summarizeEpmGridList {epm}

Summarize lists of epmGrid objects

Description

If a diversity metric was calculated for an epmGrid object that contained a phylogenetic distribution, then a list of resulting epmGrid objects was returned. This function will take that list, and apply a summary statistic, returning a single epmGrid object. If the input list is from betadiv_phylogenetic, then that list of sf or SpatRaster objects can also be summarized with this function.

Usage

summarizeEpmGridList(x, fun = mean)

Arguments

x

a list of objects of class epmGrid or sf or SpatRaster.

fun

a function to apply to grid cells across the list x.

Details

It is assumed that across the objects in list x, the only difference is the values for the grid cells.

Value

a single object of class epmGrid or sf or SpatRaster.

Author(s)

Pascal Title

Examples

tamiasEPM <- addPhylo(tamiasEPM, tamiasTreeSet)
tamiasEPM <- addTraits(tamiasEPM, tamiasTraits)

x <- gridMetrics(tamiasEPM, metric='meanPatristicNN')
z <- summarizeEpmGridList(x, fun = var)

# using a custom function
f <- function(y) sum(y) / length(y)

z <- summarizeEpmGridList(x, fun = f)

# works with square grid epmGrids too
tamiasEPM2 <- createEPMgrid(tamiasPolyList, resolution = 50000, 
	cellType = 'square', method = 'centroid')
tamiasEPM2 <- addPhylo(tamiasEPM2, tamiasTreeSet)
tamiasEPM2 <- addTraits(tamiasEPM2, tamiasTraits)

x <- gridMetrics(tamiasEPM2, metric='meanPatristicNN')

z <- summarizeEpmGridList(x, fun = median)


# With phylogenetic distribution

tamiasEPM <- addPhylo(tamiasEPM, tamiasTreeSet, replace = TRUE)
beta_phylo_turnover <- betadiv_phylogenetic(tamiasEPM, radius = 70000,
	component = 'turnover')

z <- summarizeEpmGridList(beta_phylo_turnover)

tamiasEPM2 <- createEPMgrid(tamiasPolyList, resolution = 50000,
	cellType = 'square', method = 'centroid')
tamiasEPM2 <- addPhylo(tamiasEPM2, tamiasTreeSet)

beta_phylo_turnover <- betadiv_phylogenetic(tamiasEPM2, radius = 70000,
		component = 'turnover')

z <- summarizeEpmGridList(beta_phylo_turnover, fun = median)