peruflorads43

Overview

Key Features

Intelligent Name Matching

Dual Database System

Installation

install.packages("peruflorads43")

# Using pak (recommended)pak::pak("PaulESantos/peruflorads43")# Or using remotesremotes::install_github("PaulESantos/peruflorads43")

Quick Start

Basic Usage

library(peruflorads43)# Simple vector of species namesspecies_list<- c("Cattleya maxima",# Orchid - Endangered"Polylepis incana",# Queñua tree - Vulnerable"Persea americana"# Avocado - Not threatened)# Check threat statustibble::tibble(splist=species_list)|>dplyr::mutate(ds43= is_threatened_peru(splist))#> # A tibble: 3 × 2#>   splist           ds43#>   <chr>            <chr>#> 1 Cattleya maxima  CR#> 2 Polylepis incana CR#> 3 Persea americana Not threatened

Detailed Matching Results

# Detailed results with matching metadataresults<- is_threatened_peru(species_list,return_details=TRUE)# View key columnsresults|>dplyr::select(Orig.Name,Matched.Name,Threat.Status,Match.Level)#> # A tibble: 3 × 4#>   Orig.Name        Matched.Name     Threat.Status  Match.Level#>   <chr>            <chr>            <chr>          <chr>#> 1 Cattleya maxima  Cattleya maxima  CR             Exact rank#> 2 Polylepis incana Polylepis incana CR             Exact rank#> 3 Persea americana ---              Not threatened No match

DS 043-2006-AG Validation

# Species with nomenclatural changesspecies<- c("Haageocereus acranthus subsp. olowinskianus",# Original name (2006)"Brassia ocanensis",# Updated name (was Ada)"Persea americana"# Not threatened)# Consolidated search across both databasestibble::tibble(species)|>dplyr::mutate(status= is_ds043_2006_ag(species))#> # A tibble: 3 × 2#>   species                                     status#>   <chr>                                       <chr>#> 1 Haageocereus acranthus subsp. olowinskianus VU (synonym)#> 2 Brassia ocanensis                           VU (updated name)#> 3 Persea americana                            Not threatened# Detailed reconciliationdetails<- is_ds043_2006_ag(species,return_details=TRUE)details|>dplyr::select(Input.Name,Consolidated.Status,Final.Source,Nomenclature.Status)#> # A tibble: 3 × 4#>   Input.Name                Consolidated.Status Final.Source Nomenclature.Status#>   <chr>                     <chr>               <chr>        <chr>#> 1 Haageocereus acranthus s… VU (synonym)        DS 043-2006… Synonym (name upda…#> 2 Brassia ocanensis         VU (updated name)   DS 043-2006… Name updated since…#> 3 Persea americana          Not threatened      Not in DS 0… Not applicable

Handling Fuzzy Matches

# Species with typosspecies_fuzzy<- c("Catleya maxima",# Missing 't' in Cattleya"Polylepys incana"# Wrong spelling of Polylepis)results<- is_threatened_peru(species_fuzzy,return_details=TRUE)# Check fuzzy matching qualityresults|>dplyr::select(Orig.Name,Matched.Name,Threat.Status,fuzzy_genus_dist,fuzzy_match_genus)#> # A tibble: 2 × 5#>   Orig.Name        Matched.Name Threat.Status fuzzy_genus_dist fuzzy_match_genus#>   <chr>            <chr>        <chr>                    <dbl> <lgl>#> 1 Catleya maxima   Cattleya ma… CR                           1 TRUE#> 2 Polylepys incana Polylepis i… CR                           1 TRUE

Reviewing Ambiguous Matches

# Get ambiguous matches for quality controlambiguous<- get_ambiguous_matches(results,type="all")#> No ambiguous all matches found.# Save for manual curationif (!is.null(ambiguous)) {  get_ambiguous_matches(results,type="genus",save_to_file=TRUE  )}

Database Structure

Original Database (DS 043-2006-AG 2006)

# Access original nomenclaturedb_original<- get_threatened_database(type="original")# Summary statisticsget_database_summary("original")#> # A tibble: 1 × 10#>   Database Total_Species    CR    EN    VU    NT Families Genera#>   <chr>            <int> <int> <int> <int> <int>    <int>  <int>#> 1 original           776   193    73   391   119       80    290#> # ℹ 2 more variables: Has_Infraspecies <int>, Max_Rank <dbl>

Updated Database (Current Nomenclature)

