EcoGenetics v1.2.1-5
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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
Functions in EcoGenetics
| Name | Description | |
| P | P | |
| aue.seqlist | Creation of a sequence of numbers in matrix or list format, for indexing. | |
| eco.cormantel | Mantel and partial Mantel correlograms, omnidirectional and directional | |
| show,eco.IBD-method | show eco.IBD | |
| aue.sort | 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 | plot eco.IBD | |
| aue.dataAngle | Angles for an XY coordinates matrix | |
| aue.geom.dist | Weight matrices based on different geometries | |
| aue.circle.w | Radial distance to a point. | |
| plot,eco.listlsa,ANY-method | listplot | |
| eco | eco | |
| eco.alfreq | Allelic frequency histograms for an ecogen genetic data frame | |
| plot,eco.correlog,ANY-method | globalplot | |
| eco.correlog | Moran's I, Geary's C and bivariate Moran's I correlograms, omnidirectional and directional | |
| eco.listw2ew | 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 | |
| XY | XY | |
| aue.access | EcoGenetics slot standard notation. Returns an accessor to the slot <ecoslot> of the object <X> | |
| aue.get_os | Detect operative system | |
| eco.lagweight | Obtention of a list of spatial weights for classes defined by inter-individual distances or nearest-neighbors | |
| eco.formula | Formula construction for ecogen objects | |
| eco.gsa-class | eco.gsa class | |
| eco.listlsa-class | eco.listlsa | |
| aue.fqal | Allelic frequencies | |
| aue.genlab | Generation of generic labels of constant length | |
| aue.phenosimil | 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 | |
| eco.IBD-class | eco.IBD class | |
| coordinates | coordinates | |
| aue.point | Solid circle | |
| eco.old2new | eco.old2new | |
| aue.ad2wg | Transforming an adyacency matrix into a local weight matrix for a point with coordinates (x0,y0) | |
| aue.square | Solid square | |
| eco.subset | Subsetting an ecogen object by group | |
| eco.lsa | Local spatial analysis | |
| eco.split | Splitting an ecogen object by group | |
| aue.aggregated_df | Generate aggregated dataframe | |
| eco.bearing | Angular Spatial Weights | |
| eco.variogram-class | eco.variogram class | |
| eco.NDVI | Generation of atmospherically corrected NDVI and MSAVI2 images for temporal series of Landsat 5 and 7 | |
| eco.cbind | Combining ecogen objects by column | |
| eco.fill_ecogen_with_ecopop | Importation of ecopop to ecogen | |
| eco.malecot | Global and local kinship analysis | |
| aue.rmspaces | Remove spaces and tabs at the begining and the end of each element of charvec | |
| eco.format | Format tool for genetic data | |
| eco.variogram | Empirical variogram | |
| summary,eco.mlm-method | Summary for eco.lmtree output | |
| eco.NDVI.post | Postprocessing for NDVI and MSAVI2 temporal series of Landsat 5 and 7 | |
| eco.lock,ecogen-method | Lock rows in an ecogen object | |
| eco.lsa-class | eco.lsa class | |
| eco.unlock,ecopop-method | Unlock rows in an ecogen object | |
| aue.rotate | Rotation of a matrix | |
| ecogen2genepop | Exporting an ecogen genetic data frame into Genepop format | |
| eco.detrend-class | eco.detrend class | |
| eco.correlogB-class | eco.correlogB | |
| ecogen2genind | Conversion form ecogen to genind and genind to ecogen | |
| eco.kin.hardy | Kinship and relationship estimation for dominant markers | |
| eco.kin.loiselle | Obtention of the multilocus Loiselle's Fij matrix | |
| names,ecogen-method | names | |
| ecogen | Creating a new ecogen object | |
| ecopop-class | ecopop class | |
| eco.unlock | eco.unlock | |
| check_ecogen | check_ecogen | |
| plot,eco.lsa,ANY-method | plot eco.lsa | |
| check_ecopop | check_ecopop | |
| eco.nei_dist | Estimate Nei distance matrix | |
| names,ecopop-method | names | |
| eco.clear | Clearing the working environment, maintaining only the specified objects | |
| genepop2ecogen | Importing a Genepop file | |
| eco.lock,ecopop-method | Lock rows in an ecogen object | |
| eco.forestplot | Forestplot graphs | |
| EcoGenetics-package | Management and Exploratory Analysis of Spatial Data in Landscape Genetics | |
| int.check.rownames | Check row names | |
| eco.merge | Merging two ecogen objects. Ordering the rows of an ecogen object according to the rows of another | |
| eco.lock | eco.lock | |
| G | G | |
| aue.df2image | Transforming a data frame into a raster | |
| eco.convert | Conversion utility for genetic data | |
| eco.mlm-class | eco.mlm-class | |
| int.check.to_numeric | check if elements are numbers and if not convert the matrix using eco.format | |
| int.check.con | Check a connection network | |
| int.geary | Geary internal. | |
| show,eco.detrend-method | show eco.detrend | |
| aue.dummy2af | 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 | |
| eco.rbind | 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 | |
| eco.detrend | Detrending spatial data with polynomial interpolation | |
| eco.plotCorrelogB | eco.plotCorrelogB | |
| eco.rasterplot,eco.multilsa-method | rasterplot graph for eco.lsa results | |
| eco.rasterplot | Rasterplot graphs | |
| ecogen2ecopop | Conversion form ecogen to ecopop | |
| eco.remove | Creating an updated ecogen object by removing results of the slot OUT | |
| ecogen2gstudio | Conversion from ecogen to gstudio and gstudio to ecogen | |
