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selectivity re="ar1" with model = "age-specific" options to prepare_wham_input function

11

selectivity$model = "age-specific" without random effects will estimate or fix each age-specific selectivity parameter (estimated as fixed effects) according to specifications of the asap3 dat file or (over-ridden by) selectivity$initial_pars...

timjmiller

Inputting new parameters (par = ) into simulate() function

1

I just downloaded the most recent version of WHAM (main branch) and I'm running into the following issue: When I change the input parameters in the simulate() function of a...

emilylil

Project_wham doesn't work when only 1 WAA matrix in data due to indexing error

1

This line of code generates the below error when only 1 WAA matrix is included in the ASAP input file Code: https://github.com/timjmiller/wham/blob/6c30301d5b68c2bb0c0330cc4f112432c7950dfd/R/prepare_projection.R#L181 Error: Error in apply(data$waa[, avg.yrs.ind, ], c(1, 3),...

ahart1

for age-specific selectivity allow user-specified ages that share the same parameters

5

allow user to force different ages to have the same selectivity but still estimated. This can be helpful when selectivity for some ages are inestimable. It is possible outside of...

timjmiller

allow same selectivity blocks for different fleets/indices

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For example, when considering LPUE or CPUE as indices may wish to use the same selectivity assumptions for the fleet and index. This came up in the Plaice research track...

timjmiller

Dense hessian when only NAA-1 (recruitment) are random effects

1

``` library(wham) path_to_examples

brianstock-NOAA

Plot_wham_output() missing variable yr.col

2

Line 187 of EGB_WHAM_tjm.R is: > plot_wham_output(mod=m1, out.type='html') This returns the error: Error in plot.xy(xy.coords(x, y), type = type, ...) : object 'yr.col' not found As a temporary fix this...

tcarruth

Question: should ragged IAA_mats (varying ages) work by using index_sel_start_age and index_sel_end_age?

2

Line 173 of prepare_wham_input(): temp = asap3$IAA_mats[[i]][, 3 + 1:data$n_ages] requires that all IAA mats have data for all n_ages. However, the NMFS fall survey (that I have at least)...

tcarruth

Problem could be that in models with time-varying M, there's nothing to stop M from being so high that SPR0 is driven very low? In the model I'm looking at,...

brianstock-NOAA