Occurrence density grid

calculates the part of environmental space more densely populated by species & the availability of environmental conditions in the background

Usage

espace_occDens(sp.name1, sp.name2, pca, logger = NULL)

Arguments

sp.name1

character name of species 1 to be analyzed.

sp.name2

character name of species 2 to be analyzed.

pca

pca output of pca component ( in list format)

logger

stores all notification messages to be displayed in the Log Window of Wallace GUI. Insert the logger reactive list here for running in shiny, otherwise leave the default NULL.

Value

Returns a list of 2 lists (one for each species). Each list is an ecospat niche object that contains 10 species specific slots with information outputed by ecospat::grid.clim.dyn. z.uncor is the density of occurrence of the species and z.cor the occupancy of the environment by the species. It has the input parameters as individual slots.

Details

This function implements a density estimation for each region in the environmental space (gridded at 100*100 pixels). Then an occurrence density is estimated using a kernel density approach. The density of environmental conditions in the background is calculated in the same way.

See also

espace_pca espace_nicheOv ecospat.grid.clim.dyn

Author

Jamie Kass <jamie.m.kass@gmail.com >

Olivier Broennimann <olivier.broennimann@unil.ch>

Examples

if (FALSE) { # \dontrun{
sp.name1 <- "Bassaricyon_alleni"
sp.name2 <- "Bassaricyon_neblina"
envs <- envs_userEnvs(rasPath = list.files(system.file("extdata/wc",
                                           package = "wallace"),
                      pattern = ".tif$", full.names = TRUE),
                      rasName = list.files(system.file("extdata/wc",
                                           package = "wallace"),
                      pattern = ".tif$", full.names = FALSE))

occs.z1 <- read.csv(system.file("extdata/Bassaricyon_alleni.csv",
                    package = "wallace"))
occs.z2 <- read.csv(system.file("extdata/Bassaricyon_neblina.csv",
                    package = "wallace"))

bgPts.z1 <- read.csv(system.file("extdata/Bassaricyon_alleni_bgPoints.csv",
                     package = "wallace"))
bgPts.z2 <- read.csv(system.file("extdata/Bassaricyon_neblina_bgPoints.csv",
                     package = "wallace"))

occsExt.z1 <- raster::extract(envs, occs.z1[, c("longitude", "latitude")])
occsExt.z2 <- raster::extract(envs, occs.z2[, c("longitude", "latitude")])
bgExt.z1 <- raster::extract(envs, bgPts.z1[, c("longitude", "latitude")])
bgExt.z2 <- raster::extract(envs, bgPts.z2[, c("longitude", "latitude")])
pcaZ <- espace_pca(sp.name1, sp.name2,
                   occsExt.z1, occsExt.z2,
                   bgExt.z1, bgExt.z2)
occDens <- espace_occDens(sp.name1, sp.name2, pcaZ)
} # }