Function to create a Species Temporal Data object (STD object).

Creates an object of class sp.temporal.modeling that contains a list with four attributes:

• temporal_df: A data frame with the following columns:

  • Longitude: Longitude coordinates of occurrence records.

  • Latitude: Latitude coordinates of occurrence records.

  • Date: Date variable indicating when the species were observed.

  • Layer Dates: Format of dates for each layer of environmental data.

  • Layers Path: Path to the bioclimatic layer corresponding to each year.

• sp_date_var: Name of the date variable column in the occurrence records.

• lon_lat_vars: Names of the longitude and latitude columns.

• layers_ext: Final extension format of the environmental information (e.g., ".tif").

Usage

sp_temporal_data(
  occs,
  longitude,
  latitude,
  sp_date_var,
  occ_date_format = "y",
  layers_date_format = "y",
  layers_by_date_dir,
  layers_ext = "*.tif$"
)

Arguments

occs

A data.frame with information about occurrence records of the species being modeled.

longitude

Name of the variable in 'occs' containing longitude data.

latitude

Name of the variable in 'occs' containing latitude data.

sp_date_var

Name of the date variable.

occ_date_format

Format of dates in occurrence records. Options: "y", "ym", "ymd", "mdy", "my", "dmy".

layers_date_format

Format of dates in raster layers. Options: "y", "ym", "ymd", "mdy", "my", "dmy".

layers_by_date_dir

Directory containing folders organized by date with raster layers of environmental information.

layers_ext

Extension or path of each raster layer archive (e.g., ".tif").

Value

Returns a sp.temporal.modeling object (list) with the coordinates of each occurrences points, the years of observation and the path to the temporal layers.

Details

The format of dates for each layer can be organized in a particular pattern, for example year/month/day ("ymd"), year/month ("ym"), just year ("y") or some other arrangement like month/year ("my"), month/year/day ("myd"), day/month/year ("dmy").

Examples

library(tenm)
#A data.frame with occurrences points information of Abronia graminea.
# See help(abronia)
data("abronia")
tempora_layers_dir <- system.file("extdata/bio",package = "tenm")
abt <- tenm::sp_temporal_data(occs = abronia,
                              longitude = "decimalLongitude",
                              latitude = "decimalLatitude",
                              sp_date_var = "year",
                              occ_date_format="y",
                              layers_date_format= "y",
                              layers_by_date_dir = tempora_layers_dir,
                              layers_ext="*.tif$")