EcoGenetics v1.2.1-6

0

Monthly downloads

0th

Percentile

Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Management and exploratory analysis of spatial data in landscape genetics. Easy integration of information from multiple sources with "ecogen" objects.

Readme

EcoGenetics 1.2.1-5

Linux Windows R Downloads
lin-badge win-badge R-badge dow-badge


Tutorial


Online documentation



Installation of devel version

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

Functions in EcoGenetics

Name Description
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
No Results!

Last month downloads

Details

Type Package
Date 2020-05-24
License GPL (>= 2)
URL https://github.com/cran/EcoGenetics, https://leandroroser.github.io/EcoGenetics-Tutorial
LazyLoad yes
Collate 'ZZZ.R' 'generics.R' 'auxiliar.R' 'int.genind.R' 'ecogen.1OF6.definition.R' 'ecogen.2OF6.constructor.R' 'ecogen.3OF6.basic.methods.R' 'ecogen.4OF6.brackets.R' 'ecogen.5OF6.get&set.R' 'ecogen.6OF6.converters.R' 'ecopop.1OF6.definition.R' 'ecopop.2OF6.constructor.R' 'ecopop.3OF6.basic.methods.R' 'ecopop.4OF6.brackets.R' 'ecopop.5OF6.get&set.R' 'ecopop.6OF6.converters.R' 'accessors.R' 'classes.R' 'control.R' 'deprecated.R' 'eco.formula.R' 'eco.NDVI.R' 'eco.NDVI.post.R' 'eco.alfreq.R' 'eco.association.R' 'eco.bearing.R' 'eco.cbind.R' 'eco.clear.R' 'eco.convert.R' 'eco.cormantel.R' 'eco.correlog.R' 'eco.detrend.R' 'eco.forestplot.R' 'eco.format.R' 'eco.gsa.R' 'eco.kin.loiselle.R' 'eco.lagweight.R' 'eco.lmtree.R' 'eco.lsa.R' 'eco.malecot.R' 'eco.mantel.R' 'eco.merge.R' 'eco.pairtest.R' 'eco.plotCorrelog.R' 'eco.plotGlobal.R' 'eco.plotLocal.R' 'eco.plotWeight.R' 'eco.post.geneland.R' 'eco.rankplot.R' 'eco.rasterplot.R' 'eco.rbind.R' 'eco.remove.R' 'eco.slide.con.R' 'eco.slide.matrix.R' 'eco.split.R' 'eco.subset.R' 'eco.theilsen.R' 'eco.variogram.R' 'eco.weight.R' 'int.break.R' 'int.convert.R' 'int.crosscor.R' 'int.geary.R' 'int.jackknife.R' 'int.joincount.R' 'int.kin.loiselle.R' 'int.mantel.R' 'int.moran.R' 'int.multitable.R' 'int.order.R' 'int.random.test.R' 'miscellaneous.R' 'fill_ecogen_with_pop.R' 'plot.generic.R' 'plot.methods.R' 'roxygen.auxiliar.R' 'show_summary.methods.R' 'eco.dom_af.R' 'eco.kin.hardy.R' 'eco.nei_dist.R'
RoxygenNote 7.1.0
NeedsCompilation no
Packaged 2020-05-24 06:01:19 UTC; Leandro
LazyData true
Repository CRAN
Date/Publication 2020-05-24 15:20:17 UTC

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/EcoGenetics)](http://www.rdocumentation.org/packages/EcoGenetics)