Additional families compatible with sdmTMB().
Usage
Beta(link = "logit")
lognormal(link = "log")
gamma_mix(link = "log")
lognormal_mix(link = "log")
nbinom2_mix(link = "log")
nbinom2(link = "log")
nbinom1(link = "log")
truncated_nbinom2(link = "log")
truncated_nbinom1(link = "log")
student(link = "identity", df = 3)
tweedie(link = "log")
censored_poisson(link = "log")
delta_gamma(link1 = "logit", link2 = "log")
delta_gamma_mix(link1 = "logit", link2 = "log")
delta_lognormal(link1 = "logit", link2 = "log")
delta_lognormal_mix(link1 = "logit", link2 = "log")
delta_truncated_nbinom2(link1 = "logit", link2 = "log")
delta_truncated_nbinom1(link1 = "logit", link2 = "log")
delta_poisson_link_gamma(link1 = "log", link2 = "log")
delta_poisson_link_lognormal(link1 = "log", link2 = "log")
delta_beta(link1 = "logit", link2 = "logit")Arguments
- link
Link.
- df
Student-t degrees of freedom fixed value parameter.
- link1
Link for first part of delta/hurdle model.
- link2
Link for second part of delta/hurdle model.
Value
A list with elements common to standard R family objects including family,
link, linkfun, and linkinv.
Details
The families ending in _mix() are 2-component mixtures where each
distribution has its own mean but a shared scale parameter.
(Thorson et al. 2011). See the model-description vignette for details.
The parameter plogis(log_p_mix) is the probability of the extreme (larger)
mean and exp(log_ratio_mix) + 1 is the ratio of the larger extreme
mean to the "regular" mean. You can see these parameters in
model$sd_report.
The nbinom2 negative binomial parameterization is the NB2 where the
variance grows quadratically with the mean (Hilbe 2011).
The nbinom1 negative binomial parameterization lets the variance grow
linearly with the mean (Hilbe 2011).
For student(), the degrees of freedom parameter is currently not estimated and is fixed at df.
delta_poisson_link_gamma() is the Poisson-link (complementary
log-log) delta model (Thorson 2018).
delta_poisson_link_lognormal() is the Poisson-link (complementary
log-log) delta model (Thorson 2018).
References
Families ending in _mix():
Thorson, J.T., Stewart, I.J., and Punt, A.E. 2011. Accounting for fish shoals in single- and multi-species survey data using mixture distribution models. Can. J. Fish. Aquat. Sci. 68(9): 1681–1693. doi:10.1139/f2011-086 .
Negative binomial families:
Hilbe, J. M. 2011. Negative binomial regression. Cambridge University Press.
Poisson-link families:
Thorson, J.T. 2018. Three problems with the conventional delta-model for biomass sampling data, and a computationally efficient alternative. Canadian Journal of Fisheries and Aquatic Sciences, 75(9), 1369-1382. doi:10.1139/cjfas-2017-0266
Examples
Beta(link = "logit")
#>
#> Family: Beta
#> Link function: logit
#>
lognormal(link = "log")
#>
#> Family: lognormal
#> Link function: log
#>
gamma_mix(link = "log")
#>
#> Family: gamma_mix
#> Link function: log
#>
lognormal_mix(link = "log")
#>
#> Family: lognormal_mix
#> Link function: log
#>
nbinom2_mix(link = "log")
#>
#> Family: nbinom2_mix
#> Link function: log
#>
nbinom2(link = "log")
#>
#> Family: nbinom2
#> Link function: log
#>
nbinom1(link = "log")
#>
#> Family: nbinom1
#> Link function: log
#>
truncated_nbinom2(link = "log")
#>
#> Family: truncated_nbinom2
#> Link function: log
#>
truncated_nbinom1(link = "log")
#>
#> Family: truncated_nbinom1
#> Link function: log
#>
student(link = "identity")
#>
#> Family: student
#> Link function: identity
#>
tweedie(link = "log")
#>
#> Family: tweedie
#> Link function: log
#>
censored_poisson(link = "log")
#>
#> Family: censored_poisson
#> Link function: log
#>
delta_gamma()
#>
#> Family: binomial Gamma
#> Link function: logit log
#>
delta_gamma_mix()
#>
#> Family: binomial gamma_mix
#> Link function: logit log
#>
delta_lognormal()
#>
#> Family: binomial lognormal
#> Link function: logit log
#>
delta_lognormal_mix()
#>
#> Family: binomial lognormal_mix
#> Link function: logit log
#>
delta_truncated_nbinom2()
#>
#> Family: binomial truncated_nbinom2
#> Link function: logit log
#>
delta_truncated_nbinom1()
#>
#> Family: binomial truncated_nbinom1
#> Link function: logit log
#>
delta_poisson_link_gamma()
#>
#> Family: binomial Gamma
#> Link function: log log
#>
delta_poisson_link_lognormal()
#>
#> Family: binomial lognormal
#> Link function: log log
#>
delta_beta()
#>
#> Family: binomial Beta
#> Link function: logit logit
#>