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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

142

Version

1.2.1-6

License

GPL (>= 2)

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Maintainer

Leandro Roser

Last Published

May 24th, 2020

Functions in EcoGenetics (1.2.1-6)

EcoGenetics-package

Management and Exploratory Analysis of Spatial Data in Landscape Genetics
aue.aggregated_df

Generate aggregated dataframe
aue.ad2wg

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

XY
S

S
E

E
P

P
G

G
EcoGenetics accessors

Generic accessors for EcoGenetics objects
aue.circle.w

Radial distance to a point.
aue.point

Solid circle
eco.NDVI.post

Postprocessing for NDVI and MSAVI2 temporal series of Landsat 5 and 7
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
eco.cbind

Combining ecogen objects by column
aue.rm.nonpoly

Remotion of non polymorphic loci
eco

eco
aue.ellipse

Solid ellipse
aue.dataAngle

Angles for an XY coordinates matrix
aue.formatLine

Remove spaces in a line of text
aue.fqal

Allelic frequencies
aue.seqlist

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

Ordering the content of cells in a matrix. Ordering alleles in a genetic matrix.
aue.access

EcoGenetics slot standard notation. Returns an accessor to the slot <ecoslot> of the object <X>
aue.df2image

Transforming a data frame into a raster
aue.circle

Circle perimeter
eco.correlog

Moran's I, Geary's C and bivariate Moran's I correlograms, omnidirectional and directional
aue.image2df

Transforming a raster into a data frame with cartesian coordinates
eco.association

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

coordinates
eco.alfreq

Allelic frequency histograms for an ecogen genetic data frame
aue.rmspaces

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

Compute allele frequencies for dominant data using different methods
aue.dummy2af

Converion from dummy allele matrix to frequencies
eco.detrend

Detrending spatial data with polynomial interpolation
eco.convert

Conversion utility for genetic data
aue.genlab

Generation of generic labels of constant length
eco.theilsen

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

Obtain the classes for each column of a data frame
aue.get_os

Detect operative system
eco.clear

Clearing the working environment, maintaining only the specified objects
.printaccess

printaccess
eco.gsa-class

eco.gsa class
eco.fill_ecogen_with_ecopop

Importation of ecopop to ecogen
eco.kin.loiselle

Obtention of the multilocus Loiselle's Fij matrix
aue.geom.dist

Weight matrices based on different geometries
aue.split_categorical

Split categorical variable into levels, using a second factor (hierarchy) to aggregate the data
eco.remove

Creating an updated ecogen object by removing results of the slot OUT
eco.correlog-class

eco.correlog-class
aue.square

Solid square
show,eco.gsa-method

show eco.gsa
eco.bearing

Angular Spatial Weights
eco.pairtest

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

check_ecogen
check_ecopop

check_ecopop
aue.is.poly

Identification of polymorphic loci
eco.fill_ecogen_with_df

Importation of data frames to ecogen
eco.malecot

Global and local kinship analysis
aue.rotate

Rotation of a matrix
eco.correlogB-class

eco.correlogB
int.check.rownames

Check row names
eco.listlsa-class

eco.listlsa
show,eco.lsa-method

show eco.lsa
environment

environment
eco.lock

eco.lock
eco.cormantel

Mantel and partial Mantel correlograms, omnidirectional and directional
names,ecopop-method

names
eco.format

Format tool for genetic data
eco.formula

Formula construction for ecogen objects
eco.IBD-class

eco.IBD class
eco.lsa-class

eco.lsa class
plot,eco.multilsa,ANY-method

plot eco.multilsa
eco.plotCorrelog

eco.plotCorrelog
int.genind

constructor
eco.plotLocal

eco.plotLocal
show,eco.lagweight-method

show eco.lagweight
eco.order

Functions deprecated in EcoGenetics version 1.2.0-2
plot,eco.correlog,ANY-method

globalplot
show,eco.weight-method

show eco.weight
ecogen-class

ecogen class
show,eco.IBD-method

show eco.IBD
eco.NDVI

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

genotype_dom
eco.old2new

eco.old2new
plot,eco.IBD,ANY-method

plot eco.IBD
eco.mlm-class

eco.mlm-class
names,ecogen-method

names
eco.gsa

Global spatial analysis
eco.detrend-class

eco.detrend class
misc.dlatlon2distm

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

Plot for a connection network
eco.weight

Spatial weights
eco.listw2ew

Conversion from listw to ecoweight
show,eco.detrend-method

show eco.detrend
int.check.con

Check a connection network
genepop2ecogen

Importing a Genepop file
ecogen2spagedi

Exporting an ecogen genetic data frame into SPAGeDi format
ecogen2hierfstat

Converting an ecogen genetic data frame into a hierfstat data frame
int.check.colnames

Check column names
int.multitable

Table construction for multiple test result.
eco.lock,ecogen-method

Lock rows in an ecogen object
ecogen

Creating a new ecogen object
show,eco.mlm-method

show eco.mlm
eco.lagweight

Obtention of a list of spatial weights for classes defined by inter-individual distances or nearest-neighbors
eco.lock,ecopop-method

