timeToSize: Projects how long it takes to get from a starting...

In wpetry/IPMpack2: Builds and analyses Integral Projection Models (IPMs).

Projects how long it takes to get from a starting distribution to a target continuous stage value.

Description

Provided with a starting vector reflecting starting individual sizes, this function projects forward via the provided IPM until a defined proportion of the population has reach the chosen endSize. Only works for single environment or compound matrices (not time-varying covariates apart from a single discrete one).

Usage

timeToSize(startingSizes, IPM, endSize, startingEnv = 1, maxT = 100, propReach = 0.01)

Arguments

startingSizes	vector of starting sizes reflecting sizes of individuals in the starting population (in any order).
IPM	the IPM Pmatrix.
endSize	the end size.
startingEnv	vector of starting env, same length as startingSizes, or length = 1 if compound matrices are not being used.
maxT	the max number of time steps tested.
propReach	the proportion of the starting pop that have to be > than the endSize for it to count.

Details

Plots and returned values of survivorship from preliminary runs will give a notion of how low this has to be.

Value

ts.dist	the time-series of size distribution
time.reach	the time for n.reach to be at sizes > endSize
survivorship	survivorship over the course of the time elapsed for that pop

Author(s)

C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.

References

Caswell, 2001. Matrix population models: analysis, construction and interpretation. 2nd ed. Sinauer.

Examples

#note that with the "fake data" essentially either takes 
#forever or is immediate...
dff <- generateData()
startSizes <- rnorm(1000, 2.5, 1)
Pmatrix <- makeIPMPmatrix(minSize = 1.2*min(dff$size, na.rm=TRUE),
maxSize = 1.2*max(dff$size, na.rm=TRUE), 
growObj = makeGrowthObj(dff), 
survObj = makeSurvObj(dff))

rc <- timeToSize(startingSizes = startSizes, IPM = Pmatrix, endSize = 6, 
startingEnv = 1, maxT = 1000, propReach = 0.001)

names(rc)

par(mfrow=c(2,2), bty = "l")
## Make picture with lines for distribution of 
## population on different time points
matplot(Pmatrix@meshpoints, rc$ts.dist, type = "l", xlab = "size", 
ylab = "Number of individuals")

## Examine time elapsed for propReach to attain the chosen endSize
rc$time.reach

## Plot out the survivorship
plot(rc$survivorship, type = "l", #log = "y", 
xlab = "time step", ylab = "Probability original population survival", 
ylim = c(0,1), col = "gray")

wpetry/IPMpack2 documentation built on Sept. 29, 2022, 9:41 a.m.