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Read species occurrence points from XLSX, CSV or vector files

Source: R/import_data.R
read_occurrences.Rd

Imports occurrence records from a spreadsheet (.xlsx/.xls), delimited text (.csv/.tsv/.txt) or a vector file (.shp, .gpkg, .geojson; for shapefiles you may also pass a .zip containing the .shp/.shx/.dbf/.prj set) and returns a clean point sf in WGS84 (EPSG:4326) with a standardised species column.

Usage

read_occurrences(
  path,
  species_col = NULL,
  lon_col = NULL,
  lat_col = NULL,
  crs = 4326,
  sheet = NULL,
  sep = NULL,
  dec = NULL,
  encoding = "UTF-8",
  default_species = "sp1"
)

Arguments

path

Path to the input file.

species_col, lon_col, lat_col

Optional column names to override auto-detection. lon_col/lat_col are ignored for vector files that already carry geometry.

crs

Input CRS for tabular coordinates (default 4326). Output is always reprojected to WGS84.

sheet

For Excel inputs, the sheet name or index (default first sheet).

sep

For delimited text, the field separator. If NULL (default) it is auto-detected from the header line (;, , or tab).

dec

Decimal mark for delimited text. If NULL (default) it is inferred from sep (, when sep is ;, else .), matching Brazilian Excel exports.

encoding

File encoding for delimited text (default "UTF-8"; use e.g. "latin1" for Windows-1252 files).

default_species

Species label used when no species column is found (default "sp1").

Value

An sf of POINT geometries in EPSG:4326 with a species column plus all original attributes.

Details

Longitude, latitude and species columns are auto-detected from common header names (Darwin Core decimalLongitude/decimalLatitude, lon/lat, x/y, scientificName, etc.). You can override the detection with the corresponding arguments. Rows with missing or out-of-range coordinates are dropped with a message.

For delimited text the field separator and decimal mark are auto-detected, so Brazilian-style CSVs exported from Excel (; separator, , decimals, optional UTF-8 BOM) are read correctly without extra arguments.

Examples

f <- system.file("extdata", "example_occurrences.csv", package = "mappingAS")
occ <- read_occurrences(f)
table(occ$species)
#> 
#>       Prepusa connata Gardner    Prepusa hookeriana Gardner 
#>                             5                            21 
#> Worsleya procera (Lem.) Traub 
#>                             3