kissmig: Run a simple species migration model

In kissmig: a Keep It Simple Species Migration Model

Run a simple species migration model

Description

kissmig runs a simple, raster-based, stochastic migration model to simulate species migration and range shifts. It uses a geographic area of origin along with suitability maps to iteratively run a simple 3x3 cell algorithm. Specifically, it allows for generating accessibility maps for easy integration of limited migration in species distribution models (Nobis and Normand 2014, <\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/ecog.00930")}>).

Usage

kissmig(O, S=NULL, it, type='FOC', signed=FALSE, pext=1.0, pcor=0.2, seed=NULL)

Arguments

O	a single RasterLayer of the geographic origin
S	a Raster* object of suitability, i.e., a RasterLayer, RasterStack, or RasterBrick
it	number of iteration steps
type	type of result: final distribution ('DIS'), iteration step of first occurrence ('FOC'), iteration step of last occurrence ('LOC'), or number of iteration steps with occurrence ('NOC')
signed	if TRUE, the sign indicates whether the cells was colonized (positive) or uncolonized (negative) after the last iteration step
pext	propability [0,1] a colonized cell becomes uncolonized between iteration steps, i.e., the species gets locally extinct
pcor	propability [0,1] corner cells are considered in the 3x3 cell neighborhood
seed	integer used to set the seed of the random number generator

Details

Starting from origin "O" kissmig simulates migration for "it" iteration steps in a heterogeneous environment characterised by the suitability layer(s) "S". The colonized cells of the origin "O" have value 1, uncolonized cells value 0. In case "S" consists of several suitability layers to cover environmental change, "it" is applied to each layer. Suitability ranges between 0 (unsuitable) and 1 (suitability maximum). kissmig uses a 3x3 algorithm for species spread/migration. All cells get exstinct before an iteration step with probability "pext", and for a recolonization or new colonization event corner cells within the 3x3 neighborhood are considers with probability "pcor" ("pcor"=0.2 produces more realistic circular spread patterns - see Nobis & Normand 2014). For runtime optimization, signed results are generate for "signed"=TRUE, i.e, in addtion to the result type 'FOC, 'LCO', or 'NOC', the sign indicates the final distribution ('DIS') with positive values beeing colonized and negative values beeing previously colonized but uncolonized after the last iteration step. To get reproducible results, the seed of the R random number generator can be set using the "seed" parameter.

References

• Nobis MP and Normand S (2014) KISSMig - a simple model for R to account for limited migration in analyses of species distributions. Ecography 37: 1282-1287. <\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/ecog.00930")}>

• KISSMig homepage <https://purl.oclc.org/wsl/kissmig>

See Also

kissmigAccess, kissmigOrigin

Examples

library(kissmig)

# create a suitability map and geographic origin

s <- kissmigDummyS(mean=12, sd=3)
o <- kissmigOrigin(s, x=8, y=44.5, size=0.5)
l <- s>=0 # land mask used for plotting kissmig results below
plot(s, asp=1.0, main='suitability + origin (in black)')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

# run kissmig with different type of output

k <- kissmig(o, s, it=150, type='FOC')
plot(k*l, asp=1.0, main='First iteration step of occurrence (type="FOC")')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

a <- kissmigAccess(k)
plot(a*l, asp=1.0, main='Accessibility based on "FOC", absolute values')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

a <- kissmigAccess(k, rel=TRUE)
plot(a*l, asp=1.0, main='Accessibility based on "FOC", relative values')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

k <- kissmig(o, s, it=150, type='DIS')
plot(k*l, asp=1.0, main='Final distribution (type="DIS")')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

k <- kissmig(o, s, it=150, type='LOC')
plot(k*l, asp=1.0, main='Last iteration step of occurrence (type="LOC")')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

k <- kissmig(o, s, it=150, type='NOC')
plot(k*l, asp=1.0, main='Number of iteration steps with occurrences (type="NOC")')
plot(o, col=c(NA,"black"), legend=FALSE, add=TRUE) # add origin

kissmig documentation built on Sept. 11, 2024, 5:45 p.m.