# Access updated nomenclaturedb_updated<- get_threatened_database(type="updated")# Compare with originalget_database_summary("both")#> # A tibble: 2 × 10#>   Database        Total_Species    CR    EN    VU    NT Families Genera#>   <chr>                   <int> <int> <int> <int> <int>    <int>  <int>#> 1 Original (2006)           776   193    73   391   119       80    290#> 2 Updated                   179    44    16    93    26       30     85#> # ℹ 2 more variables: Has_Infraspecies <int>, Max_Rank <dbl>

Advanced Features

Comparison Between Databases

# Side-by-side comparisoncomparison<- comparison_table_ds043(species)comparison|>dplyr::select(input_species,status_original,status_updated,nomenclature_status,protected_by_ds_043)#> # A tibble: 3 × 5#>   input_species               status_original status_updated nomenclature_status#>   <chr>                       <chr>           <chr>          <chr>#> 1 Haageocereus acranthus sub… VU              Not threatened Synonym (name upda…#> 2 Brassia ocanensis           Not threatened  VU             Name updated since…#> 3 Persea americana            Not threatened  Not threatened Not applicable#> # ℹ 1 more variable: protected_by_ds_043 <chr>

Legal Framework

IUCN Threat Categories

Use Cases

1. Environmental Assessment

# Species list from field surveyfield_species<- c("Achyrocline saturejoides","Bouteloua simplex","Jarava ichu","Cenchrus clandestinus","Grindelia boliviana","Tagetes filifolia","Bidens pilosa","Cumulopuntia boliviana","Ageratina sternbergiana","Roca","Nassella inconspicua","Dalea sp","Baccharis tricuneata","Lepechinia meyenii","Erodium cicutarium","Suelo","Ephedra rupestris","Achyrocline saturejoides","Ageratina sternbergiana","Astragalus garbancillo","Baccharis tola","Bidens pilosa","Bouteloua simplex","Cenchrus clandestinus","Cumulopuntia boliviana","Jarava ichu")tibble::tibble(field_species)|>dplyr::mutate(status= is_ds043_2006_ag(field_species))|>dplyr::filter(status!="Not threatened")#> The species list (splist) should only include binomial names. The following names were submitted at the genus level: 'ROCA', 'SUELO'#> The species list (splist) should only include binomial names. The following names were submitted at the genus level: 'ROCA', 'SUELO'#> # A tibble: 1 × 2#>   field_species     status#>   <chr>             <chr>#> 1 Ephedra rupestris CR# Check DS 043 protection statusresults<- is_ds043_2006_ag(field_species,return_details=TRUE)#> The species list (splist) should only include binomial names. The following names were submitted at the genus level: 'ROCA', 'SUELO'#> The species list (splist) should only include binomial names. The following names were submitted at the genus level: 'ROCA', 'SUELO'results#> # A tibble: 26 × 14#>    Input.Name        Consolidated.Name Consolidated.Status Consolidated.Category#>    <chr>             <chr>             <chr>               <chr>#>  1 Achyrocline satu… ---               Not threatened      <NA>#>  2 Bouteloua simplex ---               Not threatened      <NA>#>  3 Jarava ichu       ---               Not threatened      <NA>#>  4 Cenchrus clandes… ---               Not threatened      <NA>#>  5 Grindelia bolivi… ---               Not threatened      <NA>#>  6 Tagetes filifolia ---               Not threatened      <NA>#>  7 Bidens pilosa     ---               Not threatened      <NA>#>  8 Cumulopuntia bol… ---               Not threatened      <NA>#>  9 Ageratina sternb… ---               Not threatened      <NA>#> 10 Roca              ---               Not threatened      <NA>#> # ℹ 16 more rows#> # ℹ 10 more variables: Protected.DS043 <lgl>, Is.Synonym <lgl>,#> #   Accepted.Name <chr>, Final.Source <chr>, Match.Scenario <chr>,#> #   Nomenclature.Status <chr>, Original.Matched <chr>, Original.Status <chr>,#> #   Updated.Matched <chr>, Updated.Status <chr># Generate reportresults|>dplyr::filter(Protected.DS043==TRUE)|>dplyr::select(Input.Name,Consolidated.Status,Final.Source)#> # A tibble: 1 × 3#>   Input.Name        Consolidated.Status Final.Source#>   <chr>             <chr>               <chr>#> 1 Ephedra rupestris CR                  DS 043-2006-AG (original)

