speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

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.

Author
Alexander Zizka [aut, cre]
Date of publication
2015-10-18 01:20:59
Maintainer
Alexander Zizka <alexander.zizka@bioenv.gu.se>
License
GPL-3
Version
1.0-4

View on CRAN

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

Files in this package

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