reports/changesToChumModel.md

In CamFreshwater/samSim: Closed-loop salmon dynamics simulator

Summary of modifications to C. Holt's chum model

I) Addition of random number vectors within salmon-sim code (Dec. 11); replaced Jan. 17

• Originally used complex system of random number calls in vectors to ensure appropriate number called regardless of extinction events
• Removed if(extinctAg == 1) statement and instead modified model so that entire cycle run regardless of spawner abundance

II) Modifications to make model usable across species (Dec. 13/14)

Input parameters

• Include species argument within function
  • Generation length (gen) and age class distribution used to represent differences
  • Could potentially also specify stray rate and species-specific extinction thresholds
  • Adding coho should be straight forward, CK more difficult
• Note that nInit and total simulation length will change as a result of adjusting gen
• Treat odd and even year cycle lines as independent

Options for making code flexible

1. nAges argument represents species and interacts w/ external functions
2. nAges assumed to be static and relative ppn of each group changes to reflect species diversity

Option 2 selected for now

Code adjustments

• Add in species call separating pink from chum/sockeye/coho
• Allow for age-2 returns; necessary for pink obviously but may also be useful for stocks such as Harrison sox
• Estimate age class proportion, recBY, recRY accordingly

III) CU-specific estimates within model (Jan. 3/4)

• Calculate age structure, benchmarks, catches, forecasts and exploitation rates at level of individual CUs
• Will require modifications for inputs because some (e.g. ageStruc) are now matrices
• Update Jan 10: edited var-covar matrix to allow for CU-specific sigma estimates
• Update Jan 24: added CU-specific estimates of tauAge

Code adjustments

• Largely consisted of changing outputs from vectors/matrices to arrays
• E.g. ppnAges, Smsy, estRicB, ppnAge2Ret4 now have additional dimension
  • All data stored as years X CUs X trials

IV) Change model outputs (Jan. 8/9; edited: Jan. 17, Jan. 24, Mar. 23)

• Diagnostic figures currently include
  • 1)
    • a. Randomly draw one CU from one trial and plot: SR relationships and spawner abundance relative to median and quantile values
    • b. For all CUs plot (true and observed): alpha, S, obsS, recBY, recRY, Canadian catch, US catch, single catch, exploitation rate, sMSY, sGen, (saved as plotOneTrial function)
  • 2) Plot median and 20-80% CI limites for aggregate: spawners, observed spawners, recruits (BY/RY), obs recruits (BY/RY), catch, obs catch, synchrony, obs syncrhony, benchmarks, estimated benchmarks (saved as plotMedian function)
• Data exported as one .csv of aggregate values (nTrials X nVariables) and one list of CU-specific matrices (nTrials X nCUs X nVariables)
  • 1) aggDat.csv includes:
    • General info: model run, harvest control rule, trial number and targetER
    • Aggregate spawner abundance (mean and SD across years per trial)
    • Aggregate spawner abundance in first and last two generations in TS
    • Aggregate catch (mean and SD across yrs per trial)
    • Observed aggreagte catch (mean and SD)
    • Mean aggregate catch in first and last two gens
    • Mean realized and observed realized exploitation rate
    • Proportion of years aggregate is above upper/lower BMs
    • Ppn of years aggregate catch is above aggregate threshold
    • Ppn of CUs above upper/lower BMs for last generation of TS
    • Ppn of CUs extinct at end of sim
  • 2) cuDat.Rdata includes CU-specific values for:
    • General info: harvest control rule, CU name, MU name, and targetER
    • Spawner abundance (mean and SD)
    • Alpha (mean and SD)
    • Beta or B0 for Larkin (mean and SD)
    • Total true catch (mean and SD)
    • Total observed catch (mean and SD)
    • Realized exploitation rate and observed ER
    • Ppn years above upper/lower BMs
    • Ppn years observed abundance is above estimated BMs
    • Ppn years with COSEWIC or WSP decline
    • Ppn years above Canadian and single-CU catch thresholds

V) Model inputs (Jan. 15; updated Feb. 12, updated Feb. 16, updated March 6)

Required files; Additional details in inputParSummary.md

1. ...simInputs.csv contains simulation specific parameters that are shared among CUs
   • Can be modified manually by entering different values for specific simulations
2. ...CUPars.csv contains CU-specific SR parameters and age estimates, as well as entries for different initial abundances and exploitation rates
   • Age proportions are estimated using all available data; ageTau excluded age classes that are never observed (i.e. age 2 for non-Harrison CUs)

Optional files

1. To account for uncertainty in underlying SR relationship, parameters can now be input as medians (in cuPars.csv) or sampled from two additional input csvs - containing either 1000 samples per stock for Ricker or Larkin pars (e.g. fraserDat/rickerMCMCPars.csv)
   • To account for correlations among parameters, only one sample is drawn per stock, which contains each par necessary
2. ...RecDatTrim.csv contains stock and age-specific recruitment data used to set initial age proportions and prime model with abundance TS
3. ...CatchDatTrim.csv contains sector specific catch data
4. Fraser only Added file containing cycle line specific fishery reference points drawn from FRSSI (tamRefPts.csv)

