| Title: | Model-based estimation of northern fur seal pup production |
|---|---|
| Description: | Impliments methods for model-based estimation of northern fur seal pup production. |
| Authors: | Devin S. Johnson |
| Maintainer: | Devin S. Johnson <[email protected]> |
| License: | CC0 |
| Version: | 0.0.1 |
| Built: | 2024-11-21 03:04:43 UTC |
| Source: | https://github.com/dsjohnson/mbpp |
Fit asymptotic approximation of hierarchical N-mixture model for estimation of northern fur seal pup production.
asym_mbpp( det_formula = ~rcode * resample * observer, avail_formula = ~rcode, mark_data, resight_data, par, ... )asym_mbpp( det_formula = ~rcode * resample * observer, avail_formula = ~rcode, mark_data, resight_data, par, ... )
det_formula |
formula for the detection model |
avail_formula |
formula for the avaialbility model |
mark_data |
Data frame providing pups marked and dead pup counts for each site |
resight_data |
Data frame providing marked and unmarked resight counts |
par |
Optional start value specification. |
... |
additional arguments passed to nlminb() or TMB::MakeADFun() for optimization |
Devin S. Johnson
Parameteric bootstrap sample for abundance
boot_asym(object, size = 10000)boot_asym(object, size = 10000)
object |
A fitted model object from aysm_mbpp |
size |
Number of bootstrap samples to draw |
This function uses the asymtotic model fit from TMB to generate a bootstrap sample for parameter inference
Compile package TMB function
compile_mbpp_tmb()compile_mbpp_tmb()
model |
Details which model to compile |
This function is only used once after the package is installed to compile the c++ TMB code for asymptotic abundance estimation. Simply call the function to compile the source code.
Fit asymptotic approximation of hierarchical N-mixture model for estimation of northern fur seal pup production.
jags_mbpp( dp_formula = ~0 + log(harem_bulls), avail_formula = ~rcode, mark_data, resight_data, par, ... )jags_mbpp( dp_formula = ~0 + log(harem_bulls), avail_formula = ~rcode, mark_data, resight_data, par, ... )
avail_formula |
formula for the avaialbility model |
mark_data |
Data frame providing pups marked and dead pup counts for each site |
resight_data |
Data frame providing marked and unmarked resight counts |
par |
Optional start value specification. |
... |
additional arguments passed to R2jags::jags such as n.chains, n.iter, n.burnin, or n.thin for optimization |
det_formula |
formula for the detection model |
Devin S. Johnson
Northern fur seal shear marking data from 2016
A data frame with 19 observations on the following 6 variables.
Island designation
Rookery designation
Number of dead pups counted on survey
Estimated pup production using design-based method
Estimated standard error using design-based method
Number of pups shear marked
Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA 7600 Sand Point Way NE Seattle, WA 98115
Northern fur seal mark resight data from 2016
A data frame with 76 observations on the following 6 variables.
Island designation
Rookery designation
The resight occasion designation
The observer designation
Number of marked pups observed
Number of unmarked pups observed
Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA 7600 Sand Point Way NE Seattle, WA 98115