ebv_analyse {ebvcube}

Get a simple explorative analysis of an EBV netCDF datacube

Description

Get basic measurements of the data, including min, max, mean, sd, n, #NAs, q25, q50, q75 (no mean for categorical data).

Usage

ebv_analyse(
  filepath,
  datacubepath = NULL,
  entity = NULL,
  timestep = 1,
  subset = NULL,
  touches = TRUE,
  epsg = 4326,
  scenario = NULL,
  metric = NULL,
  numerical = TRUE,
  na_rm = TRUE,
  verbose = TRUE
)

Arguments

filepath

Character. Path to the netCDF file.

datacubepath

Character. Optional. Default: NULL. Path to the datacube (use ebv_datacubepaths()). Alternatively, you can use the scenario and metric argument to define which cube you want to access.

entity

Character or Integer. Default is NULL. If the structure is 3D, the entity argument is set to NULL. Else, a character string or single integer value must indicate the entity of the 4D structure of the EBV netCDFs.

timestep

Integer or character. Select one or several timestep(s). Either provide an integer value or list of values that refer(s) to the index of the timestep(s) (minimum value: 1) or provide a date or list of dates in ISO format, such as '2015-01-01'.

subset

Optional if you want measurements on a smaller subset. Possible via the path to a shapefile (character) or the indication of a bounding box (vector of four numeric values) defining the subset. Else the whole area is analysed.

touches

Logical. Optional. Default: TRUE. Only relevant if the subset is indicated by a shapefile. See ebv_read_shp().

epsg

Numeric. Optional. Only relevant if the subset is indicated by a bounding box and the coordinate reference system differs from WGS84. See ebv_read_bb().

scenario

Character or integer. Optional. Default: NULL. Define the scenario you want to access. If the EBV netCDF has no scenarios, leave the default value (NULL). You can use an integer value defining the scenario or give the name of the scenario as a character string. To check the available scenarios and their name or number (integer), use ebv_datacubepaths().

metric

Character or integer. Optional. Define the metric you want to access. You can use an integer value defining the metric or give the name of the scenario as a character string. To check the available metrics and their name or number (integer), use ebv_datacubepaths().

numerical

Logical. Default: TRUE. Change to FALSE if the data covered by the netCDF contains categorical data.

na_rm

Logical. Default: TRUE. NA values are removed in the analysis. Change to FALSE to include NAs.

verbose

Logical. Default: TRUE. Turn off additional prints by setting it to FALSE.

Value

Returns a named list containing the measurements.

See Also

ebv_read_bb() and ebv_read_shp() for the usage of subsets.

Examples

#set path to EBV netCDF
file <- system.file(file.path("extdata","martins_comcom_subset.nc"), package="ebvcube")
#get all datacubepaths of EBV netCDF
datacubes <- ebv_datacubepaths(file, verbose=FALSE)
#set path to shp file
shp_path <- system.file(file.path("extdata","cameroon.shp"), package="ebvcube")


#get measurements for full extent and the first three timesteps
data_global <- ebv_analyse(filepath = file, datacubepath = datacubes[1,1],
                           entity = 1, timestep = 1:3, verbose = FALSE)

#get measurements for subset of Africa only (using bounding box) and one timestep
data_1910 <- ebv_analyse(filepath = file, datacubepath = datacubes[1,1],
                         entity = 1, timestep = "1900-01-01",
                         subset = c(-26, 64, 30, 38), verbose = FALSE)

#get measurements for cameroon only (using shp) and one timestep
data_1930 <- ebv_analyse(filepath = file, entity = 1,
                         timestep = "1930-01-01",
                         subset = shp_path, verbose = FALSE,
                         metric = 'Absolute change in the number of species',)