VI) Divided catches across multiple fisheries (Jan. 19 and 23; updated Feb. 7)

• Assumed to be captured in either US, mixed Canadian or single-CU Canadian
• True catches estimated using three different ERs
  • usER and canER are in sims.csv; vector singER is in ...CUPars.csv
  • Also incorporate two levels of outcome uncertainty: lower for US/mixed Can, higher for single CU (reflects differences between commercial and FN/rec)
• Observed catches for US and mixed Canadian fisheries
  • Incorporate two levels of catch observation errors: lower for US/mixed Can fisheries, higher for single CU fisheries (same rationale as above)
  • Incorporate uncertainty when splitting observed aggregate catches (e.g. obsCanCatch) into CU-specific catch estimates; singObsCatch does not because these fisheries would assume all captured individuals originate in that CU
• Proportional contribution of each CU is estimated using ppnCatchErr function, which is closely related to ppnAgeErr function, and based on each year's true proportional contribution plus error associated with mis-assignment of aggregate catches to specific CUs (see catchTau below for details)
• Added an en-route migration mortality term migMort that represents fish that escape the marine American/Canadian fisheries, but die prior to spawning and terminal fisheries (could be moved if this jars with allocation issues)
  • Mortality rate enRouteMR is CU-specific and varies across years based on enRouteSig
  • In the case of Fraser River mean M is the mean proportional difference between estimates (pDBE) since 2000 and sigma is the standard deviation in pDBE over the same period
    • Full dataset in data/fraserDat/postSeasonMortality_2017.csv
  • En route mortality is observed with an error equivalent to observing spawner abundance obsSig

VII) Adjusted MSY calculation (Feb. 2)

• Following Scheuerell 2016 PeerJ, replaced linear approximation for sMSY suggested by Hilborn (1985) (ricA/ricB)*(0.5-0.07ricA) with explicit solution generated with Lambert W function: (1 - lambert_W0(exp(1-ricA)))/ricB

VIII) ageTau parameter selection (Jan. 19 and Feb. 5)

• Evaluated performance of four ageTau structures using exploreTau.R and output files in simData/exploreTau/exploreAgeTau; input files in data/tauDummySim
  • 1) High tau value (2.0) that was uniform across all CUs
  • 2) Low uniform tau value (0.5)
  • 3) Tau estimated across full TS using tauEstimator.R; mean=1.17
  • 4) Tau estimated for each cycle line; these values were 0.1-0.5 lower with mean=0.98
  • Full and cycle line specific estimates for Fraser River CUs saved in data/ fraserTauEstimates.csv
• Compared observed to generated age proportion TS ageProportion.pdf and compared SD of each age class's proportional abundance
  • Tau based on cycle lines are somewhat higher than observed, but closer than low, high or full TS tau
  • Will use cycle line specific estimates of tauAge for now
• Examined correlations between cycle line specific abundances, age structure (i.e. proportion of age-4 individuals) and SD in age structure
  • Tau values only strongly correlated with interannual variability in age structure; suggests that there is substantial variation among cycle lines in proportion of age-4 individuals (seems consistent with DD hypotheses)
• Update May 8: average, year-specific deviations in true vs. observed recruit abundance; however total observed abundance (i.e. sum of recruits observed across years doesn't change)
  • 0.1 = 1.02 (+/- 0.3)
  • 0.3 = 1.04 (+/- 0.4)
  • 0.6 = 1.09 (+/- 0.5)
  • 0.9 = 1.16 (+/- 0.7)
  • 1.5 = 1.39 (+/- 1.5)

IX) catchTau parameter selection (Jan. 19; Feb. 5; Feb. 19)

• catchTau estimated using CU-specific return data and script tauEstimator.R, which is based on get.mv.logistic.tau.R from C Holt
• Since misassignment is influenced by many factors (quality of genetic baseline, sample size in GSI runs, representativeness of test fisheries), accurate estimates of this uncertainty do not exist. As a proxy used two alternative methods
  • 1a) Estimate tauCatch based on interannual variation in observed CU-specific proportions within each cycle year; assumption is that observed deviations between years could represent misassignment rates if management is assuming set proportion will return
    • Values between 0.3 and 0.6 (mean=0.5) depending on cycle year
  • 1b) As above but instead of using spawner abundance used total catch
    • Values between 0.3 and 0.7 (mean=0.475)
  • 2) Estimate tauCatch based on intra-annual variation in observed CU- specific proportions across test-fishery surveys; assume that variation at smaller temporal scales reflects variation at larger temporal scales
    • Limited dataset (2010-2014) and for now only included data from Johnstone Strait TF, but estimated values are similar (0.3-0.7, mean=0.42)
• Additionally conducted simulation study with range of values (0.1, 0.5, 1.0 and 2.0) for tauCatch, with all other sources of variability set to 0
  • Example output figures in diagnostics/tauExplore show true/observed CU specific contributions to aggregate catch and percent error
  • Values from 0.5-1 produced spikes in error of ~10% and seemed reasonable
• Will use value of 0.5 for tauCatch for now

