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

View source: R/IPMpack-Matrices.R View source: R/IPMpack-Matrices.R

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.

1 2 3 4 5 | ```
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 |

`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`

1 | ```
## See makeCompoundFmatrix for examples
``` |

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