Rage: repro_maturity – R documentation

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repro_maturity

Age of reproductive maturity

Description

Apply Markov chain approaches to compute age-specific trajectory of reproduction for individuals in a matrix population model. Includes functions to calculate the probability of achieving reproductive maturity (mature_prob), mean age at first reproduction (mature_age), and distribution of individuals first achieving reproductive maturity among stage class (mature_distrib).

Usage

mature_prob(matU, matR, start = 1L)

mature_age(matU, matR, start = 1L)

mature_distrib(matU, start = 1L, repro_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). Optionally with named rows and columns indicating the corresponding life stage names.
`matR`	The reproductive component of a matrix population model (i.e. a square projection matrix reflecting transitions due to reproduction; either sexual, clonal, or both). Optionally with named rows and columns indicating the corresponding life stage names.
`start`	The index (or stage name) of the first stage at which the author considers the beginning of life. Defaults to 1.
`repro_stages`	A vector of stage names or indices indicating which stages are reproductive. Alternatively, a logical vector of length `ncol(matU)` indicating whether each stage is reproductive (TRUE) or not (FALSE).

Value

For mature_distrib, a vector giving the proportion of individuals that first reproduce within each stage class. For all others, a scalar trait value.

Author(s)

Roberto Salguero-Gomez <rob.salguero@zoo.ox.ac.uk>

Hal Caswell <hcaswell@whoi.edu>

Owen R. Jones <jones@biology.sdu.dk>

Patrick Barks <patrick.barks@gmail.com>

References

Caswell, H. 2001. Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates; 2nd edition. ISBN: 978-0878930968

Examples

data(mpm1)

mature_prob(mpm1$matU, mpm1$matF, start = 2)
mature_age(mpm1$matU, mpm1$matF, start = 2)

### distribution of first reproductive maturity among stage classes
repstage <- repro_stages(mpm1$matF)
mature_distrib(mpm1$matU, start = 2, repro_stages = repstage)

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