X) Replace first priming loop with true recruit/spawner abundance (Feb. 6,7)

• Instead of using constant spawner abundances in years 1 through 5 allow SR data to be used as input; used to generate initial values for S, recBY, and ppnAge
• Intended to reflect actual status of populations in recovery context and also necessary for cyclic stocks
• Input data should be .csv with following columns: stk, yr, rec2, rec3, rec4, rec5, and ets
• EDIT
  • To allow BMs to be calculated shifted to using obs spawner abundances for entire time series available (SR datasets are currently trimmed and cleaned within model)
  • Also made the assumption that observed and true abundances/benchmarks are the same during initial priming period. This allows BMs to be integrated seamlessly between priming and simulation component
  • Saved original script as SimpleSimWCatch.R and renamed recoverySim.R
• EDIT 2
  • Added marine and First Nations catch data to represent Canadian catches and single CU catches prior to sim period
• Note
  • May need additional modifications to account for differences in available input data
  • Add argument so that if a CU specific benchmark cannot be estimated in a given year it takes the last value non-NA value (e.g. estSGen[nPrime,k])

XI) Add mortCalc function (Feb. 8)

• Wrapper function that sequentially calculates usCatch, canCatch, en route mortality, and singleCatch providing output as a list

XII) Add preliminary HCRs (Feb. 8, 13, 15;)

• Add simple HCR as alternatives to fixed ER
• Intended to reflect FRSSI TAM rules
  • When forecasted recruitment below lower BM, canadian ER and singER each = 0.05 for all MUs except late which gets 0.1 for each
  • When between upper and lower BMs, Canadian and single CU ERs are calculated to allow for escapement equal to the lower BM after accounting for MU- specific average en route mortality and US exploitation
  • When above upper BM Canadian ER is 0.3 and single CU ER is 0.3 (normally 0.6 for TAM)
• Currently using cycle line and MU-specific fishery reference points provided by AMH as BMs (tamRefPts.csv)
• NOTE LARGELY DEPRECATED VIEW MAY 29 NOTE

XIII) Account for gappy input data (Mar. 9)

• If stock-recruit TS is incomplete in recent years initial error term for Ricker AR operating model cannot be estimated; similarly recBY are not available to prime recRY
• Modify B. Davis infill function to estimate recruits and spawners in last 5 years where data are missing using proportional contribution (geometric mean) from observations over past 25 years (or length of TS, whichever longer)
  • Added as an intermediate for loop between observed historical data and closed-loop forward sim

XIV) Incorporate realistic estimates of forecast error (Mar. 16, Mar. 31, Apr. 27)

• Use pre-season, in-season (3 days after 50% migration date) and post-season (meeting after TAC date) of run size from 2006-2017 for each MU as potential estimates of forecast error in the model
  • See camGenDat/forecastEstimates.csv and prepFRParInputs.R for details
• Post-season run size estimates come from fraserDat/camGenDat/frTotalCatch.csv
• Currently forecast error is normally distributed with mean equal to mean in- season estimate relative to post-season run size estimate (e.g. mu = 1.1 if mean in-season estimate 10% larger than observed) and sigma equal to sd among years
• Update: replaced MU-specific distributions with:
  • mu = 1.20 for all MUs except summer (~mean value among these MUs)
  • mu = 0.85 for summer because underestimates seem common for this MU)
  • sd = 0.15 slightly larger than observed for 3 grouped MUs
  • Modified mortCalcTAM to constrain target Canadian FR to 0.01 when realized ER is over 100%
  • Tried to apply TAC by applying ER to forecasted recruits rather than true (see mortCalcTam in simFunctions.R); however high level uncertainty, biased towards overfishing seemed to result in unrealistically large levels of extirpation
    • Moderating OU seems like a more tractable, equivalent process
• NOTE: currently there is no equivalent process for Nass chum model because a) we lack historical estimates of forecast error (likely because no forecast
• takes place) and b) TAM rules are unlikely to be applied to these CUs, therefore not necessary

XV) Generate multi-simulation run outputs (Mar. 21, 22; Apr 23)

• pmFunctions.R contain functions to produce output plots using summary lists of CU-specific and aggregate performance metrics
• Figures
  1. Trade-off dot plots that contrast catch PMs w/ various conservation PMs, but can easily incorporate greater range
     • Option to include inter-trial variability as confidences intervals is functional, but produces very "busy" figures for cu-specific plots and should likely be modified
  2. Continuous trade off plot (e.g. Walters Skeena) that show escapement and catch on the left axis, extirpation risk and benchmark status on the right
  3. Dot plots outlining aggregate and CU-specific multi-trial status across proportional performance metrics (e.g. ppn of CUs above upper BM at end of trial)
  4. Multi-operating model tradeoff plots are produced separately (compareOMsPlot) and plot agg PMs vs. MPs for multiple OMs simultaneously

