Calculate longevity (the age x at which survivorship for a synthetic cohort falls below some critical proportion) from a matrix population model
longevity(matU, start = 1L, x_max = 1000, lx_crit = 0.01)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 index (or stage name) of the first stage at which the author
considers the beginning of life. Defaults to 1. Alternately, a
numeric vector giving the starting population vector (in which case
length(start) must match ncol(matU)). See section
Starting from multiple stages.
The maximum age, in units of the MPM projection interval, to
which survivorship will be calculated. Defaults to 1000.
Proportion of initial cohort remaining before all are
considered dead (a value between 0 and 1). Defaults to 0.01.
Returns longevity, the integer age at which expected survivorship
falls below lx_crit. If survivorship doesn't reach lx_crit by
x_max, returns NA and prints a warning message.
Note that the units of time in returned values are the same as the
(ProjectionInterval) of the MPM.
Rather than specifying argument start as a single stage class from
which all individuals start life, it may sometimes be desirable to allow for
multiple starting stage classes. For example, if we want to start our
calculation of longevity from reproductive maturity (i.e., first
reproduction), we should account for the possibility that there may be
multiple stage classes in which an individual could first reproduce.
To specify multiple starting stage classes, specify argument start as
the desired starting population vector, giving the proportion
of individuals starting in each stage class (the length of start
should match the number of columns in the relevant MPM).
Caswell, H. 2001. Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates; 2nd edition. ISBN: 978-0878930968
Morris, W. F. & Doak, D. F. 2003. Quantitative Conservation Biology: Theory and Practice of Population Viability Analysis. Sinauer Associates, Sunderland, Massachusetts, USA
mature_distrib for calculating the proportion of
individuals achieving reproductive maturity in each stage class.
Other life history traits:
entropy_d(),
entropy_k_age(),
entropy_k_stage(),
entropy_k(),
gen_time(),
life_elas(),
life_expect_mean(),
net_repro_rate(),
repro_maturity,
shape_rep(),
shape_surv()
data(mpm1)
longevity(mpm1$matU, start = 2)
#> [1] 12
longevity(mpm1$matU, start = "small") # equivalent using named life stages
#> [1] 12
longevity(mpm1$matU, start = 2, lx_crit = 0.05)
#> [1] 7
# starting from first reproduction
repstages <- repro_stages(mpm1$matF)
n1 <- mature_distrib(mpm1$matU, start = 2, repro_stages = repstages)
longevity(mpm1$matU, start = n1)
#> [1] 13