Hook_and_Line_Survey_Catch_Analysis
Binary catch data analyzed at the hook level using a modified stepAIC() function from the MASS R package with a sample from the posterior distribution generated using MCMClogit() in the MCMCpack R package.
The modified stepAIC() adds a buffer to the AIC testing of the models being looped over. The new candidate model has to be better (smaller) than (AIC - buffer) of the current model for the break of the loop not to occur. So if the buffer = 1.95 (the default), then the new candidate model has to be almost 2 AIC units better for the AIC stepping to continue. If the buffer is significantly greater than 2 AIC units then the new model has to be a lot better than the current model for the AIC stepping to continue. Hook and Line Survey binary GLM models appear to need a value far greater than 2 AIC units to have parsimony with not too many variables and biologically dubious interactions terms. This need is not fully understood, but the hook level data does make the total N in the models relatively high and a large number of explanatory variables are considered. In practice the buffer works quite well once it is tuned. The buffer is a vector, with the first element being for main effects and the second element for interaction terms.
Note that the early years of the survey had less non-CCA (Cowcod Conservation Area) sites then the standard 121 unique sites used in the non-CCA part of the survey:
year numSites
1 2004 74
2 2005 90
3 2006 92
4 2007 99
5 2008 120
6 2009 118
7 2010 121
8 2011 111
9 2012 121
10 2013 120
11 2014 120
12 2015 115
13 2016 121
14 2017 120
15 2018 122
16 2019 122
For species that are caught less frequently and predominately only on certain sites, these missing sites may impact the index in the early years.
Years with less sites than 121 after 2008 are due to weather issues. A 122'nd site was added starting in 2016 but is not productive and may be removed in the future.
Reference
Analysis of fishery-independent hook and line-based data for use in the stock assessment of bocaccio rockfish (Sebastes paucispinis)
https://www.sciencedirect.com/science/article/pii/S0165783610002031