XVI) Switch from internal MVT AR to simple MVT Ricker model (Mar. 30, edited Apr. 17 w/ new function)

• Using Ricker.MVT from simFunctions.R

  Ricker.MVT<-function(S,a,b,cv,error){   
      N<-length(a)
      R<-NA
      if(a>=0){
          if(b!=0) R <- S*exp(a-b*S)*exp(err)
          if(b==0) R <- S*exp(error)
      }
      if(a<0) R<-S*exp(a)*exp(error)*exp(err)
      return(R)   
  }
  

• Justification: input SR parameters currently being estimated with hierarchical, non-AR models

• Currently structure still contains AR-model specific objects (e.g. err and arRicSig), but could be removed depending on future model goals

XVII) Pooled observation error (Mar. 31, Apr. 10)

• Add obsErrDat dataframe which contains observation error estimates
• Observations of mixed CU catch and forecast errors are MU-specific, while spawners and single CU catches are CU-specific (drawn individually but from a shared distribution)
  • In case of Fraser en route mortality shares the same error as spawner observations
  • Recruit observations do not have their own observation error because they are simply sum of observed spawners and catch
• Re-estimated each year and not stored

XVIII) Ran profiler to ID bottlenecks (Apr. 10)

• Used package profvis
• Little room for obvious improvement; largest processing times associated with 1) constructing ppnAges matrix, 2) estimating y-intercept, slope and rSq with internal SR relationship, and 3) estimating slope of decline

IXX) Streamline outputs generated by simRun.R (Apr. 14, Apr. 17)

• Add parallel processing
  • Allows different scenarios to be run in parallel using parallel, doParallel, and foreach packages
  • Note that bugs are most likely to appear when passing user defined functions that are nested within parlapply call; be sure to specify all necessary libraries, objects, and external functions using clusterExport or cluserEvalQ
• Change output functions to access combination of directories (based on scenarios run simultaneously) and subdirectories (based on specific OMs) where diagnostics, data, and output figures are now stored

XX) Changed external hierarchical model used to estimate SR pars for chum (Apr. 17)

• Instead of being passed observed recruits, passed log(R/S)
• Intended to make it consistent w/ B. Connor's PSF model, but parameter estimates still don't converge
• Compared to previous model structure, parameter estimates are basically identical except TauA is an order of magnitude larger

XXI) Separated outcome uncertainty (Apr. 18)

• Previously OU in fisheries was uniform across CUs within a year, i.e. if CUs had same target ERs in a fishery they would have same realized ERs
• Now draw mixOutErr, migMortErr and singOutErr from qnorm(runif(nCU, 0.0001, 0.9999), 0, fisheryOUSigma)

XXII) Add weighted CV and agg CV estimates (Apr. 20)

• Following Thibaut and Connolly 2013, sqrt(synch) * wtdCV provide an index of aggregate variability
• Added 10 year moving window estimates to explore how different OMs/MPs contribute to component variability/synchrony

XXIII) Identify optimal number of trials (Apr. 24; Apr. 29)

• Sampled 25-1500 trials worth of PM outputs for Fraser River frSoxVaryProd simulation runs
• Median values in aggregate and CU-specific PMs appear to stabilize at 250-500 trials, but variance can fluctuate; suggest running 500 for first checks, 1000-1500 final
• Outputs in outputs/miscSensitivity/minTrials

XXIV) Misc. productivity adjustments (May 7 - 8; May 15; May 21)

• Add varyA == FALSE term to function inputs
  • Used to constrain Ricker/Larkin alpha term to be the same across trials
  • Currently set to mean value of all CUs in the simulation
• Add realProd matrix to function outputs
  • Contains realized productivity estimates (i.e. recBY/S) - used to provide a more meaningful representation of synchrony (covary more strongly with correlCU; see simulationRunNotes.R for additional details)
  • Added to aggregate output plots as well
• Change productivity operating models and do not sample from posterior but calculate point values
  • High productivity: 90th percentile of alpha values + associated beta and sigma
  • Moderate productivity: 50th percentile
  • Low productivity: 10th percentile
  • Decline from medium to low w/ start and end date
• Edit May 21
  • Adjust above so that only alphas are sampled at different prod regimes, betas/sigmas remain at median

XXV) Add allocation variables (May 15; changed July 25)

• Added three input variables
  • ppnMixHigh - proportion of Canadian catch allocated to mixed stock fisheries by default (currently set at 0.8)
  • ppnMixLow - as above but lower value intended to test whether outcomes improve when singleCU allocations increase; only used when following true
  • varyAllocation - if TRUE then ppnMixHigh is replaced with ppnMixLow when threshold values reached
• Currently when varyAllocation is true the HCR control rule switches to ppnMixLow if agS < agSGen in 3 of previous 5 years
  • Eventually this should at the very least be replaced by observed and estimated
  • With TAM rule could be directly incorporated so that allocation shifts based on ref pts, but currently just passed same ppnMix value as fixedER would be
• NEW RULE Replaced previous version since agSGen is too easily met; now ppnLow is used whenever the average CU within an MU is not above its lower BM in at least 50% of previous generation

  meanStatus <- ifelse(length(CUs) > 1, 
                       mean(apply(lowerBM[(y - 1):(y - gen), CUs], 2, sum)),
                       sum(lowerBM[(y - 1):(y - gen), CUs]))
  poorStatusMU[y, CUs] <- ifelse(meanStatus > 0.5 * gen, 1, 0)
  

