near.threatened: Identify Near Threatened Species

In gdauby/ConR: Computation of Parameters Used in Preliminary Assessment of Species Conservation Status

Identify Near Threatened Species

Description

Implementation of IUCN list of cases that qualify species as Near Threatened (NT) instead of Least Concerned (LC) or more generally "LC or NT" (the standard output string in ConR).

Usage

near.threatened(
  cats = NULL,
  EOO = NULL,
  AOO = NULL,
  decline = NULL,
  pop.reduction = NULL,
  pop.size = NULL,
  pop.size.low = NULL,
  locations = NULL,
  sever.frag = NULL,
  ext.fluct = NULL,
  subpop = NULL,
  subcriteria = NULL,
  many.more = 3,
  extra.case = TRUE
)

Arguments

cats	a character string containing the Red List categories.
EOO	numeric vector with species extent of occurrence - EOO (i.e. sub-criterion B1)
AOO	numeric vector with species area of occupancy - AOO (i.e. sub-criterion B2)
decline	string vector providing the status of the species continuing decline in EOO, AOO, habitat, locations or subpopulations or population size (i.e. condition 'b').
pop.reduction	numeric vector with the estimated percentage of population reduction in the last three generations.
pop.size	numeric vector with the mean estimate of population size in number of mature individuals.
pop.size.low	numeric vector with the lower bound of the confidence interval of the population size in number of mature individuals.
locations	numeric vector with the number of locations where the species occur (i.e. condition 'a')
sever.frag	numeric vector with the proportion AOO which is in patches that are separated from other patches by a large distance.
ext.fluct	numeric vector with the mean order of magnitude of the differences between population minima and maxima.
subpop	numeric vector with the number of sub-populations for the species
subcriteria	character string with the sub-criteria used to perform the assessments (e.g. "A1")
many.more	numeric value to numerically express what "many more" means.
extra.case	logical. Should the extra case to detected probable "LC" be used? Default to TRUE.

Details

This function automatically identify the Near Threatened (NT) category among the "LC or NT" general category. A species qualify as NT if it is close to qualifying for the Vulnerable category (IUCN, 2019).

The function try to translate the list of cases where NT applies and does not applies (IUCN 2019, pp 76-77). Not all the cases listed were translated here, particularly those based on uncertainties of the estimates. To perform this translation some interpretation, adaptation or generalization was carried out, namely:

• "Population has declined by an estimated 20 - 25% in the last three generations: pop. reduction between 20 and 30%;

• "Population has declined by an estimated 10%": pop. reduction >10%;

• "many more": by default we use triple to numerically express many more;

• "(...) has about 15,000/1,500 mature individuals": mature individuals between 10000 and 16000/1000 and 1600, respectively;

• "The population has more than 2,000 mature individuals": pop. size <2000 &

For many of the cases listed by IUCN (2019, pp 76 - 77), there is a minimum number of arguments that should be provided so that the NT criteria can be assigned. For instance, if only EOO and AOO is given no species will be classified as NT and the function will return "LC" for all "LC" or "LC or NT" provided as an input. On the other hand, if only pop.size species can be classified as "NT". Please see all the IUCN cases for more details on this (IUCN 2019, pp 76-77).

We added one extra case to the list of cases from IUCN (2019) where species should be classified as "LC" and not "NT". This case comes from an interpretation of the IUCN (2019) guidelines and it is unofficially used by the IUCN/SSC Global Tree Specialist Group as an indication of low probability of triggering a threatened or NT categories, if the species is not cited as threatened based on other criteria (e.g. uses and threats):

• EOO > 30000 km2 or AOO > 3000 km2, and number of locations > 30. This extra case can be excluded from the separation between "LC" and "NT" by setting the argument extra.case to FALSE.

Value

A vector of the same length as cats with NT separated from the LC category. If the category provided is different than "LC" or "LC or NT" the function returns the same category.

Author(s)

Renato A. Ferreira de Lima

References

IUCN 2019. Guidelines for Using the IUCN Red List Categories and Criteria. Version 14. Standards and Petitions Committee. Downloadable from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf.

Examples

cats <- c("LC", "LC or NT", "LC or NT", "LC")
EOO <- c(35000, 10000, 10000, NA)
AOO <- c(3200, 800, 800, 32)
decline <- c("Decreasing", "Decreasing", "Increasing", "Increasing")
pop.reduction <- c(23.1, 23.1, 11, 6)
pop.size <- c(25000, 12000, 12000, 1200)
locations <- c(75, 25, 25, 9)

## Example with different species metrics
near.threatened(cats = cats, EOO = EOO, AOO = AOO, decline = decline, 
pop.reduction = pop.reduction, pop.size = pop.size, locations = locations)

## Example with only EOO, AOO and number of locations (not enough metrics)
near.threatened(cats = cats, EOO = EOO, AOO = AOO)

gdauby/ConR documentation built on Jan. 30, 2024, 11:10 p.m.