Find MRCA for data cube and call function to calculate PD metrics

This function determines the MRCA of all species in the datacube and calls the function(s) to calculate PD metrics

Usage

get_pd_cube(mcube, tree, timegroup = NULL, metric = "faith")

Arguments

mcube: An occurrence data cube with matched names appended, product of function taxonmatch()
tree: A phylogenetic tree with branch lengths
timegroup: Optional, an integer which represents the number of years over which occurrences need to be aggregated and the PD value calculated
metric: Name of the PD metric to be calculated

Value

Calculated PD value

Examples

library(dplyr)
ex_data <- retrieve_example_data()
#> Reading layer `EEA_1km_HK' from data source 
#>   `/home/runner/work/_temp/Library/pdindicatoR/extdata/EEA_1km_NPHogeKempen/EEA_1km_HK.shp' 
#>   using driver `ESRI Shapefile'
#> Simple feature collection with 4108 features and 7 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 3974000 ymin: 3068000 xmax: 4051000 ymax: 3125000
#> Projected CRS: ETRS89-extended / LAEA Europe
#> Reading layer `protected_areas_NPHogeKempen' from data source 
#>   `/home/runner/work/_temp/Library/pdindicatoR/extdata/PA_NPHogeKempen/protected_areas_NPHogeKempen.shp' 
#>   using driver `ESRI Shapefile'
#> Simple feature collection with 32 features and 6 fields
#> Geometry type: MULTIPOLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 3948585 ymin: 3065773 xmax: 4049889 ymax: 3141858
#> Projected CRS: ETRS89-extended / LAEA Europe
mcube <- append_ott_id(ex_data$tree, ex_data$cube, ex_data$matched_nona)
mcube <- dplyr::filter(mcube, !is.na(ott_id))
PD_cube <- get_pd_cube(mcube, ex_data$tree, metric="faith")