library(spatialEpisim.foundation)
#> Warning in fun(libname, pkgname): /home/runner/spatialEpisim.foundation.data
#> already exists, but option `spatialEpisim.foundation.datapath` was unset.Installation
Installation is covered in the Installation vignette.
Storage configuration
Unless the [spatialEpisim.data] package (included in the list of
suggested packages in the DESCRIPTION file of this package) is installed
and successfully attached, then the option
spatialEpisim.foundation.datapath must be set
correctly.
The path described in the option
spatialEpisim.foundation.datapath is used for storing
spatial raster and vector data that is needed for
spatialEpisim.foundation to be useful.
By default, if this option is NULL is set to
path.expand("~/spatialEpisim.foundation.data").
Setup for simulation
[SVEIRD.BayesianDataAssimilation] is used with an object referred to
as layers. This SpatRaster-classed object contains layers
for each of the compartments in an SVEIRD simulation.
Raster aggregation
[getSVEIRD.SpatRaster] is the function used to aggregate a
SpatRaster, and it will call [maskAndClassifySusceptibleSpatRaster] for
the user, masking it with the provided SpatVector object. This is the
easiest way to aggregate a SpatRaster object for use with
spatialEpisim.foundation. Aggregation without this function, id
est using terra::aggregate on a SpatRaster beforehand,
will lead to inaccurate results, because the
aggregationFactor argument of [getSVEIRD.SpatRaster] and
[SVEIRD.BayesianDataAssimilation] is used throughout various parts of
the algorithm.
If this approach to aggregation does not meet your needs, please contact the maintainer of the package and request a feature enhancement that meeds your needs, or fork the project and modify it to your needs.
It’s recommended to define a variable,
rasterAggregationFactor, to pass to both
[SVEIRD.BayesianDataAssimilation] and [getSVEIRD.SpatRaster] to ensure
it is the same. See the examples for the former function.