net_repro_rate: Calculate net reproductive rate (R0) from a matrix population...

In Rage: Life History Metrics from Matrix Population Models

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

Description

Calculate net reproductive rate (R0) from a matrix population model. The net reproduction rate (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 = NULL,
  matF = NULL,
  matC = NULL,
  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). If matR is not provided, it will be constructed by summing matF and matC.
matF	The matrix reflecting sexual reproduction. If provided without matC, matC is assumed to be a zero matrix. If matR is provided, this argument is ignored.
matC	The matrix reflecting clonal (asexual) reproduction. If provided without matF, matF is assumed to be a zero matrix. If matR is provided, this argument is ignored.
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 rate, 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 rate 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 rate 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 rate. If matU is singular (often indicating infinite life expectancy), returns NA.

Author(s)

Roberto Salguero-Gomez <[e-mail]>

Hal Caswell <[e-mail]>

References

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

See Also

Other life history traits: entropy_d(), entropy_k(), entropy_k_age(), entropy_k_stage(), gen_time(), life_elas(), life_expect_mean(), longevity(), repro_maturity, shape_rep(), shape_surv()

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 = 1)
net_repro_rate(mpm1$matU, mpm1$matF, method = "start", start = "seed")

# It is usually better to explicitly name the arguments, rather than relying
# on order.
net_repro_rate(matU = mpm1$matU, matF = mpm1$matF, 
method = "start", start = 1)

net_repro_rate(matU = mpm1$matU, matR = mpm1$matF, 
method = "start", start = "seed")

Rage documentation built on April 4, 2025, 12:51 a.m.