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

Collapse a matrix population model to a smaller number of stages. For instance, to compare properties of multiple projection matrices with different numbers of stages, one might first collapse those matrices to a standardized set of stages (e.g. propagule, pre-reproductive, reproductive, and post-reproductive). The transition rates in the collapsed matrix are a weighted average of the transition rates from the relevant stages of the original matrix, weighted by the relative proportion of each stage class expected at the stable distribution.

1 | ```
collapseMatrix(matU, matF, matC = NULL, collapse)
``` |

`matU` |
The survival component of a matrix population model (i.e. a square projection matrix reflecting survival-related transitions; e.g. progression, stasis, and retrogression) |

`matF` |
The sexual component of a matrix population model (i.e. a square projection matrix reflecting transitions due to sexual reproduction) |

`matC` |
The clonal component of a matrix population model (i.e. a square
projection matrix reflecting transitions due to clonal reproduction).
Defaults to |

`collapse` |
A list giving the mapping between stages of the original
matrix and the desired stages of the collapsed matrix (e.g. See |

A list with four elements:

`matA` |
Collapsed projection matrix |

`matU` |
Survival component of the collapsed projection matrix |

`matF` |
Sexual reproduction component of the collapsed projection matrix |

`matC` |
Clonal reproduction component of the collapsed projection matrix |

The collapsed matrix will always be of dimension `length(collapse)`

,
even if one or more elements of the `collapse`

argument is `NA`

(corresponding to a desired stage of the collapsed matrix that is not present
in the original matrix). In the collapsed matrix, any row/column
corresponding to a missing stage will be coerced to `NA`

.

This method of collapsing a matrix population model preserves the
equilibrium population growth rate (*lamda*) and relative stable
distribution, but is not expected to preserve other traits such as relative
reproductive values, sensitivities, net reproductive rates, life
expectancy, etc.

Rob Salguero-Gómez <[email protected]>

Salguero-Gomez, R. & Plotkin, J. B. (2010) Matrix dimensions bias demographic inferences: implications for comparative plant demography. The American Naturalist 176, 710-722.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
matU <- rbind(c( 0, 0, 0, 0),
c(0.5, 0, 0, 0),
c( 0, 0.3, 0, 0),
c( 0, 0, 0.2, 0.1))
matF <- rbind(c( 0, 0, 1.1, 1.6),
c( 0, 0, 0.8, 0.4),
c( 0, 0, 0, 0),
c( 0, 0, 0, 0))
matC <- rbind(c( 0, 0, 0.4, 0.5),
c( 0, 0, 0.3, 0.1),
c( 0, 0, 0, 0),
c( 0, 0, 0, 0))
# collapse reproductive stages
collapse1 <- list(1, 2, 3:4)
collapseMatrix(matU, matF, matC, collapse1)
# collapse pre-reproductive stages, and reproductive stages
collapse2 <- list(1:2, 3:4)
collapseMatrix(matU, matF, matC, collapse2)
``` |

jonesor/Rage documentation built on May 22, 2019, 1:42 p.m.

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