mpm_rearrange: Rearrange stages of a matrix population model to segregate...

In Rage: Life History Metrics from Matrix Population Models

Rearrange stages of a matrix population model to segregate reproductive and non-reproductive stages

Description

Rearrange stages of a matrix population model so that all inter-reproductive stages fall in the final rows/columns of the matrix. This is a preparatory step to collapsing the matrix model into a standardized set of stages (e.g., propagule, pre-reproductive, reproductive, and post-reproductive).

Usage

mpm_rearrange(matU, matF, matC = NULL, repro_stages, matrix_stages)

Arguments

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 NULL, indicating no clonal reproduction (i.e., matC is a matrix of zeros).
repro_stages	Logical vector of length ncol(matU) indicating which stages are reproductive. Alternatively, a vector of stage indices or stage names of the reproductive classes.
matrix_stages	A character vector identifying organized matrix stages.

Value

Returns a list with 6 elements:

matU	Rearranged survival matrix
matF	Rearranged sexual reproduction matrix
matC	Rearranged clonal reproduction matrix
matrix_stages	Rearranged vector of organized matrix stages
repro_stages	Rearranged logical vector of reproductive stages
nonRepInterRep	Numeric index for any rearranged inter-reproductive stages

Author(s)

Rob Salguero-Gómez <[e-mail]>

See Also

mpm_standardize

Other transformation: is_leslie_matrix(), leslie_collapse(), mpm_collapse(), mpm_split(), mpm_standardize(), name_stages(), repro_stages(), standard_stages()

Examples

matU <- rbind(
  c(0.1, 0, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0, 0),
  c(0, 0.3, 0.3, 0.1, 0),
  c(0, 0, 0.4, 0.4, 0.1),
  c(0, 0, 0, 0.1, 0.4)
)

matF <- rbind(
  c(0, 1.1, 0, 1.6, 0),
  c(0, 0.8, 0, 0.4, 0),
  c(0, 0, 0, 0, 0),
  c(0, 0, 0, 0, 0),
  c(0, 0, 0, 0, 0)
)

repro_stages <- c(2, 4)
matrix_stages <- c("prop", "active", "active", "active", "active")

mpm_rearrange(matU, matF,
  repro_stages = repro_stages,
  matrix_stages = matrix_stages
)

Rage documentation built on Sept. 30, 2023, 1:06 a.m.