pets: Calculate the Potential Extinction upon Time Series (PETS)...

In leondap/pets: Potential Extinction upon Time Series (PETS)

Calculate the Potential Extinction upon Time Series (PETS) index.

Description

The PETS index calculate the completeness of time series for a given community based on occurrence data. Incomplete time series for recent year can be due to local extinction and/or lack of knowledge.

Usage

pets<-function(taxa, time, obs_type=NULL, fauna=NULL, plot=T, colours=c("red","green","blue","orange","purple"),
persistence="palegreen", absence="pink", end=NULL, firsty=NULL)

Arguments

taxa	A vector indicating the species membership of each record.
time	A vector indicating the year of collection of each record
obs_type	An optional vector indicating the type of observation (e.g. collection, citizen science etc)
fauna	An optional vector indicating the reference species list to be matched with the "taxa" vector.
plot	Logical, if TRUE the plot is returned.
colours	A list of colours to be attributed to the different categories of obs_type.
persistence	The colour to be attributed to the persistence segment in the plot.
end	The last year for the calculation of the PETS index, if NULL the last year in the year vector is used.
firsty	The first year to be imposed in the graph, if NULL the first year of record is used.

Details

The difference between the first and last year of existing records is considered as the persistence of a species in a given area while time since the last observation (absence) is considered as continuos measure for potential extinction. The PETS algorithm measure which is the overall fraction in a community of the potential extinction (absence) against the total time since the first observation (persistence+absence) on the entire community.

Value

extinctionP	The value of the PETS index.
table	The table containing the list of species together with their first and last observations and with the fraction the species is unrecorded compared to time passed since the first record.

Author(s)

Leonardo Dapporto

References

Labadessa, R., Cagnetta, G., Desaphy, J. F., Bonifacino, M., Dodaro, G., Festa, D., Monterastelli, E., Papa, V., E., Zollo, L., Balletto, E., Dapporto, L. (2021). Using occurrence data to evaluate extinction reveals a strong resilience of butterflies in a National Park of Southern Europe (Alta Murgia National Park). Journal of Insect Biodiversity, 28(1), 1-12.

Examples

# Inspect the example dataset
head(gransasso)

# Run the simplest analysis with only species and years
pets_run<-pets(gransasso$scientificName,gransasso$year)
pets_run

# Impose the last year of sampling (e.g. end=2021) and visualise different kinds of observations by including a obs_type vector.

pets_run2<-pets(gransasso$scientificName,gransasso$year, obs_type=gransasso$basisOfRecord, end=2021)

leondap/pets documentation built on Oct. 12, 2024, 8:55 p.m.