Calculates total instantaneous (Z), natural mortality (M) and/or fishing mortality (F) using times-at-large data and methods of Gulland (1955) and McGarvey et al. (2009).
mort.al(relyr = NULL, tal = NULL, N = NULL, method = c(1, 2, 3),
np = 0, stper = NULL, nboot = 500)a vector of release year (or cohort) for individual times-at-large observations.
a vector of individual times-at-large observations.
a vector of number of releases for each release year (or cohort). Each individual observation from a release year should have the same N value.
1 = McGarvey et al., 2 = Gulland. Default is all (i.e., c(1,2)).
the number of periods over which to combine data to make period estimates of mortality. Set np=0 to estimate mortality for each release year.
vector of year values representing the beginning year of each period over which to estimate mortality. The first year in c() must always be the first release year.
the number of resamples for the Gulland method.
dataframe containing the M, F and Z estimates and associated standard errors by period.
The methods of Gulland (1955) and McGarvey et al (2009) are used to estimate Z, F and M (depending on the method) from tagging times-at-large data. For the Gulland method, the standard error of the Z, M, and F estimates are made using a parametric bootstrap method similar to Tanaka (2006). When periods are specified, period-specific mortality estimates and standard errors are derived by averaging release-year-specific mortality estimates. The standard errors are calculated by taking the square-root of the averaged variances of the estimates. To combine data over all years prior to estimation, change all relyr within a period to the same year value.
Gulland, J. A. 1955. On the estimation of population parameters from marked members. Biometrika 42: 269-270.
McGarvey, R., J. M. Matthews, and J. E. Feenstra. 2009. Estimating mortality from times-at-large: testing accuracy and precision using simulated single tag-recovery data. ICES Journal of Marine Science 66: 573-581.
Tanaka, E. 2006. Simultaneous estimation of instantaneous mortality coefficients and rate of effective survivors to number of released fish using multiple sets of tagging experiments. Fisheries Science 72: 710-718.
# NOT RUN {
# }
# NOT RUN {
data(tanaka)
mort.al(relyr = tanaka$relyr, tal = tanaka$tal, N = tanaka$N)
# }
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