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

Usage

finbif_occurrence_load(
  file,
  select,
  n = -1,
  count_only = FALSE,
  quiet = FALSE,
  cache = getOption("finbif_use_cache"),
  dwc = FALSE,
  date_time_method,
  tzone = getOption("finbif_tz"),
  write_file = tempfile(),
  dt,
  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.

cache

Logical. Use cached data.

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. Note that this functionality requires that the {dplyr} and {tidyr} packages are available.

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, Swedish, Russian, and Sámi (Northern). 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) {

# Get occurrence data
finbif_occurrence_load(49381)

}