XXVI) Divide catch observations by MU (May 18, 21)

• Switch observations of US and Canadian mixed stock fisheries to occur at MU level so that mis-allocations are realistic
• Prevents MUs that may contribute to large portion of run, but rarely intercepted (e.g. Early Stuart) from making up a disproportionate portion of observed catch due to catchTau
• Calculated with calcObsCatch
• As a result also downweight catchTau to 0.1 from 0.5

XXVII) Cap recruitment (May 25)

• Limit recruitment to be no more than 3x maximum observed historic recruitment
• If SR time series not available cap at 5x 75% quantile (passed in CU pars file)

XXVIII) Adjust TAM rule and exploitation rate calculations (May 29; edit Aug 16)

• Forecasts
  • To ensure consistency between HCRs, forecasts are now made in all MPs
  • In data limited scenarios, median and SD estimates for forecast accuracy are set to 1 and 0 respectively, i.e. forecasts perfectly represent reality and outcome uncertainty should be adjusted upwards to compensate
• Instead of adjusting forecasts downward based on median en route mortality, use actual management adjustment which is calibrated from same data (pDBE dataset)
  • pMA * esc goal = numerical management adjustment to add to esc.goal
  • pDBE * (run size – total catch) = number of fish that will be counted at Mission but not counted on spawning grounds (i.e., projected DBE)
  • pMA = 1 / (1 + pDBE) - 1
  • Currently using median pMA with interannual variance since 2000, pulled from postSeasonMortality_2017.csv
• NOTE In fixed exploitation rate HCRs, forecasted recruitment cannot be moderated via pMA because this requires an escapement goal which is increased by the pMA (adjusted escapement goal * harvest rate = TAC under TAM); this may lead to issues where TAM rule is more conservative than fixed independent of changes in harvest rate with abundance, but I don't know how to work around it
• Pseudo-code
  1. Forecast of recruitment is made (at MU level because this is scale at which PSC data available)
  2. If the species is not sockeye, amTAC and canTAC are calculated simultaneously from forecasted recruitment and prespecified exploitation rates
  3. If the species is sockeye and HCR = fixedER, a totalTAC is calculated based on Canadian ER and Americans get 16.5% of this total, Canadians get remainder
  4. If the species is sockeye and HCR = TAM, totalTAC depends on forecasted abundance
     • If forecast below lower reference point (RP), totalTAC = minimumER * forecast
     • If forecast above LRP and below URP, escapement target (by default LRP) is adjusted upwards using MU-specific median management adjustment (MA); if forecasted recruitment is above the adjusted target, an ER is calculated based on the difference between forecast and target; this ER is only used if it is a) larger than minimum ER and b) forecast is greater than adjusted target
     • If forecast above URP, escapement target adjusted upwards using (1 - maxER)*foreRec; ER selected as above
  5. Canadian TAC (totalTAC - amTAC; still at MU level) is distributed proportionally between mixed and single CU fisheries creating a mixTAC and singleTAC
  6. mixTAC and singleTACs are used to generate target (mixHR and singleHR) and realized harvest rates (mixHR + outcome uncertainty and singleHR + outcome uncertainty) by dividing by true recruitment at the MU level.
     • This step is necessary because outcome uncertainty is parameterized for exploitation rates, but not catches.
     • MixHR and singleHR are at the MU level (because TAC is), but because outcome uncertainty varies among CUs, the realized HRs vary among CUs
     • TACs are divided by true recruitment, rather than forecasted recruitment, because outcome uncertainty incorporates deviations between target and realized harvest rates
  7. Finally harvest rates are applied to each CU to produce catches.
• Relevant functions are calcTAC and calcHarvRate, replacing mortCalc and tamERCalc in simUtilityFunc.R
• NOTE AUG 16 Change forecast component so that forecasting error differs among MUs

XXIX) Add custom correlation matrices (June 5)

• Add argument to simPars input so that if corrMat == "custom" model looks for an input correlation matrix to use instead of applying static value passed from simPars$correlCU
• For Fraser River this correlation matrix generated from stock-specific Ricker/ Larkin models (chosen as above based on PSC report and fit using EFF not ETS) fit to all available data; however correlation matrix looks only at residuals since 1990
  • Details in fraserCovariance.R

XXX) Parameterize OU and obsCatch for Nass (June 7)

• Use deviations between two catch estimates (NBSSR model vs. hail + otolith data; 2000-2014) to get estimate of SD in observation error
• Use deviations between ERs of two methods and target ER (10%) to estimate outcome uncertainty
• Conducted simulation tests w/ different levels of obsSig and ouSig to identify values that approximated historical patterns
• Details in ncChumDoc.md and simulationRunNotes.md, as well as referenced R scripts and output files

