Retrieves the threatened plant species database for Peru. This function provides controlled access to the internal datasets used by the package.
Usage
get_threatened_database(type = c("original", "updated"))Note
This function is primarily for advanced users who need direct access
to the database structure. For most use cases, use the higher-level
functions: is_threatened_peru or is_ds043_2006_ag.
Database Structure
**Original Database** (type = "original"):
~777 species as listed in DS 043-2006-AG
Supports quaternomial names (Rank 4)
Includes both accepted names and synonyms
Columns: scientific_name, genus, species, tag, infraspecies, tag_2, infraspecies_2, threat_category, accepted_name_author, taxonomic_status, accepted_name, family, protected_ds_043
**Updated Database** (type = "updated"):
Updated nomenclature using WCVP and POWO
Supports trinomial names (Rank 3 maximum)
Only accepted names (synonyms resolved)
Columns: scientific_name, genus, species, tag_acc, infraspecies, threat_category, accepted_name_author, taxonomic_status, accepted_name, family, protected_ds_043
Legal Context
Data based on Supreme Decree DS 043-2006-AG, Ministry of Agriculture, Peru (July 13, 2006), which establishes the official list of threatened wild flora species in Peru.
See also
is_threatened_peru to check threat status of species
is_ds043_2006_ag to check DS 043 protection status
Examples
# \donttest{
# Get original database
db_original <- get_threatened_database(type = "original")
str(db_original)
#> tibble [776 × 13] (S3: tbl_df/tbl/data.frame)
#> $ scientific_name : chr [1:776] "Aphelandra cuscoensis" "Aphelandra formosa" "Aphelandra wurdackii" "Tetramerium sagasteguianum" ...
#> $ author : chr [1:776] "Wasshausen" "(Humboldt & Bonpland) Ness" "Wassh" "T.F Daniel" ...
#> $ family : chr [1:776] "Acanthaceae" "Acanthaceae" "Acanthaceae" "Acanthaceae" ...
#> $ tag : chr [1:776] NA NA NA NA ...
#> $ infraspecies_2 : chr [1:776] NA NA NA NA ...
#> $ accepted_name : chr [1:776] "Aphelandra cuscoensis" "Aphelandra formosa" "Aphelandra wurdackii" "Tetramerium sagasteguianum" ...
#> $ accepted_name_author: chr [1:776] "Wassh." "(Bonpl.) Nees" "Wassh." "T.F.Daniel" ...
#> $ accepted_family : chr [1:776] "Acanthaceae" "Acanthaceae" "Acanthaceae" "Acanthaceae" ...
#> $ taxonomic_status : chr [1:776] "Accepted" "Accepted" "Accepted" "Accepted" ...
#> $ threat_category : chr [1:776] "CR" "CR" "CR" "CR" ...
#> $ genus : chr [1:776] "APHELANDRA" "APHELANDRA" "APHELANDRA" "TETRAMERIUM" ...
#> $ species : chr [1:776] "CUSCOENSIS" "FORMOSA" "WURDACKII" "SAGASTEGUIANUM" ...
#> $ infraspecies : chr [1:776] NA NA NA NA ...
nrow(db_original)
#> [1] 776
# Get updated database
db_updated <- get_threatened_database(type = "updated")
str(db_updated)
#> tibble [179 × 12] (S3: tbl_df/tbl/data.frame)
#> $ scientific_name : chr [1:179] "Pucara leucantha" "Ceroxylon weberbaueri" "Dyssodia lopez-mirandae" "Senecio mollendoensis" ...
#> $ author : chr [1:179] "Ravenna" "Burret" "Cabrera" "Cabrera" ...
#> $ family : chr [1:179] "Amaryllidaceae" "Arecaceae" "Asteraceae" "Asteraceae" ...
#> $ accepted_name : chr [1:179] "Stenomesson leucanthum" "Ceroxylon pityrophyllum" "Schizotrichia lopez-mirandae" "Lomanthus mollendoensis" ...
#> $ accepted_name_author: chr [1:179] "(Ravenna) Meerow & van der Werff" "(Mart.) Mart. ex H.Wendl." "(Cabrera) Molinari" "(Cabrera) B.Nord." ...
#> $ accepted_family : chr [1:179] "Amaryllidaceae" "Arecaceae" "Asteraceae" "Asteraceae" ...
#> $ taxonomic_status : chr [1:179] "Synonym" "Synonym" "Synonym" "Synonym" ...
#> $ threat_category : chr [1:179] "CR" "CR" "CR" "CR" ...
#> $ genus : chr [1:179] "STENOMESSON" "CEROXYLON" "SCHIZOTRICHIA" "LOMANTHUS" ...
#> $ species : chr [1:179] "LEUCANTHUM" "PITYROPHYLLUM" "LOPEZ-MIRANDAE" "MOLLENDOENSIS" ...
#> $ tag_acc : chr [1:179] NA NA NA NA ...
#> $ infraspecies : chr [1:179] NA NA NA NA ...
# Compare number of species
n_original <- nrow(db_original)
n_updated <- nrow(db_updated)
cat("Original:", n_original, "| Updated:", n_updated, "\n")
#> Original: 776 | Updated: 179
# Count by threat category
table(db_original$threat_category)
#>
#> CR EN NT VU
#> 193 73 119 391
# Find critically endangered orchids
orchids <- db_original[db_original$family == "ORCHIDACEAE" &
db_original$threat_category == "CR", ]
head(orchids$scientific_name)
#> character(0)
# }