create.landscapes: Wrapper function to create replicate simulated landscapes

In rSPACE: Spatially-Explicit Power Analysis for Conservation and Ecology

Description

Creates a series of files with replicated complete encounter histories based on habitat and population parameters.

Usage

createReplicates(n_runs, map, Parameters, ... )

Arguments

n_runs	number of replicate encounter histories to produce
map	a raster layer with underlying habitat information
Parameters	list of parameter values for simulation (see enter.parameters)
...	optional options (see details)

Details

This function will produce n_run text files with simulated complete encounter histories. Each individual file does not contain identifying information about the parameters used to create it, so it will be good practice to create a folder structure to keep separate simulations separate. Default is to create a folder for the runs (./rSPACE_X) and name all encounter histories ./rSPACE_X/rSPACEx??.txt where ?? indicates the run number. If Parameters is not specified, enter.parameters will be called.

map raster layer defining the landscape for the population simulation. Values of map are used as weights for both selecting individual activity centers and scaling bivariate normal movement distributions. Raster layer should use either longlat or utm projections with meter units.

There are additional arguments that can be included to specify other options, but some are more sketchy than others.

Optional argument skipConfirm will bypass the user-confirmation for creating a folder structure.

Optional argument run.label changes the folder name for the run scenario. Defaults to './rSPACE_X'

Optional argument base.name can be used to change the base file name for encounter history replicate files. Defaults to 'rSPACEx'

Optional argument filter.map can be used to specify an alternative sampling frame for the landscape. The default sampling frame consists of a rectangular grid built from the habitat information in map and user-specifications for Paramters$grid_size and Parameters$sample.cutoff. By providing a secondary raster layer via filter.map, users can restrict sampling to specific areas (e.g., to exclude inaccessible private lands or restrict sampling to a single jurisdiction such as USFS, NPS, BLM, etc) or to provide a user-specific grid for the entire landscape. The raster provided in filter.map will be expanded to match the extent of map, with non-coded regions coded 0. Raster values of 0 in filter.map are treated as areas to exclude from sampling. If filter.map consists of 0/1 values only, the default rectangular grid will be restricted to areas with values of 1 in filter.map. If filter.map contains additional values, non-zero values will be treated as indentifiers for sampling cells in a user-specified grid.

Optional argument printN defaults to TRUE. Logical - prints population size by run by year to a text file.

Optional argument saveParameters defaults to TRUE. Logical - save rData file with parameter list used in run scenario.

Optional argument saveGrid defaults to TRUE. Logical - save raster layer with sampling grid used in run scenario.

Value

returns list with directory location and output file names

Author(s)

Martha Ellis

References

ELLIS, MARTHA M., JACOB S. IVAN, and MICHAEL K. SCHWARTZ. "Spatially Explicit Power Analyses for Occupancy-Based Monitoring of Wolverine in the US Rocky Mountains." Conservation Biology (2014).

rSPACE documentation built on May 29, 2017, 11:37 a.m.