IUCNest: Convert Range Sizes to IUCN Assessment

In azizka/speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

Convert Range Sizes to IUCN Assessment

Description

The function converts range sizes (Area of Occupancy and Extent of Occurrence), as calculated by CalcRange to conservation assessments based on IUCN criterion B and extinction probabilities following Mooers et al. (2008).

Usage

IUCNest(x, value = "all",
        NT.thresh = c(30000, 3000), VU.thresh = c(20000, 2000), 
        EN.thresh = c(5000, 500), CR.thresh = c(100, 10))

Arguments

x	an object of the class range.sizes, as produced by CalcRange.
value	a character string. Defining the output value, see details. One of "all", "AOO", "EOO", "IUCN50", "IUCN100", "IUCN500" Default = "all".
NT.thresh	numeric. Thresholds for categorization to near threatened, in the form (EOO, AOO). Defaults from IUCN Standards and Petitions (Subcommittee 2014).
VU.thresh	numeric. Thresholds for categorization to vulnerable, in the form (EOO, AOO). Defaults from IUCN Standards and Petitions (Subcommittee 2014).
EN.thresh	numeric. Thresholds for categorization to endangered, in the form (EOO, AOO). Defaults from IUCN Standards and Petitions Subcommittee (2014).
CR.thresh	numeric. Thresholds for categorization to critically endangered, in the form (EOO, AOO). Defaults from IUCN Standards and Petitions Subcommittee (2014).

Details

The value argument defines the type of assessment in the output: “AOO” = assessment based on the AOO, “EOO” = assessment based on the EOO, “both” = assessment based on AOO and EOO, “IUCN50” = a extra column where the assessment is converted into a probability of extinction within the next 50 years, “IUCN100” = a extra column where the assessment is converted into a probability of extinction within the next 100 years, “IUCN500” = a extra column where the assessment is converted into a probability of extinction within the next 500 years. See Mooers et al. 2008 for reference on the conversion.

Value

a data.frame, the number of columns depend on the value argument (see details).

Note

See https://github.com/azizka/speciesgeocodeR/wiki for more details and tutorials.

References

IUCN Standards and Petitions Subcommittee (2014) Guidelines for using the IUCN Red List categories and criteria. Version 11. Prepared by the Standards and Petitions Subcommittee. Downloadable from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf.

Mooers, A.O., Faith D.P. & Maddison W. P. (2008) Converting Endangered Species Categories to Probabilities if Extinction for Phylogenetic Conservation Prioritization. PLOSone, 3(11)

Examples

occ.exmpl<- data.frame(species = sample(letters, size = 250, replace = TRUE),
                       decimallongitude = runif(n = 250, min = 42, max = 51),
                       decimallatitude = runif(n = 250, min = -26, max = -11))

rang <- CalcRange(occ.exmpl, method = 'pseudospherical', terrestrial = FALSE)
IUCNest(rang)

azizka/speciesgeocodeR documentation built on Sept. 5, 2023, 3:45 a.m.