parsetting: rate vector for each species at each island, called widely by other functions

Description

set up rate matrix of species-patches for the simulation

Usage

parsetting(island, rate = 1, scale = 2, type = "decrease")

Arguments

island

number of patches

rate

basal rate for setting up the matrix

scale

controlling the parameter's low value=parameter original value/scale; while parameter's high value=parameter original value*scale. Specifically used in the spatial types.

type

a model configuration vector describing the spatial patterns of each of the paramters (default is "decrease"), for example, a vector like this, c("decrease","decrease","decrease","increase","increase","increase","mosaiclow") can be used as the input. There are 5 simple spatial types currently for the package: "decrease",the parameter will have one-time decreasing transition from source patch to other sink patches in the middle of the patches "increase",the parameter will have one-time increasing transition from source patch to other sink patches in the middle of the patches "constant",the parameter will keep in a constant value across the patches during the simulation "mosaiclow",the parameter will switch from a low value to a high value one-by-one from the source patch to sink patches, so source patch the paramter for the species there will be assigned a low value "mosaichigh",the parameter will switch from a high value to a low value one-by-one from the source patch to sink patches,so source patch the paramter for the species there will be assigned a high value

Details

will return a vector for recording species parameter value at each patch

References

Chen YH (2012) coexist: an R package for performing species coexistence modeling and analysis under asymmetric dispersal and fluctuating source-sink dynamics. http://code.google.com/p/coexist.

Examples

Run this code

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (island, rate = 1, scale = 2, type = "decrease") 
{
    parset <- vector()
    length(parset) <- island
    if (type == "decrease") {
        parset[1:as.integer(island/2)] = rate
        parset[(as.integer(island/2) + 1):island] = rate/scale
    }
    if (type == "increase") {
        parset[1:as.integer(island/2)] = rate/scale
        parset[(as.integer(island/2) + 1):island] = rate
    }
    if (type == "constant") {
        parset[1:island] = rate
    }
    if (type == "mosaiclow") {
        for (i in 1:island) {
            if (i%%2 == 0) {
                parset[i] = rate
            }
            else {
                parset[i] = rate/scale
            }
        }
    }
    if (type == "mosaichigh") {
        for (i in 1:island) {
            if (i%%2 == 0) {
                parset[i] = rate/scale
            }
            else {
                parset[i] = rate
            }
        }
    }
    return(parset)
  }