Rage: standard_stages – R documentation

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standard_stages

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 <rob.salguero@zoo.ox.ac.uk>

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

Life History Metrics from Matrix Population Models

v1.0.0

GPL-3

Authors

Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>), Danny Buss [ctb], Pol Capdevila [aut] (<https://orcid.org/0000-0002-2842-4302>), Hal Caswell [aut] (<https://orcid.org/0000-0003-4394-6894>), Judy P. Che-Castaldo [aut] (<https://orcid.org/0000-0002-9118-9202>), John Jackson [aut] (<https://orcid.org/0000-0002-4563-2840>), Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>), Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>), Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>), William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>), Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>), Caroline Schuette [ctb] (<https://orcid.org/0000-0002-2063-8736>), Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>), Chelsea C. Thomas [aut] (<https://orcid.org/0000-0002-8155-9353>)

Initial release