ebv_create_taxonomy {ebvcube} | R Documentation |
Create an EBV netCDF with taxonomy
Description
Create the core structure of the EBV netCDF based on the json
from the EBV Data Portal. Additionally,
you can add the hierarchy of the taxonomy. This is not provided in the
ebv_create()
function. Use the ebv_create()
function
if your dataset holds no taxonomic information. Data will be added
afterwards using ebv_add_data()
.
Usage
ebv_create_taxonomy(
jsonpath,
outputpath,
taxonomy,
lsid = FALSE,
epsg = 4326,
extent = c(-180, 180, -90, 90),
resolution = c(1, 1),
timesteps = NULL,
fillvalue = NULL,
prec = "double",
sep = ",",
force_4D = TRUE,
overwrite = FALSE,
verbose = TRUE
)
Arguments
jsonpath |
Character. Path to the json file downloaded from the EBV Data Portal. Login to the page and click on 'Uploads' and 'New Upload' to start the process. |
outputpath |
Character. Set path where the netCDF file should be created. |
taxonomy |
Character. Path to the csv table holding the taxonomy.
Default: comma-separated delimiter, else change the |
lsid |
Logical. Default: FALSE. Set to TRUE if the last column in your taxonomy csv file defines the lsid for each entity. For more info check CF convention 1.8: Taxon Names and Identifiers. |
epsg |
Integer. Default: 4326 (WGS84). Defines the coordinate reference system via the corresponding epsg code. |
extent |
Numeric. Default: c(-180,180,-90,90). Defines the extent of the data: c(xmin, xmax, ymin, ymax). |
resolution |
Numerical. Vector of two numerical values defining the longitudinal and latitudinal resolution of the pixel: c(lon,lat). |
timesteps |
Character. Vector of the timesteps in the dataset. Default: NULL - in this case the time will be calculated from the start-, endpoint and temporal resolution given in the metadata file (json). Else, the dates must be given in in ISO format 'YYYY-MM-DD' or shortened 'YYYY' in case of yearly timesteps. |
fillvalue |
Numeric. Value of the missing data in the array. Not mandatory but should be defined! |
prec |
Character. Default: 'double'. Precision of the data set. Valid options: 'short' 'integer' 'float' 'double' 'char' 'byte'. |
sep |
Character. Default: ','. If the delimiter of the csv specifying the entity-names differs from the default, indicate here. |
force_4D |
Logical. Default is TRUE. If the argument is TRUE, there will be 4D cubes (lon, lat, time, entity) per metric. If this argument is changed to FALSE, there will be 3D cubes (lon, lat, time) per entity (per metric). So the latter yields a higher amount of cubes and does not bundle all information per metric. In the future the standard will be restricted to the 4D version. Recommendation: go with the 4D cubes! |
overwrite |
Logical. Default: FALSE. Set to TRUE to overwrite the output file defined by 'outputpath' |
verbose |
Logical. Default: TRUE. Turn off additional prints by setting it to FALSE. #' @note To check out the results take a look at your netCDF file with Panoply provided by the NASA. |
Value
Creates the netCDF file at the 'outputpath' location including the taxonomy information.
Note
You can check the taxonomy info with ebv_properties()
in the slot
'general' under the name 'taxonomy' and 'taxonomy_lsid'.
Examples
#set path to JSON file
json <- system.file(file.path("extdata/testdata","5.json"), package="ebvcube")
#set output path of the new EBV netCDF
out <- tempfile(fileext='.nc')
#set path to the csv holding the taxonomy names
taxonomy <- file.path(system.file(package='ebvcube'),"extdata/testdata","id5_entities.csv")
#create new EBV netCDF with taxonomy
## Not run:
ebv_create_taxonomy(jsonpath = json, outputpath = out, taxonomy = taxonomy,
fillvalue = -127, resolution = c(0.25, 0.25), verbose = FALSE)
#remove file
file.remove(out)
## End(Not run)