plotHistSlice: plot a slice of the landscape history

In stranda/holoSimCell: Linked demographic/genetic simulation

plot a slice of the landscape history

Description

Plots the history of colonization events from a spatially-explicit forward simulation of population expansion up to a specified time step in the simulation.

Usage

plotHistSlice(timeslice, ph, landscape, window = c(0, timeslice))

Arguments

timeslice	the layer of the landscape that corresponds to a time step (generation) in the simulation
ph	population history object (direct output from gepophist2.cells)
landscape	the landscape object that drives the simulation (see ashSetupLandscape for a full description of the landscape object)
window	(optional, default = c(0,timeslice)) a two-element vector that defines the window of time for colonization events shown in the plot

Details

This function takes a fine-grained spatio-temporal history of a species generated by the forward-time simulator and produces a map that shows population spread through time (up to a specified time step). The input ph object includes the following named components:

• pophist a data frame with population ID, cell row, cell column, timing of colonization, and source population associated with colonists.

• Nvecs a data frame with number of generations columns and number of populations rows that provides population size through time from the forward demographic simulation.

• tmat a matrix of pairwise migration rates between populations, used in subsequent coalescent simulations.

• struct a vector summarizing the structure of the simulated landscape from the forward simulation, x and y dimensions of the grid, number of generations, disperal parameters, etc.

• hab_suit a matrix with number of generations rows and number of populations columns that provides habitat suitability through time.

• coalhist a data frame specifying historical events for the coalescent simulation, includes time of event (time), source (src) and sink (snk) IDs, and fractional colonization (prop).

• popslst a list object with one element per population from the forward-time demographic simulation. Each element includes information on location on the landscape, colonization time, source populations, and population size through time.

Value

Does not return an object, but creates a plot illustrating the history of colonization of cells on the landscape over a specified time in the simulation. Arrows indicate the direction of colonization and points are sized relative to population size in the forward simulation. Habitat suitability (at generation timeslice) is represented by a color gradient (green as highest suitability).

See Also

getpophist2.cells, plothist, ashSetupLandscape

Examples

library(holoSimCell)
parms <- drawParms(control = system.file("extdata/ashpaper","Ash_priors.csv",package="holoSimCell"))
load(file=paste0(system.file(package="holoSimCell"),"/extdata/landscapes/",pollenPulls[[1]]$file))
refpops <- pollenPulls[[1]]$refs
avgCellsz <- mean(c(res(landscape$sumrast)))

ph = getpophist2.cells(h = landscape$details$ncells, xdim = landscape$details$x.dim, ydim = landscape$details$y.dim,
                       landscape=landscape,
                       refs=refpops,   
                       refsz=parms$ref_Ne,
                       lambda=parms$lambda,
                       mix=parms$mix,  
                       shortscale=parms$shortscale*avgCellsz,  
                       shortshape=parms$shortshape, 
                       longmean=parms$longmean*avgCellsz,  
                       ysz=res(landscape$sumrast)[2], 
                       xsz=res(landscape$sumrast)[1], 
                       K = parms$Ne) 

plotHistSlice(timeslice = 20, ph = ph, landscape = landscape)
plotHistSlice(timeslice = 200, ph = ph, landscape = landscape, window = c(150,200))

stranda/holoSimCell documentation built on Aug. 4, 2023, 1:12 p.m.