EcoGenetics package - RDocumentation

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EcoGenetics 1.2.1-3

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

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Install

install.packages('EcoGenetics')

Monthly Downloads

121

Version

1.2.1-4

License

GPL (>= 2)

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Repository

https://github.com/cran/EcoGenetics

Homepage

https://leandroroser.github.io/EcoGenetics-Tutorial

Maintainer

Leandro Roser

Last Published

January 13th, 2018

Functions in EcoGenetics (1.2.1-4)

EcoGenetics slot standard notation. Returns an accessor to the slot <ecoslot> of the object <X>

Transforming an adyacency matrix into a local weight matrix for a point with coordinates (x0,y0)

Angles for an XY coordinates matrix

Transforming a data frame into a raster

Circle perimeter

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

Allelic frequencies

Generation of generic labels of constant length

Remotion of non polymorphic loci

Remove spaces and tabs at the begining and the end of each element of charvec

Scaling a data frame or matrix to [0, 1] or [-1, 1] ranges

Remove spaces in a line of text

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

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

Combining ecogen objects by column

Clearing the working environment, maintaining only the specified objects

Identification of polymorphic loci

Phenotypic similarity for vector, matrix or data frame acoording to Ritland (1996)

show,eco.lsa-method

Angular Spatial Weights

eco.detrend-class

eco.detrend class

show,eco.detrend-method

show eco.detrend

eco.plotCorrelog

eco.plotCorrelog

eco.plotCorrelogB

eco.plotCorrelogB

Sliding a window along a connection network

eco.slide.matrix

Sliding window for matrix data

Empirical variogram

eco.weight-class

eco.weight class

plot,eco.IBD,ANY-method

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

Postprocessing for NDVI and MSAVI2 temporal series of Landsat 5 and 7

show,eco.lagweight-method

show eco.lagweight

Formula construction for ecogen objects

Fitting Multiple Linear Regression models by stepwise AIC selection and Multiple Classification and Regression Trees via party

Detrending spatial data with polynomial interpolation

Format tool for genetic data

ecogen2hierfstat

Converting an ecogen genetic data frame into a hierfstat data frame

Exporting an ecogen genetic data frame into SPAGeDi format

Conversion form ecopop to genpop and genpop to ecopop

Weight matrices based on different geometries

Transforming a raster into a data frame with cartesian coordinates

Rotation of a matrix

Conversion utility for genetic data

Mantel and partial Mantel correlograms, omnidirectional and directional

show,eco.gsa-method

Creation of a sequence of numbers in matrix or list format, for indexing.

show,eco.IBD-method

Moran's I, Geary's C and bivariate Moran's I correlograms, omnidirectional and directional

Obtention of a list of spatial weights for classes defined by inter-individual distances or nearest-neighbors

Local spatial analysis

Global and local kinship analysis

eco.correlogB-class

eco.kin.loiselle

Obtention of the multilocus Loiselle's Fij matrix

eco.lagweight-class

eco.lagweight class

Multiple plot function for ggplot

int.genind-class

plot,eco.lsa,ANY-method

eco.multilsa-class

eco.multilsa class

plot,eco.multilsa,ANY-method

plot eco.multilsa

Functions deprecated in EcoGenetics version 1.2.0-2

Kruskall - Wallis + Wilcoxon (Mann-Whitney U) and aov + Tukey-HSD tests for an ecogen object

Global spatial analysis

Conversion from listw to ecoweight

show,eco.mlm-method

GSA plot methods

summary,eco.mlm-method

Summary for eco.lmtree output

Conversion form ecogen to genind and genind to ecogen

Conversion from ecogen to gstudio and gstudio to ecogen

names,ecopop-method

Creating a new ecopop object

Mantel and partial Mantel tests, with truncation option

eco.mctree-class

eco.mctree-class

Plot for a connection network

eco.post.geneland

Log posterior probability plot for Geneland repetitions with fixed K

Splitting an ecogen object by group

Subsetting an ecogen object by group

int.multiplot-class

int.multiplot class

int.multiplot method. Graphical processing of multiple correlograms

Theil-sen regression for a raster time series

eco.variogram-class

eco.variogram class

ecogenetics_devel

EcoGenetic devel site

names,ecogen-method

Forestplot graphs

Importing a Genepop file

eco.listlsa-class

plot,eco.listlsa,ANY-method

Merging two ecogen objects. Ordering the rows of an ecogen object according to the rows of another

int.check.numeric

Check numeric format in a data frame

int.check.rownames

Check row names

int.gendata-class

Metachacter to character

misc.2symmetric

Conversion of a non symmetric binary matrix into symmetric.

Rankplot graphs

int.gendata2genind

int.gendata2genind

Detection of metacharacters

test whole number

Importing a SPAGeDi file, via conversion to ecogen

ecogenetics_tutorial

EcoGenetic tutorial site

int.check.colnames

Check column names

Check a connection network

Geary internal.

[[<-,ecogen,numeric,missing-method

Combining ecogen objects by row

Creating an updated ecogen object by removing results of the slot OUT

ecogen2geneland

Creating input data for Geneland with an ecogen object

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

Check ploidy and number of digits per allele

int.corvarToDeg

eco.correlog output to degrees list

Cross correlation. Internal.

eco.rasterplot,eco.multilsa-method

rasterplot graph for eco.lsa results

Rasterplot graphs

show,eco.weight-method

show eco.weight

Mantel and partial Mantel tests, internal.

Moran internal.

int.popdata-class

int.popdata class

int.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

d-Jackknife estimation.

Join-count statistic, internal.

Table construction for multiple test result.

Ordering the rows of the data frames contained in an ecogen or ecopop object

[[,ecogen,numeric,missing-method

Spatial weights

Creating a new ecogen object

Conversion form ecogen to ecopop

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

breaks obtention

int.kin.loiselle

obtetion of multilocus Loiselle's Fij matrix

INTERNAL CONVERSION TOOLS FOR GENETIC DATA

misc.undimmattg

Creates a matrix without diagonal, in row order