# Management and Exploratory Analysis of Spatial Data in Landscape Genetics

## Documentation for package ‘EcoGenetics’ version 1.2.1-5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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