Rage: net_repro_rate – R documentation

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net_repro_rate

Calculate net reproductive value (R0) from a matrix population model

Description

Calculate net reproductive value (R0) from a matrix population model. The net reproduction value (R0) is the mean number of recruits produced during the mean life expectancy of an individual. See section 5.3.5 of Caswell (2001).

Usage

net_repro_rate(matU, matR, start = 1, method = "generation")

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 only reflecting transitions due to reproduction; either sexual, clonal, or both). Optionally with named rows and columns indicating the corresponding life stage names.
`start`	Index (or stage name) of the first stage at which the author considers the beginning of life. Only used if `method = "start"`. Defaults to 1.
`method`	The method used to calculate net reproductive value, either `"generation"` or `"start"`. Defaults to `"generation"`. See Details.

Details

The method argument controls how net reproductive rate is calculated.

If method = "generation", net reproductive value is calculated as the per-generation population growth rate (i.e. the dominant eigenvalue of matR %*% N, where N is the fundamental matrix). See Caswell (2001) Section 5.3.4.

If method = "start", net reproductive value is calculated as the expected lifetime production of offspring that start life in stage start, by an individual also starting life in stage start (i.e. (matR %*% N)[start,start]).

If offspring only arise in stage start, the two methods give the same result.

Value

Returns the net reproductive value. If matU is singular (often indicating infinite life expectancy), returns NA.

Author(s)

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

Hal Caswell <h.caswell@uva.nl>

References

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

Examples

data(mpm1)

net_repro_rate(mpm1$matU, mpm1$matF)

# calculate R0 using the start method, specifying either the life stage index
# or name
net_repro_rate(mpm1$matU, mpm1$matF, method = "start", start = 2)
net_repro_rate(mpm1$matU, mpm1$matF, method = "start", start = "small")

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