Standardize Specimen Records

Overview

The barroso_std() function is the primary tool in the barRoso package for performing full data cleaning and standardization of biodiversity specimen records. It is designed to process raw data from herbaria, virtual repositories, and field collections, ensuring harmonized fields across taxonomic, geographic, and collector-related information.

Key Features

Normalize collector names and collection numbers
Standardize geographic fields like country, state, and locality
Harmonize taxonomic names including family, genus, and species
Clean and normalize type status
Optionally remove unvouchered or duplicate records
Support for multilingual column names (e.g., Portuguese, Spanish)

Usage

library(barRoso)

df <- read.csv("raw_herbarium_data.csv")

standardized_df <- barroso_std(df,
                               unvouchered = TRUE,
                               delunkcoll = FALSE,
                               flag_missid = TRUE,
                               flag_duplicates = TRUE,
                               rm_duplicates = FALSE,
                               colname_recordedBy = "recordedBy",
                               colname_recordNumber = "recordNumber",
                               colname_country = "country",
                               colname_stateProvince = "stateProvince",
                               colname_county = "county",
                               colname_municipality = "municipality",
                               colname_locality = "locality",
                               colname_collectionCode = "collectionCode",
                               colname_institutionCode = "institutionCode",
                               colname_typeStatus = "typeStatus",
                               colname_family = "family",
                               colname_genus = "genus",
                               colname_specificEpithet = "specificEpithet",
                               rm_original_column = TRUE)

Arguments

...: A data frame or list of data frames with raw biodiversity records
unvouchered: Remove unvouchered (non-herbarium) records
delunkcoll: Optionally delete records with unknown collectors
flag_duplicates, rm_duplicates: Detect and optionally remove duplicates
rm_original_column: Remove original (uncleaned) fields after standardization

Output

Returns a cleaned and fully standardized data frame ready for:

Reconciliation and deduplication
Taxonomic and biogeographic analysis
Herbarium label generation workflows

Notes

Uses dynamic regular expressions for name harmonization rather than static dictionaries
Optimized for scalability and flexible input schema
Recommended to run before calling downstream functions like barroso_flag_duplicates() or barroso_labels()

Example

cleaned_data <- barroso_std(df,
                            colname_country = "pais",
                            colname_stateProvince = "estado",
                            rm_duplicates = TRUE)

For a complete list of supported fields, refer to the function documentation with ?barroso_std.

--- title: "Standardize Specimen Records" format: html --- ## Overview The `barroso_std()` function is the primary tool in the `barRoso` package for performing full data cleaning and standardization of biodiversity specimen records. It is designed to process raw data from herbaria, virtual repositories, and field collections, ensuring harmonized fields across taxonomic, geographic, and collector-related information. ## Key Features - Normalize collector names and collection numbers - Standardize geographic fields like country, state, and locality - Harmonize taxonomic names including family, genus, and species - Clean and normalize type status - Optionally remove unvouchered or duplicate records - Support for multilingual column names (e.g., Portuguese, Spanish) ## Usage ```r library(barRoso) df <- read.csv("raw_herbarium_data.csv") standardized_df <- barroso_std(df, unvouchered = TRUE, delunkcoll = FALSE, flag_missid = TRUE, flag_duplicates = TRUE, rm_duplicates = FALSE, colname_recordedBy = "recordedBy", colname_recordNumber = "recordNumber", colname_country = "country", colname_stateProvince = "stateProvince", colname_county = "county", colname_municipality = "municipality", colname_locality = "locality", colname_collectionCode = "collectionCode", colname_institutionCode = "institutionCode", colname_typeStatus = "typeStatus", colname_family = "family", colname_genus = "genus", colname_specificEpithet = "specificEpithet", rm_original_column = TRUE) ``` ## Arguments - `...`: A data frame or list of data frames with raw biodiversity records - `unvouchered`: Remove unvouchered (non-herbarium) records - `delunkcoll`: Optionally delete records with unknown collectors - `flag_duplicates`, `rm_duplicates`: Detect and optionally remove duplicates - `rm_original_column`: Remove original (uncleaned) fields after standardization ## Output Returns a cleaned and fully standardized data frame ready for: - Reconciliation and deduplication - Taxonomic and biogeographic analysis - Herbarium label generation workflows ## Notes - Uses dynamic regular expressions for name harmonization rather than static dictionaries - Optimized for scalability and flexible input schema - Recommended to run before calling downstream functions like `barroso_flag_duplicates()` or `barroso_labels()` ## Example ```r cleaned_data <- barroso_std(df, colname_country = "pais", colname_stateProvince = "estado", rm_duplicates = TRUE) ``` For a complete list of supported fields, refer to the function documentation with `?barroso_std`.