2. Research and Monitoring

# Historical species recordshistorical_names<- c("Lycaste locusta",# Old name"Ida locusta"# Current accepted name)# Check nomenclatural updatesnomenclature_check<- is_ds043_2006_ag(historical_names,return_details=TRUE)# Identify synonymsnomenclature_check|>dplyr::filter(Is.Synonym==TRUE)|>dplyr::select(Input.Name,Accepted.Name,Nomenclature.Status)#> # A tibble: 1 × 3#>   Input.Name      Accepted.Name Nomenclature.Status#>   <chr>           <chr>         <chr>#> 1 Lycaste locusta Ida locusta   Synonym (name updated)

Algorithm Details

Hierarchical Matching Pipeline

Rank Validation

# Example: User inputs trinomial, database has binomial# Input:  "Cattleya maxima var. alba" (Rank 3, doesn't exist)# Database: "Cattleya maxima" (Rank 2, exists)# Result: NO MATCH (correct) - prevents false positive

Performance Considerations

Duplicate Handling

# Input with duplicatesspecies_dup<- c("Cattleya maxima","Polylepis incana","Cattleya maxima"# Duplicate)results<- matching_threatenedperu(species_dup)results#>   sorter        Orig.Name     Matched.Name Threat.Status Author#> 1      1  Cattleya maxima  Cattleya maxima            CR#> 2      2 Polylepis incana Polylepis incana            CR#> 3      3  Cattleya maxima  Cattleya maxima            CR#>   accepted_name_author Matched.Rank Comp.Rank Match.Level Orig.Genus#> 1               Lindl.            2      TRUE  Exact rank   CATTLEYA#> 2                Kunth            2      TRUE  Exact rank  POLYLEPIS#> 3               Lindl.            2      TRUE  Exact rank   CATTLEYA#>   Orig.Species Orig.Infraspecies Orig.Infraspecies_2 Rank Orig.Infra.Rank#> 1       MAXIMA              <NA>                <NA>    2            <NA>#> 2       INCANA              <NA>                <NA>    2            <NA>#> 3       MAXIMA              <NA>                <NA>    2            <NA>#>   Orig.Infra.Rank_2 matched direct_match Matched.Genus Matched.Species#> 1              <NA>    TRUE         TRUE      CATTLEYA          MAXIMA#> 2              <NA>    TRUE         TRUE     POLYLEPIS          INCANA#> 3              <NA>    TRUE         TRUE      CATTLEYA          MAXIMA#>   Matched.Infra.Rank Matched.Infraspecies Matched.Infra.Rank_2#> 1               <NA>                 <NA>                 <NA>#> 2               <NA>                 <NA>                 <NA>#> 3               <NA>                 <NA>                 <NA>#>   Matched.Infraspecies_2 genus_match fuzzy_match_genus fuzzy_genus_dist#> 1                   <NA>          NA                NA               NA#> 2                   <NA>          NA                NA               NA#> 3                   <NA>          NA                NA               NA#>   direct_match_species_within_genus suffix_match_species_within_genus#> 1                                NA                                NA#> 2                                NA                                NA#> 3                                NA                                NA#>   fuzzy_match_species_within_genus fuzzy_species_dist Matched.Rank.Calculated#> 1                               NA                 NA                       2#> 2                               NA                 NA                       2#> 3                               NA                 NA                       2#>   valid_rank direct_match_infra_rank fuzzy_match_infraspecies#> 1       TRUE                      NA                       NA#> 2       TRUE                      NA                       NA#> 3       TRUE                      NA                       NA#>   fuzzy_infraspecies_dist  tag infraspecies infraspecies_2 threat_category#> 1                      NA <NA>         <NA>           <NA>              CR#> 2                      NA <NA>         <NA>           <NA>              CR#> 3                      NA <NA>         <NA>           <NA>              CR

Citation

citation("peruflorads43")#> To cite peruflorads43 in publications use:#>#>   Santos-Andrade P.E. (2025). peruflorads43: Check Threatened Plant#>   Species Status Against Peru's DS 043-2006-AG#>#> A BibTeX entry for LaTeX users is#>#>   @Manual{,#>     title = {peruflorads43: Check Threatened Plant Species Status Against Peru's DS 043-2006-AG},#>     author = {Paul E. Santos Andrade},#>     year = {2025},#>     url = {https://github.com/PaulESantos/peruflorads43},#>   }