Analysis of Phenotypic, Genotypic and Environmental Data

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Documentation for package ‘EcoGenetics’ version 1.1.0

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EcoGenetics-package Analysis of Phenotypic, Genotypic and Environmental Data
coordinates Coordinates
eco Eco
eco.2columns Converting an ecogen genetic data frame with two alleles per column into a data frame with one allele per column
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 an ecogen genetic data frame into a gstudio object
eco.2hierfstat Converting an ecogen genetic data frame into a hierfstat data frame
eco.alfreq Allelic frequency histogram for an ecogen genetic data frame
eco.append Creating an updated ecogen object by adding results to the slot OUT
eco.association Chi-square and Fisher's exact test for association of loci and alleles with a factor
eco.autocor Moran's I, Geary's C, Join-Count, local Getis-Ord's G and local Moran's I correlograms for an ecogen object
eco.boothet Heterozygosity estimates with bootstrap confidence intervals over individuals and loci, and jackkninfe estimates over populations
eco.cbind Combining the columns of two ecogen object
eco.char2num Converting data coded with characters into data coded by numbers
eco.clear Clearing the working environment, maintaining only the specified objects
eco.cormantel Mantel correlogram
eco.forestplot Plot for correlograms of Getis- Ord's G or local-Moran's I
eco.forestplot-method Plot for correlograms of Getis- Ord's G or local-Moran's I
eco.geary Geary's C statistic with Monte-Carlo test
eco.getisord Local Getis-Ord's G and G* for analysis of hot spots
eco.joincount Join-Count statistic with Monte-Carlo test
eco.laglistw Obtention of a list with weight matrices for lag distance classes
eco.lmtree Fitting Multiple Linear Regression models by stepwise AIC selection and Multiple Classification and Regression Trees via party
eco.localmoran Local Moran's I statistic with Monte-Carlo test
eco.mantel Mantel test
eco.merge Merging two ecogen objects. Ordering the rows of an ecogen object according to the rows of another
eco.moran Moran's I statistic with Monte-Carlo test
eco.NDVI Generating atmospherically corrected NDVI and MSAVI2 images for temporal series of Landsat 5 and 7
eco.NDVI.post Postprocessing for NDVI and MSAVI 2 temporal series of Landsat 5 and 7
eco.order Ordering the rows of the data frames contained in an ecogen object
eco.pairtest Wilcoxon (Mann-Whitney U) and Tukey-HSD tests for an ecogen object
eco.post.geneland Log posterior probability plot for Geneland repetitions with fixed K
eco.rankplot Plot for Getis- Ord's G or local-Moran's I analysis
eco.rankplot-method Plot for Getis- Ord's G or local-Moran's I analysis
eco.rarefact Multiple rarefaction estimates via bootstrap for ecogen genetic data frames
eco.rbind Combining the rows of two ecogen objects
eco.remove Creating an updated ecogen object by removing results of the slot OUT
eco.rescale Scaling a data frame or matrix to 0 - 1 range
eco.sort Ordering cells in a data frame or matrix
eco.subset Subsetting an ecogen object by group
eco.theilsen Theil-sen regression for a raster time series
eco.variogram Empirical variogram
ecogen Creating a new ecogen object.
ecogen2genind Conversion between genind and ecogen, and vice versa
EcoGenetics Analysis of Phenotypic, Genotypic and Environmental Data
environment environment
genind2ecogen Conversion between genind and ecogen, and vice versa
genotype genotype
latlon2distm Computing a distance matrix in meters among points in decimal degrees under a spherical Earth model
phenotype phenotype
plot-method Plot for lag objects
structure structure
summary-method Summary for eco.lmtree output
summary-method Summary for ecogen objects
tab tab