missing yellowtailflounderGB assessment history

[mle2718]

When I set

stockExclude <- c('haddockGB', 'codGB', 'pollock')

And run the model, I get this error message:

Error in get_HistAssess(stock = stock[[i]]) : 
  get_HistAssess: stock "yellowtailflounderGB" does not exist in directory "./data/data_raw/AssessmentHistory/".please add it or check spelling of file names

I looked in that folder and sure enough, those there isn't a yellowtailflounderGB assessment history file.

[samtruesdell]

I think this is related to options where the original assessment history is simulated by implementing the historical F and R estimated by the model and the assumed M. I think all that's needed here is a .csv with those estimates called yellowtailflounderGB.csv, but I believe @mdmazur and @lkerr have been working with these options recently so they would have a good sense. Alternatively you should be able to set histAssess <- FALSE in set_om_parameters_global.R to use parameters burnFmsyScalar and burnFsd along with the stock recruitment relationship during the entire burn-in period.

[mle2718]

"histAssess <- FALSE in set_om_parameters_global.R to use parameters burnFmsyScalar and burnFsd " @samtruesdell : Easy enough to do, I will give this a shot.

[lkerr]

Yes, in the short term I would suggest doing what Sam suggests-the stock magnitudes may be a little off, but we can get you the assessment history F and R values to input

[mle2718]

progress.

