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LCr: An R package to generate minimal Least Concern Red List assessments

Lifecycle: experimental R-CMD-check License: MIT Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

Overview

Generate minimal documentation for species expected to be Least Concern (see IUCN Red List). Submit to the IUCN Red List via SIS Connect (registration needed)

Installation

Not yet on CRAN, but you can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("stevenpbachman/LCr")

Usage

Primary functions:

  1. get_name_keys check name status against taxonomic name backbones
  2. get_gbif_occs gather occurrence records from GBIF
  3. check_occs & clean_occs run occurrence quality checks and clean
  4. make_sis_occs generate the SIS point files
  5. make_sis_csvs generate SIS connect csv files
  6. make_zip make a zip file for SIS Connect imports

Note the following example is for plant species. For help on processing species in other kingdoms see the vignette Fungi workflow.

Example 

library(LCr)

# create a species list
sp <- data.frame(sp_col = c("Crabbea acaulis", "Crabbea nana"))

# check names against GBIF and WCVP name backbones 
sp_keys <- LCr::get_name_keys(df = sp, name_column = "sp_col")

# get the raw GBIF occs and native ranges from Plants of the World Online
sp_occs <-  LCr::get_gbif_occs(sp_keys)
native_ranges <- LCr::get_native_range(keys = sp_keys)

# run the occurrence quality checks and clean data
checked_occs <- LCr::check_occs(sp_occs$points, native_ranges, buffer = 2000) # check
flagged_occs <- checked_occs$checked_data # flag
flagged_sum <- checked_occs$summary # summarise
cleaned_result <- LCr::clean_occs(flagged_occs) # clean

# define parameters for output files i.e. the person who is assessing the species
first_name <- "Steven"
second_name <- "Bachman"
email = "s.bachman@kew.org"
institution = "Royal Botanic Gardens, Kew"

# generate the point file
sis_point_file <- LCr::make_sis_occs(cleaned_result$clean_occs,
                                     first_name = first_name,
                                     second_name = second_name,
                                     institution = institution)

# generate output csv files
lc_sis_files <- LCr::make_sis_csvs(unique_id = sp_keys$GBIF_usageKey,
                                   wcvp_ipni_id = sp_keys$wcvp_ipni_id,
                                   first_name = "Steven",
                                   second_name = "Bachman",
                                   email = "s.bachman@kew.org",
                                   institution = "Royal Botanic Gardens, Kew",
                                   family = sp_keys$GBIF_family,
                                   genus = sp_keys$GBIF_genus,
                                   species = sp_keys$GBIF_species,
                                   gbif_ref = sp_occs,
                                   powo_ref = TRUE, 
                                   taxonomicAuthority = sp_keys$GBIF_authorship,
                                   occs = sis_point_file,
                                   kingdom = "plantae",
                                   native_ranges = native_ranges
)

# make the ZIP file to send to IUCN SIS Connect
make_zip(lc_sis_files)

Citation

To cite LCr please run:

citation("LCr")