IPMpack (version 1.6)

createIPMCmatrix: 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. Currently only pre-census clonal reproduction can be handled.

Usage

createIPMCmatrix(clonalObj, nEnvClass = 1, nBigMatrix = 50, minSize = -1, 
	maxSize = 50, chosenCov = data.frame(covariate=1), integrateType="midpoint", correction="none")

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

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

createIPMPmatrix,createIPMFmatrix

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 <- createIPMCmatrix(clonalObj = cv1, nBigMatrix = 20, 
	minSize = min(dff$size, na.rm = TRUE), maxSize = max(dff$size, na.rm = TRUE))

slotNames(Cmatrix)

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