Load FinBIF occurrence records from a file — finbif_occurrence

Load occurrence data from a file as a data.frame.

Usage

finbif_occurrence_load(
  file,
  select = NULL,
  n = -1,
  count_only = FALSE,
  quiet = getOption("finbif_hide_progress"),
  cache = getOption("finbif_use_cache"),
  dwc = FALSE,
  date_time_method = NULL,
  tzone = getOption("finbif_tz"),
  write_file = tempfile(),
  dt = NA,
  keep_tsv = FALSE,
  facts = list(),
  type_convert_facts = TRUE,
  drop_na = FALSE,
  drop_facts_na = drop_na,
  locale = getOption("finbif_locale"),
  skip = 0
)

Arguments

file: Character or Integer. Either the path to a Zip archive or tabular data file that has been downloaded from "laji.fi", a URI linking to such a data file (e.g., https://tun.fi/HBF.49381) or an integer representing the URI (i.e., 49381).
select: Character vector. Variables to return. If not specified, a default set of commonly used variables will be used. Use "default_vars" as a shortcut for this set. Variables can be deselected by prepending a - to the variable name. If only deselects are specified the default set of variables without the deselection will be returned. Use "all" to select all available variables in the file.
n: Integer. How many records to import. Negative and other invalid values are ignored causing all records to be imported.
count_only: Logical. Only return the number of records available.
quiet: Logical. Suppress the progress indicator for multipage downloads. Defaults to value of option finbif_hide_progress.
cache: Logical or Integer. If TRUE or a number greater than zero, then data-caching will be used. If not logical then the cache will be invalidated after the number of hours indicated by the argument. If a length one vector is used, its value will only apply to caching occurrence records. If the value is length two, then the second element will determine how metadata is cached.
dwc: Logical. Use Darwin Core (or Darwin Core style) variable names.
date_time_method: Character. Passed to lutz::tz_lookup_coords() when date_time and/or duration variables have been selected. Default is "fast" when less than 100,000 records are requested and "none" when more. Using method "none" assumes all records are in timezone "Europe/Helsinki", Use date_time_method = "accurate" (requires package sf) for greater accuracy at the cost of slower computation.
tzone: Character. If date_time has been selected the timezone of the outputted date-time. Defaults to system timezone.
write_file: Character. Path to write downloaded zip file to if file refers to a URI. Will be ignored if getOption("finbif_cache_path") is not NULL and will use the cache path instead.
dt: Logical. If package, data.table, is available return a data.table object rather than a data.frame.
keep_tsv: Logical. Whether to keep the TSV file if file is a ZIP archive or represents a URI. Is ignored if file is already a TSV. If TRUE the tsv file will be kept in the same directory as the ZIP archive.
facts: List. A named list of "facts" to extract from supplementary "fact" files in a local or online FinBIF data archive. Names can include one or more of "record", "event" or "document". Elements of the list are character vectors of the "facts" to be extracted and then joined to the return value.
type_convert_facts: Logical. Should facts be converted from character to numeric or integer data where applicable?
drop_na: Logical. A vector indicating which columns to check for missing data. Values recycled to the number of columns. Defaults to all columns.
drop_facts_na: Logical. Should missing or "all NA" facts be dropped? Any value other than a length one logical vector with the value of TRUE will be interpreted as FALSE. Argument is ignored if drop_na is TRUE for all variables explicitly or via recycling. To only drop some missing/NA-data facts use drop_na argument.
locale: Character. One of the supported two-letter ISO 639-1 language codes. Current supported languages are English, Finnish and Swedish. For data where more than one language is available the language denoted by locale will be preferred while falling back to the other languages in the order indicated above.
skip: Integer. The number of lines of the data file to skip before beginning to read data (not including the header).

Value

A data.frame, or if count_only = TRUE an integer.

Examples

if (FALSE) { # \dontrun{

# Get occurrence data
finbif_occurrence_load(49381)

} # }