speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses
Version 1.0-4

Preparation of species occurrences and distribution data for the use in phylogenetic analyses. SpeciesgeocodeR is built for data cleaning, data exploration and data analysis and especially suited for biogeographical and ecological questions on large datasets. The package includes the easy creation of summary-tables and -graphs and geographical maps, the automatic cleaning of geographic occurrence data, the calculating of coexistence matrices and species ranges (EOO) as well as mapping diversity in geographic areas.

AuthorAlexander Zizka [aut, cre]
Date of publication2015-10-18 01:20:59
MaintainerAlexander Zizka <alexander.zizka@bioenv.gu.se>
LicenseGPL-3
Version1.0-4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("speciesgeocodeR")

Getting started

Package overview

Popular man pages

CalcRange: Calculate the Extent of Occurrence
countryref: Country Centroids and Country Capitals
lemurs: Distribution of Lemur Species
lemurs_test: Distribution of Lemur Species with Problematic Records
mdg_poly: WWF Biomes of Madagascar in Table Format
summary.spgeoIN: Summary Method for SpgeoIN
WwfLoad: Load the WWF Terrestrial Ecoregions
See all...

All man pages Function index File listing

Man pages

CalcRange: Calculate the Extent of Occurrence
CoExClass: Species Coexistence Matrices in Given Areas.
countryref: Country Centroids and Country Capitals
GeoClean: Automated Cleaning of Geographic Coordinates
GetElevation: Elevation Data for Multiple Species
lemurs: Distribution of Lemur Species
lemurs_in: Example for an spgeoIN Object
lemurs_test: Distribution of Lemur Species with Problematic Records
MapGrid: Plotting Rasters in the Geographical Context
MapRichness: Plotting Species Richness in a Set of Polygons
mdg_biomes: WWF Biomes of Madagascar
mdg_poly: WWF Biomes of Madagascar in Table Format
PlotHull: Plotting Species Ranges
plot.spgeoIN: Plot Method for SpgeoIN Objects
plot.spgeoOUT: Plot Method for SpgeoOUT Objects
RangeRichness: Species Richness Raster from Range Polygons
ReadPoints: Loading Data into SpeciesgeocodeR
RichnessGrid: Species Richness and Abundance Grids from Point Records
SpeciesGeoCoder: A Complete SpeciesgeocodeR Analysis
speciesgeocodeR-package: Prepare Species Distributions for the Use in Phylogenetic...
Spgc2Biogeobears: Geography Input for BioGeoBEARS
SpGeoCod: Point to Polygon Classification from Text Files
SpGeoCodH: A Standard a SpeciesgeocodeR Area Classification
summary.spgeoIN: Summary Method for SpgeoIN
summary.spgeoOUT: Summary Method for SpgeoOUT
WriteOut: Write SpeciesgeocodeR results to the Working Directory
WwfLoad: Load the WWF Terrestrial Ecoregions

Functions

BarChartPoly Source code
BarChartSpec Source code
CalcRange Man page Source code
CoExClass Man page Source code
CoExClassH Source code
ConvHull Source code
ConvertPoly Source code
Cord2Polygon Source code
GeoClean Man page Source code
GetElevation Man page Source code
GetPythonIn Source code
HeatPlotCoEx Source code
MapAll Source code
MapGrid Man page Source code
MapPerPoly Source code
MapPerSpecies Source code
MapRichness Man page Source code
MapUnclassified Source code
NexusOut Source code
OutBarChartPoly Source code
OutBarChartSpec Source code
OutHeatCoEx Source code
OutMapAll Source code
OutMapPerPoly Source code
OutMapPerSpecies Source code
OutPlotSpPoly Source code
PipSamp Source code
PlotHull Man page Source code
PlotSpPoly Source code
RangeRichness Man page Source code
ReadPoints Man page Source code
RichnessGrid Man page Source code
SpGeoCod Man page Source code
SpGeoCodH Man page Source code
SpPerPolH Source code
SpSumH Source code
SpeciesGeoCoder Man page Source code
Spgc2BioGeoBEARS Man page Source code
WriteOut Man page Source code
WriteTablesSpGeo Source code
WwfLoad Man page Source code
adjFormat Source code
countryref Man page
eoo Source code
getEle Source code
lemurs Man page
lemurs_in Man page
lemurs_test Man page
mdg_biomes Man page
mdg_poly Man page
perc Source code
plot.spgeoIN Man page Source code
plot.spgeoOUT Man page Source code
rasterSum Source code
speciesgeocodeR Man page
speciesgeocodeR-package Man page
summary.spgeoIN Man page Source code
summary.spgeoOUT Man page Source code
testcordcap Source code
testcordcountr Source code

Files

inst
inst/extdata
inst/extdata/mdg_biomes_simple.shx
inst/extdata/mdg_biomes_simple.dbf
inst/extdata/mdg_biomes_simple.txt
inst/extdata/mdg_biomes_simple.qpj
inst/extdata/lemur_test.txt
inst/extdata/lemurs.txt
inst/extdata/mdg_biomes_simple.prj
inst/extdata/mdg_biomes_simple.shp
inst/doc
inst/doc/data_cleaning_and_exploration.pdf
NAMESPACE
data
data/lemurs.rda
data/lemurs_test.rda
data/mdg_biomes.rda
data/lemurs_in.rda
data/countryref.rda
data/mdg_poly.rda
R
R/CalcRange.R
R/GetElevation.R
R/MapGrid.R
R/Spgc2BioGeoBEARS.R
R/summary.spgeoOUT.R
R/PlotHull.R
R/SpeciesGeoCoder.R
R/RangeRichness.R
R/MapRichness.R
R/WriteOut.R
R/plot.spgeoIN.R
R/ReadPoints.R
R/RichnessGrid.R
R/SpGeoCodH.R
R/plot.spgeoOUT.R
R/CoExClass.R
R/summary.spgeoIN.R
R/speciesgeocodeR-internal.R
R/WwfLoad.R
R/SpGeoCod.R
R/GeoClean.R
MD5
DESCRIPTION
man
man/summary.spgeoIN.Rd
man/plot.spgeoIN.Rd
man/RichnessGrid.Rd
man/plot.spgeoOUT.Rd
man/GetElevation.Rd
man/PlotHull.Rd
man/mdg_poly.Rd
man/lemurs_test.Rd
man/SpGeoCod.Rd
man/speciesgeocodeR-package.Rd
man/countryref.Rd
man/CalcRange.Rd
man/WriteOut.Rd
man/summary.spgeoOUT.Rd
man/RangeRichness.Rd
man/lemurs.Rd
man/SpGeoCodH.Rd
man/WwfLoad.Rd
man/SpeciesGeoCoder.Rd
man/mdg_biomes.Rd
man/GeoClean.Rd
man/ReadPoints.Rd
man/Spgc2Biogeobears.Rd
man/MapGrid.Rd
man/CoExClass.Rd
man/MapRichness.Rd
man/lemurs_in.Rd
speciesgeocodeR documentation built on May 19, 2017, 10:46 p.m.

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