XXXI) Add single stock ER HCR (June 11; edited July 30)

OBSOLETE SEE NEW NOTE FOR SEP 25 - Single CU ERs coded to remove fixed proportion of Canadian TAC (currently fixed at 20%) - Added simple management lever so that this TAC is only exploited when recruitment has greater than lower benchmark in at least 50% of years in previous generation - Currently uses true recruitment and true sGen, but would be more realistic to switch to observed and estimated respectively

    singTAC[y, k] <- ifelse(sum(lowerBM[(y-gen):(y-1), k]) > (0.5 * gen), tacs[[3]], 0)

• Note that second ifelse() used to define singCatch is separate and helps constrain realized ERs < 1

XXXII) Identified bottlenecks part II (June 20)

• After discussion with S Anderson decide additional performance required
  1. Remove aggregate diagnostic plot - very inefficient and rarely useful since most information in single trial plot
  2. Remove moving window estimates of synchrony/CV due to high overhead with rollapplyr; instead export a list of 2 arrays (nYears x nCUs x nTrials) for recBY and spawners that can be used to generate these posthoc
  3. Replace standard lm() with quickLM() which is a wrapper for a C++ equivalent that is trimmed down and much faster
• Overall runtime decreases by ~40%

XXXIII) Re-introduce temporal autocorrelation (June 21)

• Concerned that forward simulated populations don't have sufficiently strong recruitment deviations so reintroduce autocorrelation
• Use modRickerAR1.MVT, which is modified version of C. Holts function but modified to account for CU-specific recruitment deviations being estimated outside model
  • When rho = 0, results are equivalent to Ricker.MVT
• Details of simulation tests w/ different ranges of rho are in simulationRunNotes.md
• Reducing sigma helps, but makes dynamics overly deterministic

XXXIV) Add proportion of fisheries open PM (July 19)

• Add a new PM to track how frequently the fishery is closed
• Calculated for each MU and follows different rules depending on species and statistical area
  • In Fraser, an MU's fishery is open if the true recruit abundance recRY in a given year is above the cycle-specific fishery reference point ID'd by TAM rule
  • in Nass, the MU's fishery is open if the previous years Canadian catch (i.e. mix catch + single catch) did not exceed 0.1 (target maximum exploitation rate for SA)
• Final PM is the proportion of fisheries that are open in a given year; this is also used to calculate the proportion of years that all fisheries are open in aggDat.csv
• EDIT Aug 14 Additional fishery PMs and adjustments
  • AMH suggested adding Fraser specific fishery PMs representing TAC values corresponding to stressed (500k TAC across all MUs) and healthy fisheries (1 million across all MUs)
    • Added as inputs (lowCatchThresh and highCatchThresh to simInput files)
    • Note that these values incorporate forecast error when TAM HCR is being used
  • However given current framework these thresholds are met in vast majority of years and are unlikely to be sensitive to different MPs/OMs
  • As alternative modified ppnFisheryOpen stat so that it no longer flips on/ off, but instead a mean proportion of MUs that are open each year is estimated for full sampling period

XXXV) Add skewness operating model option (July 24)

• NOTE UPDATED OCTOBER SEE SECTION 41
• Some evidence that declines in sockeye productivity might be triggered by synchronous negative recruitment deviations rather than declines in mean productivity
  • Plots of histograms indicate some CUs have marginally non-normal residuals
• To simulate specify a time period (equivalent to method used for decline scenario); during these years recruitment deviations are drawn from a skewed multivariate t-distribution
• Currently generated using sn package with rmst(n = 1, xi = rep(0, nCU), alpha = rep(-0.5, nCU), nu = 7, Omega = corMat)
• Generally results in higher median performance but also greater variance among trials

XXXVI) Adjust BMs for cyclic benchmarks (Aug 17)

• Change cyclic BMs so that status is only assessed on dominant cycle lines otherwise status assumed to be the same as that of previous year
• Requires estimating status in priming loop as well

XXXVII) Add harvest constraints to pseudo-TAM rule (Aug 30)

• Because there is considerable overlap in MU migration phenology (and hence exploitation rates), FRSSI will constrain harvest by reducing TAC
• In reality, this is explicitly modeled based on MU-specific overlaps and how close each MU is to its upper fishery reference point
• We simplified the process, reducing TAC by 25% unless one of the following
  • 1) All adjacent MUs are above their upper FRP (after incorporating the management adjustment for en route mortality)
  • 2) A MU's TAC is calculated based on minimum exploitation rate
• See constrain and calcTAC functions in simUtilityFuc.R for details

XXXVIII) Added catch PMs (Aug 30)

• catchChange calculates the relative difference in total catch between years, then inverts the value to provide an index of catch stability (i.e. lower is better)
• lowCatchThresh and highCatchThresh are Fraser specific PMs that represent minimum TACs corresponding to higher levels of management strain (500k and 1 million fish)

