standard_stages: Identify stages corresponding to different parts of the...

In Rage: Life History Metrics from Matrix Population Models

Identify stages corresponding to different parts of the reproductive life cycle

Description

Identify the stages of a matrix population model that correspond to different parts of the reproductive life cycle, namely propagule, pre-reproductive, reproductive and post-reproductive. These classifications are used to standardise matrices to allow comparisons across species with different life cycle structures, see mpm_standardize.

Usage

standard_stages(matF, repro_stages, matrix_stages)

Arguments

matF	The sexual component of a matrix population model (i.e., a square projection matrix reflecting transitions only due to sexual reproduction). It assumes that it has been rearranged so that non-reproductive stages are in the final rows/columns.
repro_stages	Logical vector identifying which stages are reproductive.
matrix_stages	(character) vector of stages, values are prop (propagule), active, and dorm (dormant).

Details

Assumes that fecundity and mean fecundity matrices have been rearranged so that non-reproductive stages are in the final rows/columns. Output indicates groupings to be used when collapsing the matrix model.

Value

A list with four elements:

propStages	Position of the propagule stages
preRepStages	Position of the pre-reproductive stages
repStages	Position of the reproductive stages
postRepStages	Position of the post-reproductive stages

Note

Dormant stages are not currently handled.

Author(s)

Rob Salguero-Gomez <[e-mail]>

See Also

mpm_standardize

Other transformation: is_leslie_matrix(), leslie_collapse(), mpm_collapse(), mpm_rearrange(), mpm_split(), mpm_standardize(), name_stages(), repro_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(FALSE, TRUE, FALSE, TRUE, FALSE)
matrix_stages <- c("prop", "active", "active", "active", "active")

r <- mpm_rearrange(matU, matF,
  repro_stages = repro_stages,
  matrix_stages = matrix_stages
)

standard_stages(r$matF, r$repro_stages, r$matrix_stages)

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