| ecogen2geneland | Creating input data for Geneland with an ecogen object | |
| aue.rescale | Scaling a data frame or matrix to [0, 1] or [-1, 1] ranges | |
| eco.mantel | Mantel and partial Mantel tests, with truncation option | |
| int.gendata2genind | int.gendata2genind | |
| eco.weight | Spatial weights | |
| aue.rm.nonpoly | Remotion of non polymorphic loci | |
| eco_dom | eco_dom | |
| eco.mctree-class | eco.mctree-class | |
| int.multiplot | int.multiplot method. Graphical processing of multiple correlograms | |
| meta2char | Metachacter to character | |
| eco2 | eco2 | |
| ecogen-class | ecogen class | |
| int.gendata-class | int.gendata | |
| int.multitable | Table construction for multiple test result. | |
| eco.order | Functions deprecated in EcoGenetics version 1.2.0-2 | |
| int.genind-class | int.genind | |
| eco.plotWeight | 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 | |
| eco.theilsen | Theil-sen regression for a raster time series, with parallelization available | |
| int.order | Ordering the rows of the data frames contained in an ecogen or ecopop object | |
| eco.unlock,ecogen-method | Unlock rows in an ecogen object | |
| eco.pairtest | 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. | |
| int.break | breaks obtention | |
| plot,eco.gsa,ANY-method | Plot for eco.gsa objects | |
| ecogenetics_tutorial | EcoGenetic tutorial site | |
| ecolist-class | ecolist class | |
| plot,eco.weight,ANY-method | Plot for a connection network | |
| int.popdata-class | int.popdata class | |
| ecogen2spagedi | Exporting an ecogen genetic data frame into SPAGeDi format | |
| int.check.colnames | Check column names | |
| ecogenetics_devel | EcoGenetic devel site | |
| genotype | genotype | |
| genotype_dom | genotype_dom | |
| eco.association | Chi-square and Fisher's exact test for association of loci and alleles with a factor | |
| int.genind2gendata | int.genind2gendata | |
| is.meta | Detection of metacharacters | |
| int.check.vnames | Check a vector of names | |
| grf.multiplot | Multiple plot function for ggplot | |
| is.wholenumber | test whole number | |
| structure | structure | |
| int.jackknife | 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 | |
| int.check.ncod | 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 | show eco.lsa | |
| int.random.test | random test | |
| int.check.numeric | Check numeric format in a data frame | |
| [[<-,ecogen,numeric,missing-method | [[<- | |
| eco.dom_af | Compute allele frequencies for dominant data using different methods | |
| int.genind | constructor | |
| tab | tab | |
| [[,ecogen,numeric,missing-method | [[ | |
| eco.fill_ecogen_with_df | Importation of data frames to ecogen | |
| is.locked | is.locked | |
| show,eco.gsa-method | show eco.gsa | |
| int.genind2df | export | |
| table.sokal | table.sokal | |
| phenotype | phenotype | |
| eco.gsa | Global spatial analysis | |
| int.moran | Moran internal. | |
| show,eco.mlm-method | show eco.mlm | |
| eco.lmtree | 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 | |
| %>% | Pipe operator | |
| misc.undimmattg | Creates a matrix without diagonal, in row order | |
| eco.plotGlobal | GSA plot methods | |
| eco.plotLocal | eco.plotLocal | |
| eco.slide.con | 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 | |
| eco3 | eco3 | |
| my_ecopop | my_ecopop | |
| spagedi2ecogen | Importing a SPAGeDi file, via conversion to ecogen | |
| eco.rankplot | Rankplot graphs | |
| eco4 | eco4 | |
| ecopop | Creating a new ecopop object | |
| ecopop2genpop | Conversion form ecopop to genpop and genpop to ecopop | |
| ecopop_counts2af | ecopop_counts2af | |
| environment | environment | |
| int.crosscor | Cross correlation. Internal. | |
| int.df2genind | importer | |
| int.joincount | Join-count statistic, internal. | |
| int.kin.loiselle | obtetion of multilocus Loiselle's Fij matrix | |
| int.loc2al | INTERNAL CONVERSION TOOLS FOR GENETIC DATA | |
| misc.parse.filter | Filter a raster using a conditional expression and values in a conditional vector | |
| int.mantel | Mantel and partial Mantel tests, internal. | |
| misc.dlatlon2distm | Computing a distance matrix in meters among points in decimal degrees under a spherical Earth model | |
| S | S | |
| aue.check_class | Obtain the classes for each column of a data frame | |
| E | E | |
| aue.ellipse | Solid ellipse | |
| aue.formatLine | Remove spaces in a line of text | |
| aue.image2df | Transforming a raster into a data frame with cartesian coordinates | |
| aue.is.poly | Identification of polymorphic loci | |
| aue.circle | Circle perimeter | |
| No Results! | ||
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Details
| Type | Package |
| Date | 2018-06-23 |
| 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 | 6.0.1 |
| NeedsCompilation | no |
| Packaged | 2018-06-24 05:42:15 UTC; leandro |
| Repository | CRAN |
| Date/Publication | 2018-06-24 06:13:31 UTC |
| suggests | adegenet , covr , hierfstat , testthat , vegan |
| imports | d3heatmap , doParallel , edgebundleR , foreach , ggplot2 , grid , htmlwidgets , igraph , jsonlite , magrittr , networkD3 , parallel , party , pheatmap , plotly , raster , reshape2 , rgdal , rkt , SoDA , sp |
| depends | methods , R (>= 3.0) |
| Contributors | Juan Vilardi, Beatriz Saidman, Laura Ferreyra, Winston Chang, Thibaut Jombart |
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