XXXIX) Adjust calcTAC and calcHarvRate functions (Sep 25)

Goal was to ensure that TACs that are calculated based on TAM rule and relative allocation to mixed vs. single-CU fisheries result in harvest rates that do not decline as fishery progresses

1. Calculate TAC based on forecasted abundance at MU level relative to fishery reference points (cycle/MU-specific), after accounting for management adjustment for en route mortality calcTAC function
2. Multiply calcTAC output by true proportional contribution of each CU (for mixed stock fisheries) or forecasted proportion (for single CU fisheries)
   • Accounts for fact that this is a managed process only in the latter case
3. Convert adjusted TACs into harvest rates so that outcome uncertainty can be applied, then back convert to TACs; otherwise en route mortality results in single CU fisheries underharvesting
   • To ensure that harvest rates result in catches equivalent to TACs, the denominator of the HR calculation (i.e. recruit abundance) needs to decrease as we move from mixed to single stock fisheries
   • See calcHarvRate for details
4. Subtract realized TAC from recruits with the constraint that the remaining

Potential issues - Because outcome uncertainty applied at multiple steps (both mixed stock fisheries, en route mortality) it is very possible that realized catch rates will not reflect proportions that are pre-specified - Management adjustment in TAM rule may not be sufficient to prevent overharvest in single stock CUs

XXXIX) Remove bias corrections (Sep 27)

• Observed strong effect of bias corrections on recruitment deviations (i.e. - sigma^2/2 to center mean on true value)
  • Detailed comparison of OMs with and without bias correction are in outputs/miscSensitivity/biasCorrection
• Ultimately removed from both recruitment deviations and other log-normal based distributions (e.g. observation error) because the original parameter values were not estimated with bias estimators (and medians not means are being used to seed anyways)
• C. Holt's opinion on issue from email on Sep25
  • Sean, yes, the Ricker parameters are estimated with normal errors using the linearized form of he Ricker. However, recruitment is forward simulated with log-normal errors. That step of the forward simulation is similar to the one used in Anderson et al. 2015 (portfolio paper). Likewise, we initially included a –sig2/2 correction when simulating recruitment because of the log-normal errors, to ensure that the arithmetic mean of the error term =1 when exponentiated . However, we noticed that very few salmon simulation papers actually do this correction. Papers estimating Ricker parameters and using them subsequently to predict/forecast recruitment generally include a +sig2/2 correction to the recruitment predictions or the Ricker a value itself to provide the arithmetic mean prediction (expected value) instead of the median prediction (e.g., Dorner et al. 2009, Haeseker et al. 2005, Parken et al. 2006). My understanding was that if variable x is log-normally distributed (e.g., recruitment), then in the distribution of log(x) is normal with mean=mu and SD=sig (like the linearized Ricker model). In this case, then exp(mu) = median (x) AND the expected value or arithmetic mean of (x) = exp(mu+sig2/2). Others have justified omitting the bias corrections because they have simulated, estimated, and reported medians exclusively and not worried about providing expected values. I guess I’m trying to assess if this is consistent with FRSSI and SBC Chinook MSE thinking, and/or any other simulation/estimation projects any of you have been involved with. `

XXXX) Add correlated en route mortality (Oct 3)

• Attempt to increase synchrony in recruit abundance by add correlations in en route mortality deviations (multivariate normal)
• Use both a uniform strong correlation (0.75) and a custom covariance matrix intended to represent pairwise relationships among CUs
• Although both options resulted in correlated migration mortality rates neither produced strong correlations in en route losses, spawner abundances, or recruit abundances
  • E.g. mean pairwise correlation in mortality rates increased from 0.18 to 0.21
• Unsure why, although likely due to dilution effects moving from deviations to mortality rates to en route losses
• Accept minimal correlations among recruits for now

XXXXI) Update skewed and student-t operating model (Oct 3)

• Use skewed normal and skewed student-t versions of Ricker/Larkin models to generate parameters for alternative productivity regime operatin models
• Parameters estimated in synchSalmon repo using skewedModels.R script; stan models written by S. Anderson
• Median skewness parameter estimate = 0.85; to represent a more severe scenario use 75th percentile = ~0.65
• Weak evidence for heavy tails except for Weaver however given relatively short time series not unexpected; use nu = 2.5 or 3 to represent heavy tail scenario (i.e. catastrophic OM)

XXXXII) Update single stock HCR (Oct 15)

• Addition 1)
  • Secondary harvest control rule - single stock TAC is only removed if a new CU-specific OCP is passed
  • For Ricker models this is median spawner abundance in previous generation must be greater than lower BM
  • For Larkin models single stock harvest only occurs on dominant cycle lines and abundance of previous dominant cycle line has to exceed upper BM
• Addition 2)
  • Secondary HCR can also be used to re-assign TAC from low status to high status stocks
  • CU X, Y and Z are in the same MU; CU X is below its lower RP, CU Y is above its upper RP and CU Z is between the two
  • CU Z receives its own single stock TAC
  • The single stock TAC from CU X is shifted to CU Y, which also receives its own TAC; since CU Y may not be able to sustain the full TAC from X, it receives a proportion based on its abundance in the run
    • For simplicity's sake, if CU Y makes up 25% of the run, it will receive 25% of any other CU's TAC
• Addition 3)
  • Add toggle so that single stock fisheries can occur before or after en route mortality
  • Allows sensitivity analyses to identify relative efficacy of fisheries in different locations without explicitly endorsing a specific allocation scheme

