makeCompoundCmatrix: Builds a compound C matrix.
In IPMpack: Builds and analyses Integral Projection Models (IPMs).

Description Usage Arguments Value Author(s) References See Also Examples

Uses clonality object, and environmental transition objects to construct a matrix defining probabilities for transitions between sizes due to clonal reporudction given both a continuous state (e.g. size) and environmental state, as well as a discrete stage if necessary. Currently only pre-census clonal reproduction can be handled. NOTE - old createCompoundCmatrix is being deprecated; use makeCompoundCmatrix instead.

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

`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.
`clonalObj`	clonality 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).

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

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

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.

makeCompoundPmatrix,makeIPMCmatrix