SpatialDemography: SpatialDemography = Main function for running the spatially...
In akeyel/spatialdemography: A Spatially Explicit Metacommunity Model

Description Usage Arguments Details Value Author(s) References

This function implements a spatially explicit matrix model based on input options. Inputs are pointers to files, which contain additional inputs used by the function to run the model.

SpatialDemography(scn, s.lbl, file.ending, DispPath, run.path, opath,
  ResultsFile, initial.conditions.file, settings.file, env.file, spfile,
  sp.instr.file = "none", sp.resp.instr.file = "none",
  landscape.dir = "default", locations.file = "none",
  scale.vec = c("landscape"), scale.cells.lst = "default",
  out.metrics = c("Sp.Rich", "Beta.Div", "Biomass", "FTD.UTC", "RTD.UTC"),
  testing = F)

`scn`	Indicator variable to denote scenario and to extract appropriate row from initial.conditions.file and settings.file.
`s.lbl`	A label used in the construction of the Species file and new landscape files.
`file.ending`	A text string that matches the end of the species file (either to be gener-ated or that already exists).
`DispPath`	The path of the dispersal tables (if existing) or the path where dispersal tables should be created.
`run.path`	The main path for the specific overall model run.
`opath`	The path for model outputs.
`ResultsFile`	A file to be created containing the model results.
`initial.conditions.file`	A file to specify the initial model conditions. See initial.conditions.file for details.
`settings.file`	A file to specify overall model settings. See settings.file for details.
`env.file`	A file to describe environmental layers and how they change. See env.file for details.
`spfile`	A file specifying species traits. See sp.file for details.
`sp.instr.file`	A file to describe how generation of species' base vital rates is to occur (Optional - not needed if using pre-existing species file). See sp.instr.file for details.
`sp.resp.instr.file`	A file to describe how generation of species' response traits is to occur (Optional - not needed if using pre-existing species file). See sp.resp.instr.file for details.
`landscape.dir`	(not used if generating new landscapes) The directory where the landscape files may be found or a list object containing the landscape information. See landscape.files for more information on the files, and see landscape.object for information on using a landscape generated in R.
`locations.file`	(should be 'none' if spatialdemography is assigning species to the landscape) A file containing initial locations of species. See (locations.file) for more information about the species locations file itself.
`scale.vec`	A list of spatial scales at which to evaluate the model. See scale.vec for more details.
`scale.cells.lst`	A list of cells from the landscape included in each of the above spatial scales. See scale.vec for more details.
`out.metrics`	Metrics to calculate for the model run. See out.metrics for details.
`testing`	An indicator for whether test files are being run. Defaults to F.

Details for each of the inputs in the input files: Please see Overview, Design concepts, Details (ODD, Grimm et al. 2006, 2010) description for SpatialDemography

The main purpose of the model is to produce files, however, the core results are also returned. See Results.Outputs for a summary.

A.C. Keyel

Keyel, A. C., J. L. K. Gerstenlauer, and K. Wiegand. (in prep) spatialdemography: an R package for implementing spatially explicit, matrix-based, metacommunity models.

akeyel/spatialdemography documentation built on May 12, 2019, 4:43 a.m.