XXXXIII) Add AFE to TAM rule (Oct 16)

• Add Aboriginal Fisheries Exclusion to Fraser TAM rule
• This guarantees 400k fish to Canadian TAC prior to US TAC being calculated
  • I.e. AM TAC is calculated with US ER assuming that aggregate abundance is 400k smaller and that those 400k fish are distributed proportionally across MUs

XXXXIV) Add forecast based secondary HCR (Nov 9)

• As alternative to retrospective HCR (i.e. based on median obs S over prev generation), add one based on forecasted spawner abundance
• Calculated using CU-specific forecasts of recruitment, adjusted downward by mean mortality rate if ER occurs before the fishery does, minus amTAC minus mixTAC
• Reference points are still the same, i.e. TAC is only taken if forecast is above lower BM

XXXXV) Switched outcome uncertainty to additive (Jan 4)

• Following C. Holt's suggestion OU is now additive (i.e. 1 + rnorm) rather than multiplicative
• Also considered switching forecast error to additive but it appears to be commonly applied multiplicatively (e.g. Catalano and Jones 2014)

XXXXVI) Switched outcome uncertainty to beta distribution (Jan 16)

• Parameterized harvest rate outcome uncertainty for Fraser River sockeye using deviations between mid-season TAC and run size estimates vs. post-season catch and run size estimates
  • Could not parameterize TAC because target TAC is often 0 creating a bimodal distribution that is complicated to replicate
  • Details in salmon-sim/estimateOU.R
• As a result modified samSim/recoverySim.R to apply OU on ER rather than TAC by adding a calcRealCatch function that receives target TAC as inputs
  • Also switched from additive normal to beta distribution following S. Anderson's advice
  • Parameterized w/ data in estimateOU.R script
  • Requires back-calculation; see synchSalmon/ouSimulationTests.Rmd for details
  • Note even though the observed data indicate a positive bias in realized exploitation rates (i.e. target often 0, realized never is) the beta distribution is centered on 0 so overfishing may be unrealistically uncommon

XXXXVII) Remove forecast uncertainty from overlap constraint and TAM rule calculations (Jan 16)

• K Holt noted that using forecasted recruitment to set TAC and then applying outcome uncertainty from observed data would result in inflated error rates
• As a result ER relative to FRPs are now set based on true abundance
  • Secondary benefit is that now OU in fixed ER and TAM rules are more closely equivalent
  • Applies to calcTAC and constrain functions
• Note that forecasts of recruitment are still generated for use in single stock harvest control rules

XXXXVIII) Add capacity for independent parallel chains (Feb. 1)

• Added random = TRUE argument to recoverySim() which disables the set seed function. As a result each simulation run begins on a random number, which allows for multiple identical scenarios to be run simultaneously.
• When comparing OMs or MPs this should always be set to FALSE (the default)

49) Adjust upper and lower productivity treatments (Feb 8.)

• Change highProd and lowProd defaults to + or - 35% of median value
• Based on observed difference between average productivity and max/min estimates from Kalman filter productivity estimates
• Details in salmon-sim/scripts/frKalmanAClear.R

50) Stabilize BMs relative to productivity changes (Feb 13)

• Previously Smsy and Sgen were calculated based on realized productivity
• However since reductions in alpha lead to reductions in Smsy, this resulted in PMs such as the ppn of CUs above their BM appearing relatively optimistic, particularly if management is not able to accurately update those markers
• Instead always calculate BMs relative to default (i.e. median) productivity to maximize comparisons among OMs

51) Add divergent productivity trends (Feb 27; March 9)

• Add generic divergent productivity scenario where CUs are selected at random and assigned either increasing, decreasing or stable trends
• Increasing and decreasing productivity are currently set at 1.35 and 0.65 the reference productivity value
• Also include
• divergentSmall: all CUs below median spawner abundance assigned declining trend
• oneUp/oneDown: one CU is assigned an opposite trend
• Eventually plan to add a CU-specific option, but will require adjusting cuPars input file and holding off until we decide whether this OM is worth keeping

52) Add normative period argument for benchmarks (Mar 15)

• When TRUE (default) benchmarks are "frozen" after observation period so that comparisons among OMs and MPs are directly comparable
• Side effect is that many calculations (true BMs and est BMs) do not have to be performed during sim period
• NOTE estimated BMs are assumed to be equal to true when normative period is being used because they will diverge from true due to time series
• SR model parameters still estimated for diagnostics
• In the case of Larkin stocks cycle-line specific BMs from the last observed generation are used

CamFreshwater/samSim documentation built on Jan. 19, 2025, 11:39 a.m.