R/vr_mat.R
vr_mat.RdDivides columns of a matrix population model by the corresponding
stage-specific survival probability, to obtain lower-level vital rates for
growth, stasis, shrinkage, and reproduction. Vital rates corresponding to
biologically impossible transitions are coerced to NA.
These decompositions assume that all transition rates are products of a
stage-specific survival term (column sums of matU) and a lower level
vital rate that is conditional on survival (growth, shrinkage, stasis, or
reproduction). Reproductive vital rates that are not conditional on survival
(i.e., within a stage class from which there is no survival) are also
allowed.
vr_mat_U(matU, posU = matU > 0, surv_only_na = TRUE)
vr_mat_R(matU, matR, posR = matR > 0)The survival component of a matrix population model (i.e., a square projection matrix reflecting survival-related transitions; e.g. progression, stasis, and retrogression)
A logical matrix of the same dimension as matU, with
elements indicating whether a given matU transition is possible
(TRUE) or not (FALSE). Defaults to matU > 0 (see
Details).
If there is only one possible matU transition in a
given column, should that transition be attributed exclusively to survival?
If TRUE, the vital rate of growth/stasis/shrinkage in that column
will be coerced to NA. If FALSE, dividing the single
transition by the stage-specific survival probability will always yield a
value of 1. Defaults to TRUE.
The reproductive component of a matrix population model (i.e., a square projection matrix reflecting transitions due to reproduction; either sexual, clonal, or both)
A logical matrix of the same dimension as matR, with
elements indicating whether a given matR transition is possible
(TRUE) or not (FALSE). Defaults to matR > 0 (see
Details).
A matrix of vital rates. Vital rates corresponding to impossible
transitions will be coerced to NA (see Details).
A transition rate of 0 within a matrix population model may indicate
that the transition is not possible in the given life cycle (e.g., tadpoles
never revert to eggs), or that the transition is possible but was estimated
to be 0 in the relevant population and time period. If vital rates are
to be averaged across multiple stage classes, or compared across populations,
it may be important to distinguish between these two types of zeros.
By default, vr_mat assumes that a transition rate of
0 indicates an impossible transition, in which case a value of
NA will be returned in the relevant matrix cell. Specifically, the
arguments posU and posR are specified by the logical
expressions (matU > 0) and (matR > 0), respectively. If the
matrix population model includes transitions that are possible but estimated
to be 0, one should specify the posU and/or posR
arguments manually.
Caswell, H. 2001. Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates; 2nd edition. ISBN: 978-0878930968
Other vital rates:
vital_rates(),
vr_vec,
vr
matU <- rbind(
c(0.1, 0, 0, 0),
c(0.5, 0.2, 0.1, 0),
c(0, 0.3, 0.3, 0.1),
c(0, 0, 0.5, 0.6)
)
matR <- rbind(
c(0, 0, 1.1, 1.6),
c(0, 0, 0.8, 0.4),
c(0, 0, 0, 0),
c(0, 0, 0, 0)
)
# extract vital rates of survival from matU
vr_mat_U(matU)
#> [,1] [,2] [,3] [,4]
#> [1,] 0.1666667 NA NA NA
#> [2,] 0.8333333 0.4 0.1111111 NA
#> [3,] NA 0.6 0.3333333 0.1428571
#> [4,] NA NA 0.5555556 0.8571429
# extract vital rates of reproduction from matR
vr_mat_R(matU, matR)
#> [,1] [,2] [,3] [,4]
#> [1,] NA NA 1.2222222 2.2857143
#> [2,] NA NA 0.8888889 0.5714286
#> [3,] NA NA NA NA
#> [4,] NA NA NA NA