barroso_std

Standardize Biodiversity Records Across Multiple Fields

barRoso::barroso_std()

Description

A wrapper function that performs integrated cleaning and standardization of biodiversity collection records using the barRoso package. This includes harmonizing taxonomic, geographic, collector, and type status information, as well as flagging or removing unvouchered and duplicate specimens. Determiner names in identifiedBy are standardized with the same rules of collector names.

Details

This function orchestrates several std_* functions from the barRoso package to clean records from virtual herbaria and biodiversity portals. It handles multilingual field names, missing data, inconsistent formatting, and dataset chunking for large inputs. The function also detects and optionally removes duplicate records and specimens lacking voucher information.

Arguments

Argument	Description
…	Input data frame containing raw biodiversity records.
unvouchered	Logical; if `TRUE`, remove records of wood, seed, fruit, pollen and spirit collections (e.g. `"INPAw"`, `"INPA-Carpoteca"`), and observations without a specimen (`basisOfRecord` like `"HUMAN_OBSERVATION"`) (default: `TRUE`).
delunkcoll	Logical; if `TRUE`, removes records with unknown collectors (default: `FALSE`).
flag_missid	Reserved for future use. Currently not implemented.
flag_duplicates	Logical; if `TRUE`, flags duplicates with a logical column (default: `TRUE`).
rm_duplicates	Logical; if `TRUE`, removes duplicate specimens (default: `FALSE`).
colname_recordedBy	Column name for collector names.
colname_recordNumber	Column name for collector number.
colname_identifiedBy	Column name for determiner names. The column is standardized with `std_identifiedBy()` only when present in the data.
colname_continent	Column name for continent.
colname_country	Column name for country.
colname_stateProvince	Column name for state/province.
colname_county	Column name for county.
colname_municipality	Column name for municipality.
colname_locality	Column name for locality.
colname_collectionCode	Column name for collection code.
colname_institutionCode	Column name for institution code.
colname_typeStatus	Column name for type status.
colname_family	Column name for family.
colname_genus	Column name for genus.
colname_specificEpithet	Column name for specific epithet.
rm_original_column	Logical; if `TRUE`, remove original columns after standardization.

Value

A fully cleaned and standardized data frame ready for downstream reconciliation, duplicate handling, and label generation.

Examples

df <- read.csv("raw_herbarium_data.csv")
df_std <- barroso_std(df,
                      colname_country = "pais",
                      colname_stateProvince = "estado",
                      rm_duplicates = TRUE)

--- title: 'barroso_std' description: 'Standardize Biodiversity Records Across Multiple Fields' toc: true toc-depth: 3 --- ```{r} #| eval: false barRoso::barroso_std() ``` ### Description A wrapper function that performs integrated cleaning and standardization of biodiversity collection records using the `barRoso` package. This includes harmonizing taxonomic, geographic, collector, and type status information, as well as flagging or removing unvouchered and duplicate specimens. Determiner names in `identifiedBy` are standardized with the same rules of collector names. ### Details This function orchestrates several std_* functions from the `barRoso` package to clean records from virtual herbaria and biodiversity portals. It handles multilingual field names, missing data, inconsistent formatting, and dataset chunking for large inputs. The function also detects and optionally removes duplicate records and specimens lacking voucher information. ### Arguments | Argument | Description | |---|---| | ... | Input data frame containing raw biodiversity records. | | unvouchered | Logical; if `TRUE`, remove records of wood, seed, fruit, pollen and spirit collections (e.g. `"INPAw"`, `"INPA-Carpoteca"`), and observations without a specimen (`basisOfRecord` like `"HUMAN_OBSERVATION"`) (default: `TRUE`). | | delunkcoll | Logical; if `TRUE`, removes records with unknown collectors (default: `FALSE`). | | flag_missid | Reserved for future use. Currently not implemented. | | flag_duplicates | Logical; if `TRUE`, flags duplicates with a logical column (default: `TRUE`). | | rm_duplicates | Logical; if `TRUE`, removes duplicate specimens (default: `FALSE`). | | colname_recordedBy | Column name for collector names. | | colname_recordNumber | Column name for collector number. | | colname_identifiedBy | Column name for determiner names. The column is standardized with `std_identifiedBy()` only when present in the data. | | colname_continent | Column name for continent. | | colname_country | Column name for country. | | colname_stateProvince | Column name for state/province. | | colname_county | Column name for county. | | colname_municipality | Column name for municipality. | | colname_locality | Column name for locality. | | colname_collectionCode | Column name for collection code. | | colname_institutionCode | Column name for institution code. | | colname_typeStatus | Column name for type status. | | colname_family | Column name for family. | | colname_genus | Column name for genus. | | colname_specificEpithet | Column name for specific epithet. | | rm_original_column | Logical; if `TRUE`, remove original columns after standardization. | ### Value A fully cleaned and standardized data frame ready for downstream reconciliation, duplicate handling, and label generation. ### Examples ```r df <- read.csv("raw_herbarium_data.csv") df_std <- barroso_std(df, colname_country = "pais", colname_stateProvince = "estado", rm_duplicates = TRUE) ```