sampleIndicator {ecochange}

Sample Biodiversity indicator

Description

This function divides into fixed-size grids each of the scenes of a stack of ecosystem-spatial data and samples a biodiversity indicator by every grid. To compute biodiversity indicators at the class and landscape levels, see gaugeIndicator

Usage

sampleIndicator(ps = NULL, 
    ..., metric = "condent", 
    classes = 5, min = 1, 
    max = 100, side, 
    smp_lsm = list(level = "landscape"), 
    mc.cores = round(detectCores() * 
        0.6, 0))

Arguments

ps

SpatialPolygonsDataFrame or RasterStack. Polygon geometry used to produce ecosystem-change maps via the implementation of echanges or the stack of ecosystem-change maps.

...

If ps is a polygon then additional arguments in echanges or rsp2ebv.

metric

character. The name of an indicator other than ecosystem extent. This can be cohesion ('cohesion'), conditional entropy ('condent'), perimeter-area fractal dimension ('pafrac'), among others, see package list_lsm. Default 'condent'.

classes

numeric; or NULL. Number of evenly spaced classes used to reclassify the layers. Default 5. If NULL then the layers are not reclassified.

min

numeric. If classes != NULL then minimum cell value in the layers. Default 1

max

numeric. If classes != NULL then maximum cell value in the layers. Default 100

side

numeric. Side of the sampling grid (m). If missing the function tries to find a grid size the samples at least a grid with a non-NA value of the indicator.

smp_lsm

List. Additional arguments in sample_lsm

mc.cores

numeric. The number of cores. Default uses 60 percent of the cores.

Value

Class echanges

Author(s)

Wilson Lara Henao <[e-mail]> [aut, cre], Victor Gutierrez-Velez [aut], Ivan Gonzalez [ctb], Maria C. Londono [ctb]

References

Hesselbarth, M. H., Sciaini, M., With, K. A., Wiegand, K., & Nowosad, J. (2019). landscapemetrics: an open source R tool to calculate landscape metrics. Ecography, 42(10), 1648-1657.

O'Connor, B., Secades, C., Penner, J., Sonnenschein, R., Skidmore, A., Burgess, N. D., & Hutton, J. M. (2015). Earth observation as a tool for tracking progress towards the Aichi Biodiversity Targets. Remote sensing in ecology and conservation, 1(1), 19-28.

Skidmore, A. K., & Pettorelli, N. (2015). Agree on biodiversity metrics to track from space: Ecologists and space agencies must forge a global monitoring strategy. Nature, 523(7561), 403-406.

Examples

## RasterBrick of structural Essential Biodiversity Variables
## covering the extent of a location in the northern Amazon basin
## (Colombia) is imported:
path. <- system.file('amazon.grd',package = 'ecochange')
amazon <- brick(path.)

## Changes in layers of tree-canopy cover (TC) in the 'amazon'
## brick are computed:
def <- echanges(amazon, eco = 'TC',
                change = 'lossyear',
                eco_range = c(1,80),
                get_unaffected = TRUE,
                binary_output = FALSE,
                mc.cores = 2)


plot.echanges(amazon)

## Function 'sampleIndicator' is implemented to sample a metric of
## conditional entropy (default):

    def_condent <- sampleIndicator(def, side = 400, mc.cores = 2)

plot.echanges(def_condent, cex = 1.5)