stats_eval: Statistics of environmental conditions in M and for...

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

Statistics of environmental conditions in M and for occurrences (one variable)

Description

stats_eval helps in creating tables of descriptive statistics of environmental conditions in accessible areas (M) and occurrence records for one environmental variable at a time.

Usage

stats_eval(stats = c("median", "range"), Ms, occurrences, species,
           longitude, latitude, variable, percentage_out = 0, verbose = TRUE)

Arguments

stats	(character) name or vector of names of functions to be applied to get basic statistics of environmental values.
Ms	a list of SpatVector objects representing the accessible area (M) for each species to be analyzed. The order of species represented by each object here must coincide with the one in occurrences. See details.
occurrences	a list of data.frames of occurrence records for all species. The order of species represented by each data.frame must coincide with the one in Ms. See details.
species	(character) name of the column in occurrence data.frames that contains the name of the species.
longitude	(character) name of the column in occurrence files containing values of longitude.
latitude	(character) name of the column in occurrence files containing values of latitude.
variable	a single SpatRaster layer of an environmental variable of interest. See details.
percentage_out	(numeric) percentage of extreme environmental data in M to be excluded in bin creation for further analyses. See details. Default = 0.
verbose	(logical) whether messages should be printed. Default = TRUE.

Details

Coordinates in occurrences, SpatVector objects in Ms, and SpatRaster in variable must coincide in the geographic projection in which they are represented. WGS84 with no planar projection is recommended.

Accessible area (M) is understood as the geographic area that has been accessible for a species for relevant periods of time. Defining M is usually a hard task, but also a very important one, because it allows identifying uncertainties about the ability of a species to maintain populations in certain environmental conditions. For further details on this topic, see Barve et al. (2011) doi:10.1016/j.ecolmodel.2011.02.011 and Machado-Stredel et al. (2021) doi:10.21425/F5FBG48814.

The percentage to be defined in percentage_out excludes a percentage of extreme environmental values to prevent from considering extremely rare environmental values in the accessible area for the species (M). Being too rare, these values may have never been explored by the species; therefore, including them in the process of preparation of the table of characters (bin table) is risky.

Value

A list containing tables with statistics of the values in variable, for the species M and occurrences.

Examples

# example data
## list of species records
data("occ_list", package = "nichevol")

## list of species accessible areas
m_files <- list.files(system.file("extdata", package = "nichevol"),
                      pattern = "m\\d.gpkg", full.names = TRUE)

m_list <- lapply(m_files, terra::vect)

## raster variable
temp <- terra::rast(system.file("extdata", "temp.tif", package = "nichevol"))

# running stats
stat <- stats_eval(stats = c("mean", "sd", "median", "range", "quantile"),
                   Ms = m_list, occurrences = occ_list, species = "species",
                   longitude = "x", latitude = "y", variable = temp,
                   percentage_out = 0)

nichevol documentation built on March 31, 2023, 5:38 p.m.