Get data using robis::occurrence()

Requires an aoi. i.e. aoi is not optional for this implementation of get_obis

get_obis(
  aoi = NULL,
  save_dir = NULL,
  get_new = FALSE,
  name = "obis",
  data_map = NULL,
  filter_inconsistent = TRUE,
  removes = list(basisOfRecord = c("LIVING_SPECIMEN", "FOSSIL_SPECIMEN",
    "MATERIAL_CITATION")),
  ...
)

Arguments

aoi

Optional simple feature (sf). Used to limit the occurrences returned via obis::occurence()

save_dir

Character. Path to directory into which to save outputs. If NULL results will be saved to here::here("out", "ds", "obis"). File will be named obis.parquet

get_new

Logical. If FALSE, will attempt to load from existing save_dir.

name

Character. data_name value in envImport::data_map (or other data_map)

data_map

Dataframe or NULL. Mapping of fields to retrieve. See example envImport::data_map

filter_inconsistent

Logical. If TRUE, inconsistencies between the occurrenceStatus column and either organismQuantity or individualCount are removed. e.g. a record with occurrenceStatus == "ABSENT" but individualCount == 1 would be filtered.

removes

Named list. Names need to match column names in the result of a call to robis::occurrence() (i.e. generally Darwin core column names). Levels within each name are matched and, if present, removed. Note that this filtering occurs after download so it does not save on download time and can also be done after a call to get_obis(). It does enable filtering on columns that are not passed through to the return value as they are not in the data_map.

...

Passed to envImport::file_prep()

Value

Dataframe of occurrences and file saved to save_dir.

Examples

aoi <- sf::st_read(file.path(system.file(package = "envImport"), "aoi.shp"))
#> Reading layer `aoi' from data source 
#>   `C:\temp\joel\RtmpKSVQ8v\temp_libpath23d833687f18\envImport\aoi.shp' 
#>   using driver `ESRI Shapefile'
#> Simple feature collection with 1 feature and 1 field
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 138.3357 ymin: -35.41119 xmax: 138.5762 ymax: -35.19546
#> Geodetic CRS:  WGS 84

obis_data <- get_obis(aoi
                      , save_dir = tempdir()
                      , data_map = envImport::data_map
                      , get_new = TRUE
                      )
#> save_file will be C:/temp/joel/RtmpknG3J8/obis/obis.parquet
#> 
Retrieved 3692 records of approximately 3692 (100%)
#> Warning: basisOfRecord is not a column so will not be filtered of values: LIVING_SPECIMEN, FOSSIL_SPECIMEN and MATERIAL_CITATION
#> Joining with `by = join_by(decimalLongitude, decimalLatitude)`
#> Warning: obis :  establishmentMeans are not columns in the dataframe, so won't be renamed.
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `dplyr::across(...)`.
#> Caused by warning:
#> !  5 failed to parse.
#> Joining with `by = join_by(date)`
#> Joining with `by = join_by(date)`

obis_data |>
  dplyr::count()
#> # A tibble: 1 × 1
#>       n
#>   <int>
#> 1  1681

# Removing certain methods
obis_data <- get_obis(aoi
                      , save_dir = tempdir()
                      , data_map = envImport::data_map
                      , removes = list(basisOfRecord = c("PreservedSpecimen"))
                      , get_new = TRUE
                      )
#> save_file will be C:/temp/joel/RtmpknG3J8/obis/obis.parquet
#> 
Retrieved 3692 records of approximately 3692 (100%)
#> Warning: basisOfRecord is not a column so will not be filtered of values: PreservedSpecimen
#> Joining with `by = join_by(decimalLongitude, decimalLatitude)`
#> Warning: obis :  establishmentMeans are not columns in the dataframe, so won't be renamed.
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `dplyr::across(...)`.
#> Caused by warning:
#> !  5 failed to parse.
#> Joining with `by = join_by(date)`
#> Joining with `by = join_by(date)`

obis_data |>
  dplyr::count()
#> # A tibble: 1 × 1
#>       n
#>   <int>
#> 1  1681