IPMpack (version 2.1)

makeIPMFmatrix: Builds F matrices.

Description

Uses fecundity objects to construct a matrix defining per-capita contribution to recruitment stages (e.g., propagules [seed, spore], seedlings, calves) by reproductive stages due to sexual reproduction. NOTE - old createIPMFmatrix is being deprecated; use makeIPMFmatrix instead.

Usage

makeIPMFmatrix(fecObj, nEnvClass = 1, nBigMatrix = 50, minSize = -1, 
	maxSize = 50, chosenCov = data.frame(covariate=1), 
	integrateType="midpoint", correction="none", 
	preCensus = TRUE, survObj = NULL, growObj = NULL, offspringObj=NULL)

Arguments

fecObj

fecundity object.

nEnvClass

numeric, number of environmental classes, always = 1 for non-compound matrices.

nBigMatrix

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

minSize

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

maxSize

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

chosenCov

data-frame indicating level of the discrete covariate, or range of values where multiple covariates are modeled.

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

survival object, describing the survival of parents from a census until the reproduction event starts (at some point during the inter-census time step). If preCensus = FALSE but no survival object is provided, it is assumed that all individuals survive to the breeding event.

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. So far it is assumed that at time of breeding the individuals have the same size as at the beginning of the time interval.

offspringObj

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

Value

an object of class IPMmatrix of dimensions nBigMatrix or nBigMatrix+nDiscrete classes (defined by fecObj@offspringSplitter-1).

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.

For information on unintentional eviction from IPMs (which the various corrections try and account for) see Williams et al. 2012 Avoiding unintentional eviction from integral projection models. Ecology.

See Also

makeIPMPmatrix,makeIPMCmatrix,makeIPMmatrix

Examples

# Data with only continuous stage and one habitat
dff <- generateData()
dff$fec[dff$fec==0] <- NA
fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log")
Fmatrix <- makeIPMFmatrix(fecObj = fv1, nBigMatrix = 20, 
	minSize = min(dff$size, na.rm = TRUE), 
	maxSize = max(dff$size, na.rm = TRUE), correction="constant")

slotNames(Fmatrix)

image(Fmatrix@meshpoints, Fmatrix@meshpoints, t(Fmatrix), 
	xlab = "Continuous (e.g. size) stage at t", 
		ylab = "Continous (e.g. size) stage at t+1")