Lock rows in an ecogen object
meta2char

Metachacter to character
genotype

genotype
int.order

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

Rankplot graphs
int.jackknife

d-Jackknife estimation.
eco.post.geneland

Log posterior probability plot for Geneland repetitions with fixed K
eco.slide.con

Sliding a window along a connection network
is.wholenumber

test whole number
plot,eco.weight,ANY-method

Plot for a connection network
int.joincount

Join-count statistic, internal.
eco.multilsa-class

eco.multilsa class
eco.old2new,ecopop-method

Update an old ecogen or ecopop object to a version compatible with EcoGenetics >= 1.5.0-1
eco.unlock,ecogen-method

Unlock rows in an ecogen object
eco.mantel

Mantel and partial Mantel tests, with truncation option
eco.slide.matrix

Sliding window for matrix data
plot,eco.listlsa,ANY-method

listplot
eco.old2new,ecogen-method

Update an old ecogen or ecopop object to version >= 1.5.0-1
eco.kin.hardy

Kinship and relationship estimation for dominant markers
eco.lmtree

Fitting Multiple Linear Regression models by stepwise AIC selection and Multiple Classification and Regression Trees via party
summary,eco.mlm-method

Summary for eco.lmtree output
ecogen2ecopop

Conversion form ecogen to ecopop
plot,eco.lsa,ANY-method

plot eco.lsa
eco.nei_dist

Estimate Nei distance matrix
eco.subset

Subsetting an ecogen object by group
ecogen2geneland

Creating input data for Geneland with an ecogen object
structure

structure
ecopop2genpop

Conversion form ecopop to genpop and genpop to ecopop
int.geary

Geary internal.
eco.lagweight-class

eco.lagweight class
ecopop

Creating a new ecopop object
eco.rasterplot

Rasterplot graphs
ecopop_counts2af

ecopop_counts2af
is.locked,ecogen-method

Test if rows of an ecogen object are locked
int.check.group

Check factor name consistency in a data frame and returns the corresponding column
eco.rbind

Combining ecogen objects by row
eco.lsa

Local spatial analysis
ecogen2genepop

Exporting an ecogen genetic data frame into Genepop format
eco.mctree-class

eco.mctree-class
eco.split

Splitting an ecogen object by group
eco.unlock,ecopop-method

Unlock rows in an ecogen object
ecogenetics_tutorial

EcoGenetic tutorial site
int.genind2df

export
eco.merge

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
eco.plotCorrelogB

eco.plotCorrelogB
eco_dom

eco_dom
eco.weight-class

eco.weight class
eco.plotGlobal

GSA plot methods
eco.rasterplot,eco.multilsa-method

rasterplot graph for eco.lsa results
eco.variogram

Empirical variogram
int.moran

Moran internal.
is.meta

Detection of metacharacters
ecogen2genind

Conversion form ecogen to genind and genind to ecogen
ecogen2gstudio

Conversion from ecogen to gstudio and gstudio to ecogen
eco4

eco4
int.check.ncod

Check ploidy and number of digits per allele
ecopop-class

ecopop class
int.break

breaks obtention
int.corvarToDeg

eco.correlog output to degrees list
int.crosscor

Cross correlation. Internal.
eco3

eco3
int.loc2al

INTERNAL CONVERSION TOOLS FOR GENETIC DATA
is.locked,ecopop-method

Test if rows of an ecopop object are locked
grf.seqmultiplot

Plot a ggplot sequence in layers of n plots arranged in k rows
misc.undimmattg

Creates a matrix without diagonal, in row order
my_ecopop

my_ecopop
is.locked

is.locked
ecolist-class

ecolist class
int.genind2gendata

int.genind2gendata
spagedi2ecogen

Importing a SPAGeDi file, via conversion to ecogen
int.kin.loiselle

obtetion of multilocus Loiselle's Fij matrix
int.gendata-class

int.gendata
table.sokal

table.sokal
int.gendata2genind

int.gendata2genind
eco.forestplot

Forestplot graphs
eco2

eco2
tab

tab
ecogenetics_devel

EcoGenetic devel site
eco.variogram-class

eco.variogram class
int.check.to_numeric

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

random test
int.genind-class

int.genind
misc.parse.filter

Filter a raster using a conditional expression and values in a conditional vector
eco.unlock

eco.unlock
int.check.vnames

Check a vector of names
grf.multiplot

Multiple plot function for ggplot
misc.2symmetric

Conversion of a non symmetric binary matrix into symmetric.
int.popdata-class

int.popdata class
phenotype

phenotype
int.mantel

Mantel and partial Mantel tests, internal.
%>%

Pipe operator
int.df2genind

importer
plot,eco.gsa,ANY-method

Plot for eco.gsa objects
int.multiplot-class

int.multiplot class
[[,ecogen,numeric,missing-method

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

[[<-
int.multiplot

int.multiplot method. Graphical processing of multiple correlograms