Error in eval(substitute(expr), e) : object 'waa_mis' not found

> traceback()
6: eval(substitute(expr), e)
5: eval(substitute(expr), e)
4: within.list(stock, {
       dat_file <- ReadASAP3DatFile(paste("assessment/ASAP/", stockName, 
           ".dat", sep = ""))
       dat_file$dat$year1 <- fmyearIdx - ncaayear
       styear <- fmyearIdx - ncaayear
       if (mproc[m, "Lag"] == "TRUE") {
           endyear <- y - 2
       }
       else if (mproc[m, "Lag"] == "FALSE") {
           endyear <- y - 1
       }
       N_rows <- length(styear:endyear)
       dat_file$dat$n_years <- N_rows
       dat_file$dat$M <- matrix(get_dwindow(natM, styear, endyear), 
           nrow = N_rows, ncol = page)
       if (M_mis == TRUE) {
           dat_file$dat$M <- matrix(M_mis_val, nrow = N_rows, ncol = page)
       }
       dat_file$dat$maturity <- matrix(get_dwindow(mat, styear, 
           endyear), nrow = N_rows)
       dat_file$dat$WAA_mats <- matrix(get_dwindow(waa, styear, 
           endyear), nrow = N_rows)
       if (waa_mis == TRUE) {
           dat_file$dat$WAA_mats <- t(replicate(N_rows, waa[1, ]))
       }
       dat_file$dat$sel_block_assign <- matrix(1, nrow = N_rows, 
           1)
       dat_file$dat$CAA_mats <- cbind(get_dwindow(obs_paaCN, styear, 
           endyear), get_dwindow(obs_sumCW, styear, endyear))
       dat_file$dat$DAA_mats <- matrix(0, nrow = N_rows, ncol = page + 
           1)
       dat_file$dat$prop_rel_mats <- matrix(0, nrow = N_rows, ncol = page)
       dat_file$dat$IAA_mats <- cbind(seq(styear, endyear), get_dwindow(obs_sumIN, 
           styear, endyear), rep(oe_sumIN, N_rows), get_dwindow(obs_paaIN, 
           styear, endyear), rep(oe_paaIN, N_rows))
       dat_file$dat$recruit_cv <- matrix(pe_RSA, nrow = N_rows, 
           1)
       dat_file$dat$catch_cv <- matrix(0.05, nrow = N_rows, 1)
       dat_file$dat$discard_cv <- matrix(0, nrow = N_rows, 1)
       dat_file$dat$catch_Neff <- matrix(oe_paaCN, nrow = N_rows, 
           1)
       dat_file$dat$discard_Neff <- matrix(0, nrow = N_rows, 1)
       if (mproc[m, "Lag"] == "TRUE") {
           dat_file$dat$nfinalyear <- y - 1
       }
       else if (mproc[m, "Lag"] == "FALSE") {
           dat_file$dat$nfinalyear <- y
       }
       dat_file$dat$proj_ini <- c((y), -1, 3, -99, 1)
       dat_file$dat$R_avg_start <- styear
       dat_file$dat$R_avg_end <- endyear - 10
       if (Sys.info()["sysname"] == "Windows") {
           WriteASAP3DatFile(fname = paste("assessment/ASAP/", stockName, 
               "_", r, "_", y, ".dat", sep = ""), dat.object = dat_file, 
               header.text = paste(stockName, "Simulation", r, "Year", 
                   y, sep = "_"))
           WriteASAP3DatFile(fname = paste("assessment/ASAP/ASAP3.dat", 
               sep = ""), dat.object = dat_file, header.text = paste(stockName, 
               "Simulation", r, "Year", y, sep = "_"))
           asapEst <- try(system("assessment/ASAP/ASAP3.exe", show.output.on.console = FALSE))
           res <- dget("assessment/ASAP/ASAP3.rdat")
           saveRDS(res, file = paste("assessment/ASAP/", stockName, 
               "_", r, "_", y, ".rdat", sep = ""))
       }
       if (Sys.info()["sysname"] == "Linux") {
           WriteASAP3DatFile(fname = paste(rundir, "/", stockName, 
               "_", r, "_", y, ".dat", sep = ""), dat.object = dat_file, 
               header.text = paste(stockName, "Simulation", r, "Year", 
                   y, sep = "_"))
           WriteASAP3DatFile(fname = paste(rundir, "/ASAP3.dat", 
               sep = ""), dat.object = dat_file, header.text = paste(stockName, 
               "Simulation", r, "Year", y, sep = "_"))
           tempwd <- getwd()
           setwd(rundir)
           if (runClass == "HPCC") {
               asapEst <- try(system("singularity exec $WINEIMG wine ASAP3.EXE", 
                   wait = TRUE))
           }
           else if (runClass == "neptune") {
               asapEst <- try(system("./ASAP3", wait = TRUE))
           }
           while (!file.exists("ASAP3.rdat")) {
               Sys.sleep(1)
           }
           res <- dget("ASAP3.rdat")
           saveRDS(res, file = paste(rundir, "/", stockName, "_", 
               r, "_", y, ".rdat", sep = ""))
           setwd(tempwd)
       }
   })
3: within(stock, {
       dat_file <- ReadASAP3DatFile(paste("assessment/ASAP/", stockName, 
           ".dat", sep = ""))
       dat_file$dat$year1 <- fmyearIdx - ncaayear
       styear <- fmyearIdx - ncaayear
       if (mproc[m, "Lag"] == "TRUE") {
           endyear <- y - 2
       }
       else if (mproc[m, "Lag"] == "FALSE") {
           endyear <- y - 1
       }
       N_rows <- length(styear:endyear)
       dat_file$dat$n_years <- N_rows
       dat_file$dat$M <- matrix(get_dwindow(natM, styear, endyear), 
           nrow = N_rows, ncol = page)
       if (M_mis == TRUE) {
           dat_file$dat$M <- matrix(M_mis_val, nrow = N_rows, ncol = page)
       }
       dat_file$dat$maturity <- matrix(get_dwindow(mat, styear, 
           endyear), nrow = N_rows)
       dat_file$dat$WAA_mats <- matrix(get_dwindow(waa, styear, 
           endyear), nrow = N_rows)
       if (waa_mis == TRUE) {
           dat_file$dat$WAA_mats <- t(replicate(N_rows, waa[1, ]))
       }
       dat_file$dat$sel_block_assign <- matrix(1, nrow = N_rows, 
           1)
       dat_file$dat$CAA_mats <- cbind(get_dwindow(obs_paaCN, styear, 
           endyear), get_dwindow(obs_sumCW, styear, endyear))
       dat_file$dat$DAA_mats <- matrix(0, nrow = N_rows, ncol = page + 
           1)
       dat_file$dat$prop_rel_mats <- matrix(0, nrow = N_rows, ncol = page)
       dat_file$dat$IAA_mats <- cbind(seq(styear, endyear), get_dwindow(obs_sumIN, 
           styear, endyear), rep(oe_sumIN, N_rows), get_dwindow(obs_paaIN, 
           styear, endyear), rep(oe_paaIN, N_rows))
       dat_file$dat$recruit_cv <- matrix(pe_RSA, nrow = N_rows, 
           1)
       dat_file$dat$catch_cv <- matrix(0.05, nrow = N_rows, 1)
       dat_file$dat$discard_cv <- matrix(0, nrow = N_rows, 1)
       dat_file$dat$catch_Neff <- matrix(oe_paaCN, nrow = N_rows, 
           1)
       dat_file$dat$discard_Neff <- matrix(0, nrow = N_rows, 1)
       if (mproc[m, "Lag"] == "TRUE") {
           dat_file$dat$nfinalyear <- y - 1
       }
       else if (mproc[m, "Lag"] == "FALSE") {
           dat_file$dat$nfinalyear <- y
       }
       dat_file$dat$proj_ini <- c((y), -1, 3, -99, 1)
       dat_file$dat$R_avg_start <- styear
       dat_file$dat$R_avg_end <- endyear - 10
       if (Sys.info()["sysname"] == "Windows") {
           WriteASAP3DatFile(fname = paste("assessment/ASAP/", stockName, 
               "_", r, "_", y, ".dat", sep = ""), dat.object = dat_file, 
               header.text = paste(stockName, "Simulation", r, "Year", 
                   y, sep = "_"))
           WriteASAP3DatFile(fname = paste("assessment/ASAP/ASAP3.dat", 
               sep = ""), dat.object = dat_file, header.text = paste(stockName, 
               "Simulation", r, "Year", y, sep = "_"))
           asapEst <- try(system("assessment/ASAP/ASAP3.exe", show.output.on.console = FALSE))
           res <- dget("assessment/ASAP/ASAP3.rdat")
           saveRDS(res, file = paste("assessment/ASAP/", stockName, 
               "_", r, "_", y, ".rdat", sep = ""))
       }
       if (Sys.info()["sysname"] == "Linux") {
           WriteASAP3DatFile(fname = paste(rundir, "/", stockName, 
               "_", r, "_", y, ".dat", sep = ""), dat.object = dat_file, 
               header.text = paste(stockName, "Simulation", r, "Year", 
                   y, sep = "_"))
           WriteASAP3DatFile(fname = paste(rundir, "/ASAP3.dat", 
               sep = ""), dat.object = dat_file, header.text = paste(stockName, 
               "Simulation", r, "Year", y, sep = "_"))
           tempwd <- getwd()
           setwd(rundir)
           if (runClass == "HPCC") {
               asapEst <- try(system("singularity exec $WINEIMG wine ASAP3.EXE", 
                   wait = TRUE))
           }
           else if (runClass == "neptune") {
               asapEst <- try(system("./ASAP3", wait = TRUE))
           }
           while (!file.exists("ASAP3.rdat")) {
               Sys.sleep(1)
           }
           res <- dget("ASAP3.rdat")
           saveRDS(res, file = paste(rundir, "/", stockName, "_", 
               r, "_", y, ".rdat", sep = ""))
           setwd(tempwd)
       }
   }) at get_ASAP.R#6
2: get_ASAP(stock = tempStock) at get_advice.R#24
1: get_advice(stock = stock[[i]])

