcoGenetics >= 1.5.0-1
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.plotCorrelog eco.plotCorrelog
eco.plotCorrelogB eco.plotCorrelogB
eco.plotGlobal GSA plot methods
eco.plotLocal eco.plotLocal
eco.plotWeight Plot for a connection network
eco.post.geneland Log posterior probability plot for Geneland repetitions with fixed K
eco.rankplot Rankplot graphs
eco.rankplot-method Rankplot graphs
eco.rasterplot Rasterplot graphs
eco.rasterplot-method rasterplot graph for eco.lsa results
eco.rbind Combining ecogen objects by row
eco.remove Creating an updated ecogen object by removing results of the slot OUT
eco.slide.con Sliding a window along a connection network
eco.slide.matrix Sliding window for matrix data
eco.split Splitting an ecogen object by group
eco.subset Subsetting an ecogen object by group
eco.theilsen Theil-sen regression for a raster time series, with parallelization available
eco.unlock,ecogen Unlock rows in an ecogen object
eco.unlock,ecopop Unlock rows in an ecogen object
eco.unlock-method Unlock rows in an ecogen object
eco.unlock-method Unlock rows in an ecogen object
eco.variogram Empirical variogram
eco.weight Spatial weights
eco2 eco2
eco3 eco3
eco4 eco4
ecogen Creating a new ecogen object
ecogen2ecopop Conversion form ecogen to ecopop
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 frame
ecogen2spagedi Exporting an ecogen genetic data frame into SPAGeDi format
EcoGenetics Management and Exploratory Analysis of Spatial Data in Landscape Genetics
ecogenetics_devel EcoGenetic devel site
ecogenetics_tutorial EcoGenetic tutorial site
ecopop Creating a new ecopop object
ecopop2genpop Conversion form ecopop to genpop and genpop to ecopop
ecopop_counts2af ecopop_counts2af
eco_dom eco_dom
environment environment

-- G --

G G
genepop2ecogen Importing a Genepop file
genind2ecogen Conversion form ecogen to genind and genind to ecogen
genotype genotype
genotype_dom genotype_dom
genpop2ecopop Conversion form ecopop to genpop and genpop to ecopop
grf.multiplot Multiple plot function for ggplot
grf.seqmultiplot Plot a ggplot sequence in layers of n plots arranged in k rows
gstudio2ecogen Conversion from ecogen to gstudio and gstudio to ecogen

-- I --

is.locked,ecogen Test if rows of an ecogen object are locked
is.locked,ecopop Test if rows of an ecopop object are locked
is.locked-method Test if rows of an ecogen object are locked
is.locked-method Test if rows of an ecopop object are locked

-- M --

my_ecopop my_ecopop

-- P --

P P
phenotype phenotype
plot-method plot eco.multilsa

-- S --

S S
spagedi2ecogen Importing a SPAGeDi file, via conversion to ecogen
structure structure
summary-method Summary for eco.lmtree output

-- T --

tab tab
table.sokal table.sokal

-- X --

XY XY