GeoRarefaction_MultiTaxa: Calculates six geographic range measures at resampled a...

Description Usage Arguments Details Value Note See Also Examples

View source: R/GeoRarefaction_MultiTaxa.R

Description

Calculates six geographic range measures at resampled a number of time from specified sample sizes

Usage

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GeoRarefaction_MultiTaxa(nLocCut = 3, OccMatrix, TaxaStart, LongPos = 1,
  LatPos = 2, iter = 10, CellSize = 5, longBounds = c(-180, 180),
  latBounds = c(-90, 90), steps = c(1, 50, 40, 30, 20, 10, 5),
  replacePts = FALSE)

Arguments

nLocCut

- The minimum number of locations a taxon must be seen at to have geographic range measures calculated

OccMatrix

- A matrix where columns are taxon occurrences and also having at least longitude and latitude values

TaxaStart

- The column index value where taxon records start

LongPos

- The column index value of longitudinal coordinates in the OccMatrix

LatPos

- The column index value of latitudinal coordinates in the OccMatrix

iter

- The number of times a taxon's locations are resampled at each step size

CellSize

- The size of each cell in degree X degree

longBounds

- Array of longitudinal boundaries in decimal degrees

latBounds

- Array of latitudinal boundaries in decimal degrees

steps

- Array of the values representing the number of points to be subsampled for each taxon

replacePts

- A logical value indicating whether points are allowed to be sampled more than once during each subsampling iteration

Details

The nLocCut parameter is the minimum number of distinct geographic locations a taxon must be observed at to have geographic range measures calcualted, if below retruns NA. The steps parameter typically begins with a 1 representing that all points should be used in calculations but this is not required. The replacePts parameter must be set to TRUE if any of the steps require a greater number of points to be sampled than there are actual locations for a taxon, otherwise the function will fail.

Value

Returns a vector where each element is a taxon with a list of each geographic range measure as a separate matrix of values. Measures include minimum spanning tree distance, minimum convex hull area, maxmimum pairwise great circle distance, latitudinal range, longitudinal range, and number of degree X degree cells occupied.

Note

If PEE values are to be calculated as a next step the steps parameter needs to have a value of 1 as its first value

See Also

See the velociraptr package for details of the downloadPBDB() function

Examples

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## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
GeoRarefaction_MultiTaxa(nLocCut=20,OccMatrix=BivalveMatrix,TaxaStart=3,replacePts=TRUE)

## End(Not run)

GeoRange documentation built on June 20, 2017, 9:03 a.m.