std_place

Standardize Place-Related Columns in Biodiversity Data

barRoso::std_place()

Description

Cleans and standardizes the geographic columns of a biodiversity collection dataset. This includes unifying column names and harmonizing values for continent, country, stateProvince, county, municipality, and locality. The function handles translations, synonyms, upper-case anomalies, ISO country codes, and common geographic aliases.

Details

This function is used internally by the barRoso package to support record reconciliation, duplicate detection, and label generation across different biodiversity databases. It ensures consistency of location fields by correcting common mistakes and variations. Country names are translated to English and harmonized using countrycode, and country codes like "BR" or "BRA" are converted into names. Missing countries are taken from the Brazilian state (e.g. "Bahia"), from a country name in the locality (e.g. "Manaus, Brasil"), or from other records with the same state and county. Brazilian and U.S. state abbreviations are expanded to full names. Missing municipalities are taken from the county. Words for municipality in county and municipality, e.g. "Manaus Mun.", "Mun. de Castelo", "Município de Mucugê" or "Arriaga Municipio", are removed, leaving just the name.

Arguments

Argument	Description
df	A data frame containing biodiversity records.
colname_continent	Column name for continent (default: `"continent"`).
colname_country	Column name for country (default: `"country"`).
colname_stateProvince	Column name for state or province (default: `"stateProvince"`).
colname_county	Column name for county (default: `"county"`).
colname_municipality	Column name for municipality (default: `"municipality"`).
colname_locality	Column name for locality (default: `"locality"`).
rm_original_column	Logical; if `TRUE`, original columns are removed after cleaning (default: `TRUE`).

Value

A data frame with standardized geographic information. If rm_original_column = FALSE, the original columns are retained with *Original suffixes.

Examples

df <- read.csv("herbarium_records.csv")
df_clean <- std_place(df,
                      colname_country = "pais",
                      colname_stateProvince = "estado",
                      rm_original_column = FALSE)

--- title: 'std_place' description: 'Standardize Place-Related Columns in Biodiversity Data' toc: true toc-depth: 3 --- ```{r} #| eval: false barRoso::std_place() ``` ### Description Cleans and standardizes the geographic columns of a biodiversity collection dataset. This includes unifying column names and harmonizing values for `continent`, `country`, `stateProvince`, `county`, `municipality`, and `locality`. The function handles translations, synonyms, upper-case anomalies, ISO country codes, and common geographic aliases. ### Details This function is used internally by the `barRoso` package to support record reconciliation, duplicate detection, and label generation across different biodiversity databases. It ensures consistency of location fields by correcting common mistakes and variations. Country names are translated to English and harmonized using `countrycode`, and country codes like `"BR"` or `"BRA"` are converted into names. Missing countries are taken from the Brazilian state (e.g. `"Bahia"`), from a country name in the locality (e.g. `"Manaus, Brasil"`), or from other records with the same state and county. Brazilian and U.S. state abbreviations are expanded to full names. Missing municipalities are taken from the county. Words for municipality in `county` and `municipality`, e.g. `"Manaus Mun."`, `"Mun. de Castelo"`, `"Município de Mucugê"` or `"Arriaga Municipio"`, are removed, leaving just the name. ### Arguments | Argument | Description | |---|---| | df | A data frame containing biodiversity records. | | colname_continent | Column name for continent (default: `"continent"`). | | colname_country | Column name for country (default: `"country"`). | | colname_stateProvince | Column name for state or province (default: `"stateProvince"`). | | colname_county | Column name for county (default: `"county"`). | | colname_municipality | Column name for municipality (default: `"municipality"`). | | colname_locality | Column name for locality (default: `"locality"`). | | rm_original_column | Logical; if `TRUE`, original columns are removed after cleaning (default: `TRUE`). | ### Value A data frame with standardized geographic information. If `rm_original_column = FALSE`, the original columns are retained with *Original suffixes. ### Examples ```r df <- read.csv("herbarium_records.csv") df_clean <- std_place(df, colname_country = "pais", colname_stateProvince = "estado", rm_original_column = FALSE) ```