R/net_repro_rate.R
net_repro_rate.RdCalculate 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).
net_repro_rate(
matU,
matR = NULL,
matF = NULL,
matC = NULL,
start = 1,
method = "generation"
)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.
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.
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.
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.
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.
The method used to calculate net reproductive rate, either
"generation" or "start". Defaults to "generation".
See Details.
Returns the net reproductive rate. If matU is singular (often
indicating infinite life expectancy), returns NA.
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.
Caswell, H. 2001. Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates; 2nd edition. ISBN: 978-0878930968
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()
data(mpm1)
net_repro_rate(mpm1$matU, mpm1$matF)
#> [1] 1.852091
# 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)
#> [1] 1.852091
net_repro_rate(mpm1$matU, mpm1$matF, method = "start", start = "seed")
#> [1] 1.852091
# 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)
#> [1] 1.852091
net_repro_rate(matU = mpm1$matU, matR = mpm1$matF,
method = "start", start = "seed")
#> [1] 1.852091