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Exploring specimens data

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,
  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

con

Database connection (if NULL, creates new connection)

con.taxa

Taxa database connection (if NULL, creates new connection)

genus_searched

string specimens of genus searched

tax_esp_searched

string specimens of species searched

tax_fam_searched

string specimens of family searched

integer id searched

show_previous_modif

logical if you want to see previous modification of the entry - useful to see previous identification for example

generate_labels

logical if labels should be produced

project_title

string if labels are produced title of the label

file_labels

string if labels are produced name of the rtf file

Value

A tibble

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

Details

Exploring specimens data and if necessary export labels

Author

Gilles Dauby, gilles.dauby@ird.fr

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
} # }