makeCompoundFmatrix: Builds a compound F matrix.

Description

Uses fecundity object, and environmental transition objects to construct a matrix defining probabilities for transitions between sizes due to fecundity given both a continuous state (e.g. size) and environmental state, as well as a discrete stage if necessary (e.g. seedbank). NOTE - old createCompoundFmatrix is being deprecated; use makeCompoundFmatrix instead.

Usage

makeCompoundFmatrix(nEnvClass = 2, nBigMatrix = 50,
minSize = -1, maxSize = 50, envMatrix, fecObj, integrateType="midpoint", 
correction="none",
preCensus = TRUE, survObj = NULL, growObj = NULL, offspringObj=NULL)

Arguments

nEnvClass

numeric, number of environmental classes, defaults to 2.

nBigMatrix

numeric, number of size bins in the P matrix, defaults to 50.

minSize

numeric, minimum size of the P matrix, defaults to -1.

maxSize

numeric, maximum size of the P matrix, defaults to 50.

envMatrix

envMatrix object defining transitions between environmental states for each size.

fecObj

fecundity object.

integrateType

integration type, defaults to "midpoint" (which uses probability density function); other option is "cumul" (which uses the cumulative density function).

correction

correction type, defaults to none. The first option is constant which will multiply every column of the IPM by a constant sufficient to adjust values to those predicted for total fertility at that size. The second option is discretizeExtremes which will place all transitions to sizes smaller than minSize into the smallest bin, and transitions to sizes larger than maxSize into the largest bin.

preCensus

logical (TRUE or FALSE), indicating whether the fecundity object should represent an interval between pre-breeding or a post-breeding censusses. defaults to TRUE (pre-breeding census), meaning that all reproduction and offspring rates required for the F matrix are embedded in fecObj. Alternatively, an F matrix based on post-breeding census (preCensus=FALSE) requires additional survObj and growObj, to cover the survival and growth of the parents until the reproduction event.

survObj

suvival object, describing the survival of parents from a census until the reproduction event starts (at some point during the inter-census time step.

growObj

growth object, describing the growth of parents that survive until the reproduction event starts. Warning: this growth object is still ignored in makeIPMFmatrix in the current version of IPMpack. It will become functional in coming versions.

offspringObj

growth object, describing the size of offspring (this process may alternatively appear in fecObj).

Value

an object of class IPMmatrix with dimensions nBigMatrix*nEnvClass, or if discrete transitions exist (nBigMatrix+nDisc)*nEnvClass

References

For information on F matrix: Caswell. 2001. Matrix population models: construction, analysis, and interpretation. 2nd ed. Sinauer. p110-112.

For midpoint: Zuidema, Jongejans, Chien, During & Schieving. Integral projection models for trees: a new parameterization method and a validation of model output. Journal of Ecology 98, p345-355.

For multiple-vital rate integration on fecundity: Yang, Jongejans, Yang & Bishop. 2011. The effect of consumers and mutualists of Vaccinum membranaceum at Mount St. Helens: dependence on successional context. PLoS One 10, p1-11.

Examples

Run this code

# Data with only continuous stage and two habitats
dff <- generateData()
dff$fec[dff$fec==0] <- NA
Fmatrix <-makeCompoundFmatrix(nBigMatrix = 20, 
	minSize = min(dff$size, na.rm = TRUE), 
		maxSize = max(dff$size, na.rm=TRUE), 
			envMatrix = makeEnvObj(dff), 
				fecObj = makeFecObj(dff, Formula = fec~size+size2+covariate, 
					Transform = "log"))

image(1:nrow(Fmatrix), 1:ncol(Fmatrix), t(log(Fmatrix)), 
	xlab="Continuous state (e.g. size) at t", 
		ylab="Continuous state (e.g. size) at t+1", axes = FALSE)
axis(1, at = 1:nrow(Fmatrix), lab = round(rep(Fmatrix@meshpoints, 
    Fmatrix@nEnvClass), 2))
axis(2,at = 1:nrow(Fmatrix), lab = round(rep(Fmatrix@meshpoints,
    Fmatrix@nEnvClass), 2))
abline(h = length(Fmatrix@meshpoints)*(1:Fmatrix@nEnvClass))
abline(v = length(Fmatrix@meshpoints)*(1:Fmatrix@nEnvClass))

# Data with continuous and discrete stages
dff <- generateData(type="discrete")
dff$fec[dff$fec==0] <- NA
dff$covariate <- sample(1:3, size = nrow(dff), replace = TRUE)
dff$covariateNext <- sample(1:3, size = nrow(dff), replace = TRUE)
fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log", 
	offspringSplitter=data.frame(continuous = 0.9, dormant = 0.1))
Fmatrix <- makeCompoundFmatrix(minSize = min(dff$size, na.rm=TRUE),
maxSize = max(dff$size, na.rm = TRUE), envMatrix = makeEnvObj(dff), 
    fecObj = fv1)