IPMpack (version 2.0)

makeIPMCmatrix: Builds C matrices.

Description

Uses clonality objects to construct a matrix defining per-capita contribution to clonal stages (e.g., propagules [seed, spore], seedlings, calves) by clonal reproduction. NOTE - old createIPMCmatrix is being deprecated; use makeIPMCmatrix instead.

Usage

makeIPMCmatrix(clonalObj, 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

clonalObj

clonal reproduction object; currently essentially identical to a fecundity reproduction object

nEnvClass

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

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.

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

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 require

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 individu

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 of dimensions nBigMatrix or nBigMatrix+nDiscrete classes (defined by clonalObj@offspringSplitter-1).

References

For information on C 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.

See Also

makeIPMPmatrix,makeIPMFmatrix,makeIPMmatrix

Examples

# Data with only continuous stage and one habitat
dff <- generateData()
dff$fec[dff$fec==0] <- NA
cv1 <- makeClonalObj(dff, Formula = fec~size, Transform = "log")
Cmatrix <- makeIPMCmatrix(clonalObj = cv1, nBigMatrix = 20, 
	minSize = min(dff$size, na.rm = TRUE), maxSize = max(dff$size, na.rm = TRUE))

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