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EcoGenetics 1.2.1-5

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Installation of devel version

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

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install.packages('EcoGenetics')

Monthly Downloads

121

Version

1.2.1-5

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

June 24th, 2018

Functions in EcoGenetics (1.2.1-5)

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

Mantel and partial Mantel correlograms, omnidirectional and directional

show,eco.IBD-method

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

Angles for an XY coordinates matrix

Weight matrices based on different geometries

Radial distance to a point.

plot,eco.listlsa,ANY-method

Allelic frequency histograms for an ecogen genetic data frame

plot,eco.correlog,ANY-method

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

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

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

Detect operative system

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

Formula construction for ecogen objects

eco.listlsa-class

Allelic frequencies

Generation of generic labels of constant length

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

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

Subsetting an ecogen object by group

Local spatial analysis

Splitting an ecogen object by group

aue.aggregated_df

Generate aggregated dataframe

Angular Spatial Weights

eco.variogram-class

eco.variogram class

Generation of atmospherically corrected NDVI and MSAVI2 images for temporal series of Landsat 5 and 7

Combining ecogen objects by column

eco.fill_ecogen_with_ecopop

Importation of ecopop to ecogen

Global and local kinship analysis

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

Format tool for genetic data

Empirical variogram

summary,eco.mlm-method

Summary for eco.lmtree output

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

eco.lock,ecogen-method

Lock rows in an ecogen object

eco.unlock,ecopop-method

Unlock rows in an ecogen object

Rotation of a matrix

Exporting an ecogen genetic data frame into Genepop format

eco.detrend-class

eco.detrend class

eco.correlogB-class

Conversion form ecogen to genind and genind to ecogen

Kinship and relationship estimation for dominant markers

eco.kin.loiselle

Obtention of the multilocus Loiselle's Fij matrix

names,ecogen-method

Creating a new ecogen object

plot,eco.lsa,ANY-method

Estimate Nei distance matrix

names,ecopop-method

Clearing the working environment, maintaining only the specified objects

Importing a Genepop file

eco.lock,ecopop-method

Lock rows in an ecogen object

Forestplot graphs

EcoGenetics-package

Management and Exploratory Analysis of Spatial Data in Landscape Genetics

int.check.rownames

Check row names

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

Transforming a data frame into a raster

Conversion utility for genetic data

int.check.to_numeric

check if elements are numbers and if not convert the matrix using eco.format

Check a connection network

Geary internal.

show,eco.detrend-method

show eco.detrend

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

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

Detrending spatial data with polynomial interpolation

eco.plotCorrelogB

eco.plotCorrelogB

eco.rasterplot,eco.multilsa-method

rasterplot graph for eco.lsa results

Rasterplot graphs

Conversion form ecogen to ecopop

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

Conversion from ecogen to gstudio and gstudio to ecogen

ecogen2geneland

Creating input data for Geneland with an ecogen object

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

Mantel and partial Mantel tests, with truncation option

int.gendata2genind

int.gendata2genind

Spatial weights

Remotion of non polymorphic loci

eco.mctree-class

eco.mctree-class

int.multiplot method. Graphical processing of multiple correlograms

Metachacter to character

int.gendata-class

Table construction for multiple test result.

Functions deprecated in EcoGenetics version 1.2.0-2

int.genind-class

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

Theil-sen regression for a raster time series, with parallelization available

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

eco.unlock,ecogen-method

Unlock rows in an ecogen object

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.

breaks obtention

plot,eco.gsa,ANY-method

Plot for eco.gsa objects

ecogenetics_tutorial

EcoGenetic tutorial site

plot,eco.weight,ANY-method

Plot for a connection network

int.popdata-class

int.popdata class

Exporting an ecogen genetic data frame into SPAGeDi format

int.check.colnames

Check column names

ecogenetics_devel

EcoGenetic devel site

eco.association

Chi-square and Fisher's exact test for association of loci and alleles with a factor

int.genind2gendata

int.genind2gendata

Detection of metacharacters

int.check.vnames

Check a vector of names

Multiple plot function for ggplot

test whole number

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

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

int.random.test

int.check.numeric

Check numeric format in a data frame

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

Compute allele frequencies for dominant data using different methods

[[,ecogen,numeric,missing-method

eco.fill_ecogen_with_df

Importation of data frames to ecogen

show,eco.gsa-method

Global spatial analysis

Moran internal.

show,eco.mlm-method

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

misc.undimmattg

Creates a matrix without diagonal, in row order

GSA plot methods

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

Importing a SPAGeDi file, via conversion to ecogen

Rankplot graphs

Creating a new ecopop object

Conversion form ecopop to genpop and genpop to ecopop

ecopop_counts2af

ecopop_counts2af

Cross correlation. Internal.

Join-count statistic, internal.

int.kin.loiselle

obtetion of multilocus Loiselle's Fij matrix

INTERNAL CONVERSION TOOLS FOR GENETIC DATA

misc.parse.filter

Filter a raster using a conditional expression and values in a conditional vector

Mantel and partial Mantel tests, internal.

misc.dlatlon2distm

Computing a distance matrix in meters among points in decimal degrees under a spherical Earth model

aue.check_class

Obtain the classes for each column of a data frame

Remove spaces in a line of text

Transforming a raster into a data frame with cartesian coordinates

Identification of polymorphic loci

Circle perimeter