ConR package



The ConR package aims at assisting the preliminary assessment of species conservation status based on the International Union for Conservation of Nature (IUCN) Red List Categories and Criteria. More specifically, it helps users to calculate the population metrics related to the IUCN criteria A, B, C and D and to assign one of the IUCN categories (i.e. EX, EW, CR, EN, VU, NT, LC, DD). It was developed speed up the assessment of hundreds to thousands of species at the same time.

The ideas behind this package, and its testing involved many people and institutes.

The package it not available anymore on CRAN because of the recent retirement of various packages (rgdal, rgeos). The new version is nevertheless available on github and will soon be available on CRAN.

To install the github version :

install.packages("devtools")
devtools::install_github("gdauby/ConR")

Install R, ConR and dependent packages

First step. Install R.

Loading ConR

Attach ConR package This should be done everytime you open an R session.

Help files Any function in R is documented by a help file which can be obtained by the following code:

?EOO.computing
?AOO.computing
?subpop.comp
?locations.comp
?criterion_A
?EOO.sensitivity

A mode detailed manual on how to use this package is available here.

A quick example

Occurrence data are given as a data.frame whose first three columns are, in this order, latitude, longitude and taxon name. Column names do not matter, but their positions do. The package ships a small example dataset:

data(dataset.ex)
MyData <- dataset.ex[!dataset.ex$tax %in% c("species_1", "species_2"), ]
MyData$tax <- as.character(MyData$tax)
str(MyData)
#> 'data.frame':    316 obs. of  3 variables:
#>  $ ddlat: num  0.75 3.57 1.18 3.24 4.09 ...
#>  $ ddlon: num  29.75 16.12 9.87 10.58 9.05 ...
#>  $ tax  : chr  "Psychotria minuta" "Psychotria minuta" "Psychotria minuta" "Psychotria minuta" ...

The extent of occurrence (EOO, in km2) is computed for every taxon at once:

EOO.computing(MyData, show_progress = FALSE)
#>                      tax     eoo issue_eoo
#> 1     Berlinia bruneelii 2646614        NA
#> 2     Oncocalamus mannii  660638        NA
#> 3 Platycoryne guingangae 3437198        NA
#> 4      Psychotria minuta  763732        NA

So is the area of occupancy (AOO, in km2), here on the 2 km grid recommended by IUCN:

AOO.computing(MyData, show_progress = FALSE)
#>                      tax aoo issue_aoo
#> 1     Berlinia bruneelii 404        NA
#> 2     Oncocalamus mannii 172        NA
#> 3 Platycoryne guingangae 148        NA
#> 4      Psychotria minuta  40        NA

And the number of subpopulations, using a 5 km circular buffer around each occurrence:

subpop.comp(MyData, resol_sub_pop = 5, show_progress = FALSE)
#>                      tax subpop
#> 1     Berlinia bruneelii     88
#> 2     Oncocalamus mannii     29
#> 3 Platycoryne guingangae     34
#> 4      Psychotria minuta     10

These metrics, along with the number of locations, feed the assessment functions criterion_A(), criterion_B(), criterion_C() and criterion_D(). See the manual linked above for the full workflow.

Funding

The development of this package was supported by:

  • the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 795114 (THREAT project)

  • CESAB (Centre for the Synthesis and Analysis of Biodiversity). Research program of the FRB (Foundation for Research on Biodiversity) under the RAINBIO project.

Citation

G. Dauby & R. A. F. de Lima (2023). ConR: Computation of Parameters Used in Preliminary Assessment of Species Conservation Status. R package (version 2.1).

See Also

Other R packages related to IUCN assessments: