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Query Specimens

query_specimens.Rd

Modern query interface for specimens with builder pattern support

Usage

query_specimens(
  collector = NULL,
  id_colnam = NULL,
  number = NULL,
  number_min = NULL,
  number_max = NULL,
  genus = NULL,
  species = NULL,
  family = NULL,
  id_specimen = NULL,
  idtax_n = NULL,
  interactive = TRUE,
  extract_linked_individuals = FALSE,
  subset_columns = TRUE,
  show_html = TRUE,
  html_max = 20,
  con = NULL,
  con.taxa = NULL
)

Arguments

collector

Character vector of collector names (fuzzy match)

id_colnam

Integer vector of collector IDs (exact match)

number

Integer vector of specimen numbers (exact match)

number_min

Minimum specimen number (range query)

number_max

Maximum specimen number (range query)

genus

Character vector of genus names to filter

species

Character vector of species names to filter

family

Character vector of family names to filter

id_specimen

Integer vector of specimen IDs (direct fetch)

idtax_n

Integer vector of taxonomy IDs

interactive

Logical, use interactive fuzzy matching for collectors

extract_linked_individuals

Logical, also fetch linked individuals

subset_columns

Logical, return subset of columns vs all columns

show_html

Logical. If TRUE (default) and the number of returned specimens is at most html_max, the results are displayed as a transposed HTML table in the RStudio Viewer (one column per specimen) using print_table().

html_max

Integer. Maximum number of specimens for which the HTML visualisation is triggered automatically (default 20).

con

Database connection (if NULL, creates new connection)

con.taxa

Taxa database connection (if NULL, creates new connection)

Value

Data frame with specimen records, or list if extract_linked_individuals=TRUE

Examples

if (FALSE) { # \dontrun{
# Query by collector name
query_specimens(collector = "Dauby")

# Query by collector ID and number range
query_specimens(id_colnam = 123, number_min = 1000, number_max = 2000)

# Query by specimen IDs
query_specimens(id_specimen = c(123, 456, 789))

# Query with linked individuals
result <- query_specimens(collector = "Dauby", extract_linked_individuals = TRUE)
result$specimens  # Specimen records
result$linked_individuals  # Linked individual records
} # }