mmm_ellipsoid: Mean, min, and max ellipsoids

In marlonecobos/ellipsenm: Ecological Niche's Characterizations Using Ellipsoids

Mean, min, and max ellipsoids

Description

mmm_ellipsoid helps in finding the mean, minimum, and maximum ellipsoids of a list of ellipsoid objects.

Usage

mmm_ellipsoid(ellipsoid_list)

Arguments

ellipsoid_list

list of ellipsoid objects created with the function ellipsoid_fit.

Details

Minimum and maximum ellipsoids are calculated based on the volumes of all elements in ellipsoid_list.

The mean ellipsoid is calculated by finsing the mean of all centroids and all covariance matrices of all elements in ellipsoid_list.

Examples

# reading data
occurrences <- read.csv(system.file("extdata", "occurrences.csv",
                                    package = "ellipsenm"))

# raster layers of environmental data
vars <- raster::stack(list.files(system.file("extdata", package = "ellipsenm"),
                                 pattern = "bio", full.names = TRUE))

# getting values of variables in data
occurrences1 <- cbind(occurrences[, 2:3], raster::extract(vars, occurrences[, 2:3]))

# subsampling data for construction of multiple ellipsoids
subsamples <- data_subsample(data = occurrences1, replicates = 10,
                             replicate_type = "bootstrap")

# fitting ellipsoids for the 10 subsamples
ellipsoids <- lapply(subsamples, function (x) {
  ellipsoid_fit(data = x, longitude = "longitude",
                latitude = "latitude", method = "mve1",
                level = 99)
})
length(ellipsoids)
names(ellipsoids) <- paste0("replicate_", 1:10)

class(ellipsoids$replicate_1)

# mean, minumum, and maximum ellipsoids
mmm_ellips <- mmm_ellipsoid(ellipsoid_list = ellipsoids)

length(mmm_ellips)
names(mmm_ellips)
class(mmm_ellips$mean_ellipsoid)

marlonecobos/ellipsenm documentation built on Oct. 18, 2023, 8:09 a.m.