Package: epm 1.1.2

Pascal Title

epm: EcoPhyloMapper

Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.

Authors:Pascal Title [aut, cre], Donald Swiderski [aut], Miriam Zelditch [aut]

epm_1.1.2.tar.gz
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epm.pdf |epm.html✨
epm/json (API)

# Install 'epm' in R:
install.packages('epm', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ptitle/epm/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

4.74 score 12 stars 13 scripts 417 downloads 36 exports 21 dependencies

Last updated 5 months agofrom:e44d4f6a94. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-win-x86_64OKNov 15 2024
R-4.5-linux-x86_64OKNov 15 2024
R-4.4-win-x86_64OKNov 15 2024
R-4.4-mac-x86_64OKNov 15 2024
R-4.4-mac-aarch64OKNov 15 2024
R-4.3-win-x86_64OKNov 15 2024
R-4.3-mac-x86_64OKNov 15 2024
R-4.3-mac-aarch64OKNov 15 2024

Exports:addLegendaddPhyloaddTraitsbetadiv_disparitybetadiv_phylogeneticbetadiv_taxonomiccalcMeanShapecoordsFromEpmGridcreateEPMgridcustomBetaDivcustomGridMetricdropSpeciesDRstatepmToPhyloCommexpandSpeciesCellListextractFromEpmGridfaithPDgenerateOccurrenceMatrixgetExtentOfListgetMultiMapRampgetSpPartialDisparitiesgridMetricsidentify.epmGridinteractiveExtentplot.epmGridplotDispersionFieldplotSpRangerasterToGridread.epmGridreduceToCommonTaxasingleSpCellIndexspCountIndexsummarizeEpmGridListtableFromEpmGridwrite.epmGridwriteEpmSpatial

Dependencies:apeclassclassIntDBIdigeste1071KernSmoothlatticemagrittrMASSnlmepbapplyproxyRcppRcppProgresss2sfterraunitsviridisLitewk

Readme and manuals

Help Manual

Help pageTopics
addLegendaddLegend
addPhyloaddPhylo
addTraitsaddTraits
Map change in morphological disparitybetadiv_disparity
Map phylogenetic turnover in species communitiesbetadiv_phylogenetic
Map turnover in species communitiesbetadiv_taxonomic
Calculate mean shape per grid cellcalcMeanShape
Retrieve coordinates from epmGridcoordsFromEpmGrid
Create epmGrid objectcreateEPMgrid
Custom beta diversity metricscustomBetaDiv
Custom grid metricscustomGridMetric
Drop species from epmGriddropSpecies
Calculate the DR statisticDRstat
EcoPhyloMapper (epm)epm-package epm
Eco Phylo Mapper datasetsepm-example tamiasEPM tamiasPolyList tamiasTraits tamiasTree tamiasTreeSet
Convert epmGrid to community matrixepmToPhyloComm
Expand species listexpandSpeciesCellList
Extract from epmGridextractFromEpmGrid
Calculate Faith's Phylogenetic DiversityfaithPD
Convert epmGrid to community matrixgenerateOccurrenceMatrix
Get extent of listgetExtentOfList
Extract min and max for multiple epmGridsgetMultiMapRamp
Partial DisparitygetSpPartialDisparities
Grid MetricsgridMetrics
Interactively identify species in epmGrididentify.epmGrid
Interactively choose extentinteractiveExtent
Plot epmGridplot.epmGrid
Plot dispersion fieldsplotDispersionField
plot a single species' rangeplotSpRange
Convert raster to sf gridrasterToGrid
Read a epmGrid objectread.epmGrid
Subset epmGrid to shared taxareduceToCommonTaxa
Identify single-species cellssingleSpCellIndex
Identify cells that have a certain number of taxaspCountIndex
Summarize lists of epmGrid objectssummarizeEpmGridList
epmGrid summarysummary.epmGrid
Data table from epmGridtableFromEpmGrid
Save epmGrid objectwrite.epmGrid
Write epmGrid Spatial Object to DiskwriteEpmSpatial