[mdmazur]

To fix that error somehwere in yellowtailflounderGB.R put a line that reads: waa_mis<-FALSE. You can set it to true if you want there to be a weight-at-age misspecification in the stock assessment.

[mle2718]

@mdmazur this is something that I can safely commit to master, right? ~M

On Mon, May 16, 2022 at 6:14 PM mdmazur @.***> wrote:

To fix that error somehwere in yellowtailflounderGB.R put a line that reads: waa_mis<-FALSE. You can set it to true if you want there to be a weight-at-age misspecification in the stock assessment.

— Reply to this email directly, view it on GitHub https://github.com/lkerr/groundfish-MSE/issues/214#issuecomment-1128189109, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIT5KA7W4HQWXNC3LLXBTF3VKLCB7ANCNFSM5VWLMHHA . You are receiving this because you authored the thread.Message ID: @.***>

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Economist, Northeast Fisheries Science Center

NOAA Fisheries | U.S. Department of Commerce

Office: ‪(508) 495-4704

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[mle2718]

I've created the branch https://github.com/lkerr/groundfish-MSE/tree/ytfGB_fix from the ml_ASAP branch to troubleshoot ytfGB

hist_assess<-FALSE waa_mis<-FALSE

still get some error messages,

Error in eval(substitute(expr), e) : object 'Rpar_mis' not found. It looks like there's a few other parameters that need to get set in yellowtailflounderGB.R. I'm not comfortable setting them myself: I'm sure I'll do something ridiculous while getting it to run that will be overlooked and that will cause some problems later on.

[mdmazur]

Those changes can be committed to the master branch. Rpar_mis can be set the same as Rpar in yellowtailflounderGB.R. Rpar_mis are the recruitment parameters that are used if there is a recruitment misspecification. If there is no misspecification, they will not be used. So it does not matter what it is set to unless the recruitment misspecification is turned on.

[jerellejesse]

I think I already did this in the dev branch, as well as adding pe_RSA and pe_IA. I'll double check that I pushed it!

[mle2718]

@jerellejesse the waa_mis, M_mis, R_mis are in dev for pollock and yellowtailflounderGB da96032d3f353591f8c48d48e6f59129ca4ffaa4. Also for haddockGB in b75ef42c06d3dbcb13259e121c7fdb8187f8b906.

I don't see pe_RSA or pe_IA but I might be looking in the wrong place.

those changes should close this issue.

[jerellejesse]

Yellowtail will work if histAssess <- FALSE in set_om_parameters_global and minCatch is FALSE in mproc. It is still on my list to grab the data need for this functionality.

[mle2718]

Still get this for just yellowtailGB when I set those options:

Error in matrix(pe_RSA, nrow = N_rows, 1) : object 'pe_RSA' not found traceback points to

in get_ASAP dat_file$dat$recruit_cv <- matrix(pe_RSA, nrow = N_rows, 1)

[jerellejesse]

Sorry, you might have to update from the dev branch!

[mle2718]

@jerellejesse thanks! Of course I'd need to do that. Works now.