Calculates a 'shape' value of survival lifespan inequality by comparing the area under a survival curve (over age) with the area under a constant survival function.
shape_surv(surv, xmin = NULL, xmax = NULL, trunc = FALSE, ...)Either 1) a numeric vector describing a survival curve (lx), 2) a
data.frame / list with one column / element titled 'lx'
describing a survival curve, optionally a column / element 'x' containing
age classes (each element a number representing the age at the start of the
class), or 3), a matrix, specifically the U submatrix of a matrix
population model (A).
In case (2) If x is not supplied, the function will assume age
classes starting at 0 with time steps of 1 unit of the
ProjectionInterval. If x begins at 0 then lx[1]
should equal 1. If x ends at maximum longevity, then
lx[which.max(x)] should equal 0; however it is possible to
supply partial survivorship curves.
The minimum and maximum age respectively over which to
evaluate shape. If not given, these default to min(x) and
max(x) respectively.
logical determining whether to truncate life tables or not when
any lx == 0. Usually this is the case only for the final value of
lx. As the function calculates log(lx), these value(s) cannot
be handled. trunc == TRUE strips out the zero value(s). An
alternative to this is to transform the zeroes to something approximating
zero (e.g., 1e-7).
Additional variables passed to `mpm_to_lx`, if data are supplied as a matrix.
a shape value describing lifespan inequality by comparing the area
under a survival (lx) curve over age with the area under a constant
(Type II) survival function. The shape value may take any real value
between -0.5 and +0.5. A value of 0 indicates negligible ageing (neither
generally increasing nor generally decreasing survival with age); negative
values indicate negative senescence (generally increasing survival with
age); positive values indicate senescence (generally decreasing survival
with age). A value of +0.5 indicates that all individuals die at age of
maximum longevity; a value of -0.5 indicates that (hypothetically) all
individuals die at birth.
Wrycza, T.F. and Baudisch, A., 2014. The pace of aging: Intrinsic time scales in demography. Demographic Research, 30, pp.1571-1590. <doi:10.4054/DemRes.2014.30.57>
Baudisch, A. 2011, The pace and shape of ageing. Methods in Ecology and Evolution, 2: 375-382. <doi:10.1111/j.2041-210X.2010.00087.x>
Baudisch, A, Stott, I. 2019. A pace and shape perspective on fertility. Methods Ecol Evol. 10: 1941– 1951. <doi:10.1111/2041-210X.13289>
Other life history traits:
entropy_d(),
entropy_k_age(),
entropy_k_stage(),
entropy_k(),
gen_time(),
life_elas(),
life_expect_mean(),
longevity(),
net_repro_rate(),
repro_maturity,
shape_rep()