The rceattle from grantdadams

nselages is currently set to 8 for all species

Map out gam_ua

gam_ua will need to be mapped out if predation mortality from Kinzey are not used. Prey ages not observed will also have to be mapped out.

Add sterring committee and readme

Add readme and contact sheet
Think about governance structure
Communications with developers
Have points of contact with users
Steering committee - group of people that help decide what to include in the code
DOI needs versioning
Version control
Naming convention
Code-checking, tests
Doxygen
User manual
List of publications
Testthat
Include in NOAA toolbox?
Feature set
Possible steering committee: Jim, Kerim, Steve, Ingrid, Martin, Dana
How to facilitate communication between users/developers
Examples/tests for how to do each feature

Have projected F in fsh control

Initialization of plus group

@kholsman do we want the plus group to be initialized at N(sp,1,nages(sp)) /= (1.-mfexp(-M1(sp,nages(sp)))); on line 2335 of the ADMB code/ Line 277 of the TMB code, or as N(sp,1,nages(sp)) /= (1.-mfexp(-nages(sp) * M1(sp,nages(sp))))

Add flexibility for ragged arrays in readdat_fun.R

readdat currently has flexibility for ragged matrices, will need to add flexibility for ragged arrays.

Double check with @kholsman if there are other 3D array data inputs besides c("obs_catch", "wt", "srv_age_obs", "age_trans_matrix")

Change (i, j, y) to (y, j, i) throughout for indexing arrays

It would be easier to work with the arrays as [year, age, species] for matrix multiplication

Likelihood components to do

N and NByage are the same in ADMB, change names?

Get eit_age_hat

ask @kholsman for eit_age_hat to be included in output from ADMB model

Ragged array use vector<vector<Type> >?

May bomb out

UobsWt named Uobs.Wt in .dat files

Uobs.Wt will not work in c++, will have to change names of within .dat files

Check indexing of surveys

Remove years from the BSAI data and see if it fits to evaluate if there is an indexing issue.

Recruitment of the last year

Two years of age-1s are defined as the same in the ADMB file
lines 2330-2331

for (int yr=1;yr<=nyrs;yr++)
N(sp,yr,1) = R(sp,yr); // Recruitment
N(sp,nyrs+1,1) = R(sp,nyrs); // Recruitment in nyrs+1

Should avgsel_srv be the mean up to nselages or across all ages?

E.g.

log(mean(mfexp(fsh_sel_coff(sp))));
log(mean(mfexp(fsh_sel(sp))));

UobsWtAge default to include years in data

Default to have UobsWtAge include years in dataframe. Currently can include year column or not. But better to have all data include years and set year = 0 if its an average across all years.

Model Objects to Incorporate/Rename

Weighting fishery age comp by offset each year

The offset is added to the fishery age comp likelihood each year rather than across the board with each species. What does changing this weighting scheme do?

fsh_age_hat flexible size for bins or ages

Change Catch_kg to Catch_tonne or change biomass plots

Rename TempC, Diet_Mat, phi_p_bp, bLW, d, Winf, Prop_Mat in CPP file

I will need to rename TempC, Diet_Mat, phi_p_bp, bLW, d, Winf, Prop_Mat in the cpp file to that of the .dat inputs.

Convergence issues

Put bounds on parameter estimates
build a mfexp function
Phasing

tc_age_hat is indexed by yrs_tc_biom rather than yrs_fsh_comp

In the ADMB version of CEATTLE, tc_age_hat is generated by using 'yrs_tc_biom' as a yr_ind and then yrs_fsh_comp is then used to index tc_age_hat in the likelihood. However, if there are any years where total catch is not available but fish age comp is this may be problematic.

Data different in ms and ss mode

Add fitting vignette

Survey selectivity likelihood

No mid-year adjustment for survey_age_hat

EIT Selectivity Function and Data

Do we want EIT biomass to have the mid-year penalty?
Also where are the estimates of EIT selectivity?

To index a row in TMB of a matrix take the transpose and index the column?

Convert estimated parameters to log-space

I have several parameters related to selectivity and SPR-based F rates that should probably be estimated in log space.

nyrs_fsh_comp in test_0jim.dat and length of yrs_fsh_comp do not match

In the data set test_0jim.dat the nyrs_fsh_comp does not match the length of years in yrs_fsh_comp. Will have to include a test function to make sure they match or replace nyrs_fsh_comp(i) for yrs_fsh_comp.row(i).size() in cpp file.
@kholsman

Easy simulate

http://kaskr.github.io/adcomp/Simulation.html

Update selectivities for EIT survey

Ask the bioacoustic team about updating selectivities.

Downstream: reorganize tc_obs and tc_obs_age if changing data input source

tc_obs and tc_obs_age are not in the .dat files. For future reference, if I start taking data in from the .dat files rather than the tmp output from the ADMB model, will have to change both to internal data types and calculate locally.

Calculate age_comp in house

will need to calculate fsh_age_obs and srv_age_obs in TMB code

Installing Rceattle from github

I'm trying to install the Rceattle package according to the vignette instructions: devtools::install_github("grantdadams/Rceattle", auth_token = "4925b42ac46f1e0aefd671e9dc0c1cf1b3157017", build_vignettes = TRUE) but am getting an error:
Error: Failed to install 'Rceattle' from GitHub: arguments imply differing number of rows: 0, 1

Any ideas? Thanks!

Estimate MSVPA Type 2/3 exponent - Also have estDiet switch

In the MSVPA Holling Type Equation change msmMode in the pow(AvgN, msmMode) to a parameter that can be estimable. Also have a switch that will include diet likelihood.

Will need to change suit_tmp divisor and instances of pow(AvgN(ksp, k_sex, k_age, yr), msmMode)

One possibility is to us H_4

Survey Time Adjustment exp(-Z * survey_mo)

In the estimates of survey biomass and age composition have an input that adjusted mortality based on the timing of the survey. This would allow increased flexibility.

Input length bins - Francis weighting

Age bins are implicitly included via minage and nages for each species. Nlengths is included, but specific length bins are needed to calculate Francis composition weights. Will need to include the length bins to calculate expected length.

Update map for selectivity blocks

Update map for selectivity blocks when data provided include years after nyrs. Will need to subset.

Things to do to cpp file

Data to extract from .dat files

Add Fishery Selectivity Penalty?

// ----Selectivity penalties...for smooth second diff etc
// Invoke a penalty when the partial F's go down with sp_age
for (int sp_age=1;sp_age<nages(sp);sp_age++)
if (fsh_sel(sp,sp_age)>fsh_sel(sp,sp_age+1))
fsh_sel_like(sp) += 20.*square(log(fsh_sel(sp,sp_age)/fsh_sel(sp,sp_age+1)));
fsh_sel_like(sp) += curv_pen_fsh(sp)*norm2(first_difference( first_difference(log(fsh_sel(sp)))));

2017 PCod age_trans_matrix rows dont sum to 1 - underestimate fishery catch-at-length

The rows of age transition matrix for pcod do not sum to 1, they sum to values below 1
However, for the fishery catch-at-length for PCod, catch-at-length is divided by the sum of catch-at-age to get age comp, leading to under estimates of length-comp for PCod.
Will need to add check for age-trans-matrix rows sum to 1
And/or have the catch-at-length divided by sum of catch-at-length

Follow Grant Thompson's method

grantdadams / rceattle Goto Github PK

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