addscenario: Add a protection scenario
In remi-daigle/BESTMPA:

Description Usage Arguments Value Examples

Adds protection scenarios to the SpatialPolygonsDataFrame grid. Variables in the dataframe of the SpatialPolygonsDataFrame that should otherwise be logical (e.g. scenarios) are converted to numeric since logical variables are incompatible with ESRI shapefiles.

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addscenario(domain, included = NA, priority = NA, excluded = NA,
  MPA_coverage = 0.1, replicates = 25, dist = NA, name = "MPA_SQ",
  cell_size, cells = 1)

`domain`	the gridded model domain (SpatialPolygonsDataFrame) as generated by inigrid
`included`	A logical vector indicating which grid cells are to be included in MPA assignment. This accomodates the pre-existing MPAs.
`priority`	A logical vector indicating which grid cells are to be prioritized when assigning MPA protection. The algorithm will select all priority cells regardless of distance/spacing before selecting non-priority cells.
`excluded`	A logical vector indicating which grid cells are to be excluded from MPA assignment
`MPA_coverage`	Target protection level as a proportion (e.g. 0.2 is 20% protection)
`replicates`	A vector of replicates for the main body of the model
`dist`	The fixed distance for setting MPA distance in m in fixed distance scenarios.
`name`	The name of the scenario to be added. While any character string will be accepted, using the format "MPA_XX" where XX is any 2 letters which indicates treatment type is suggested to minimize conflict with other functions in the BESTMPA package.
`cell_size`	cell size of the grid used in initgrid
`cells`	minimum number of cells that can be considered as an MPA. defaults to 1

SpatialPolygonsDataFrame

proj  <- "+proj=utm +zone=20 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"
p <- initgrid(EEZ=EEZ,cell_size=20000,proj=proj,areas=c(Habitats=Habitats,Breeding=Breeding))
# set targeted scenario
p <- addscenario(domain=p,included=oldMPA,priority=p$Habitats,excluded=p$Breeding,MPA_coverage=0.1,replicates=1:3,dist=75000,name="MPA_TR",cell_size=20000,cells=3)