DOI: 10.6078/d16t59
title: Sacramento River winter-run Chinook salmon cohort reconstruction – data and code

description: Maturation schedules shape a population’s age structure and influence
 productivity and exposure to fishing. Fish cultivated and raised in
 artificial environments like hatcheries may mature at different ages
 compared to their natural-origin counterparts. We evaluated whether
 endangered Sacramento River winter-run Chinook salmon (Oncorhynchus
 tshawytscha) produced in a conservation hatchery had different maturation
 schedules compared to natural-origin fish, and how differences affected
 their exposure to, and impact from, the ocean salmon fishery. Using
 coded-wire tags collected from hatchery fish in the ocean and in-river
 fisheries and on the spawning grounds, and scales collected from
 natural-origin spawner carcasses, we reconstructed the life history of
 hatchery and natural-origin cohorts from 2002–2015 brood years. Hatchery
 fish had similar age-2 maturation rates but higher age-3 maturation rates
 compared to natural-origin fish, resulting in fewer age-4 individuals and
 an overall more truncated age structure. Because natural-origin winter-run
 Chinook salmon were more likely to remain at sea until age-4, they were
 exposed to fishing for an additional year and experienced greater
 reduction in escapement. Compared to natural-origin males, hatchery-origin
 males were much less likely to return at an older age, possibly because
 sexual selection that is occurring on the spawning grounds is not
 occurring to the same extent in the hatchery. Identifying how reproductive
 maturation differs across sources, sex, and life histories is critical to
 understanding how fisheries can disproportionately impact subsets of a
 population and affect its long-term population dynamics and
 sustainability.
description: # Readme **Scripts** 1\. CWT Spawning Data Prep\.R – Preparing coded\-wire
 tag recovery data from spawning grounds and hatchery for hatchery\-origin
 cohort reconstruction 2\. CWT Harvest Data Prep\.R – Preparing coded\-wire
 tag recovery data from ocean and in\-river harvest\. Calculating the
 age\-aggregated encounter rate\. 3\. Hatchery Cohort Reconstruction\.R –
 Cohort reconstruction code for hatchery cohorts from CWT data\. Calculates
 hatchery\-origin maturation and impact rates\. 4\. Impact rates shared\.R
 – Calculating impact rates based on encounter rate and average
 harvestability and release mortality\. 5\. Hatchery Cohort Reconstruction
 by sex\.R – Sex\-specific cohort reconstruction code for hatchery cohorts
 using impact rates from hatchery cohort reconstruction\. 6\. Natural
 Cohort Reconstruction Prep\.R – Age specific escapement based on scale
 data\.  Kimura Chikuni adjustments 7\. Natural Cohort Reconstruction\.R \-
 Cohort reconstruction code for natural cohorts\. Calculates
 hatchery\-origin maturation and impact rates\. Can be done for males
 only\, females only\, or both\. 8\. Comparing Vital Rates\.R – code for
 generating figure 1 and 2 9\. SRR\.R – spawner reduction rate calculations
 and visualizations 10\. Sensitivity Analysis\.R – sensitivity of impact
 rates\, maturation rates\, and spawner reduction rates to changes in size
 at age and release mortality\. ## **1\. CWT Spawning Data Prep\.R** **Data
 input** **CWTReleased.csv** – coded wire batch data for winter-run Chinook
 salmon for brood year from 2000-2017. Obtained from RMIS database.
 Variable descriptions tag\_code\_or\_release\_id: the batch code.
 brood\_year: the year in which eggs were laid (the summer prior to
 release). cwt\_1st\_mark\_count: fish with CWT and Ad Clip.
 cwt\_2nd\_mark\_count: fish with CWT and No clip.
 non\_cwt\_1st\_mark\_count: fish with no CWT and Ad Clip.
 non\_cwt\_2nd\_mark\_count: fish with no CWT and No Clip
 **CWTRecoveries.csv** – all recoveries of winter-run Chinook salmon for
 brood year from 1999-2018.  Obtained from RMIS database. Variable
 descriptions run\_year: the year in which tag was recovered.
 recovery\_date: the date in which tag was recovered. fishery: 10 =
 commercial fishery; 40 = recreational fishery; 46 = in-river fishery 50 =
 hatchery; 54 = spawning ground. recovery\_location\_code: recovery
 location code. sampling\_site: sampling site location code. sex: M = male
 F = female. length: length in mm. tag code: the batch code.
 estimated\_number: expanded tag value based on sampling effort.
 recovery\_location\_name: recovery location name. brood\_year: the year in
 which eggs were laid (the summer prior to release).   **CWT Recoveries
 SG.csv** –recoveries of winter-run Chinook salmon from spawning ground
 surveys for brood year from 1998-2017. Missing data in RMIS database
 filled in by USFWS from Mike O’Farrell. Variable descriptions brood\_year:
 the year in which eggs were laid (the summer prior to release). Age: in
 years, run year - brood year (age 2 - 5) recdate: the date in which tag
 was recovered. fishery: 54 = spawning ground. survey: survey method.
 numtags: expanded tag value based on sampling effort. Value\_Expanded:
 expansion based on tagging frequency. cwtcode: the batch code.  
 **SexRatioSG.csv** – Observed sex ratio on the spawning grounds. From Doug
 Killam. Variable descriptions run\_year: the year in which tag was
 recovered. RatioF: proportion female   **Total to Escapement to
 Hatchery.csv –** Hatchery and natural-origin fish taken to the hatchery
 and used as broodstock Variable descriptions run\_year: the year in which
 tag was recovered. Hatchery Escapement: Hatchery and natural-origin fish
 taken to the hatchery     **Data output** **Escapement to Hatchery.csv** –
 CWT recovered at hatcheries and expanded. Grouped by brood year so each
 line is the age distribution each brood comes back as. Used in *Hatchery
 Cohort Reconstruction.R* Variable descriptions brood\_year: the year in
 which eggs were laid (the summer prior to release). Age1Hat: Age 1
 spawners to hatchery Age2Hat: Age 2 spawners to hatchery Age3Hat: Age 3
 spawners to hatchery Age4Hat: Age 4 spawners to hatchery   **Escapement to
 Hatchery\_F.csv** – CWT recovered at hatcheries from females and expanded.
 Grouped by brood year so each line is the age distribution each brood
 comes back as. Used in *Hatchery Cohort Reconstruction by Sex.R* Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Age2Hat: Age 2 spawners to hatchery Age3Hat: Age 3
 spawners to hatchery Age4Hat: Age 4 spawners to hatchery   **Escapement to
 Hatchery\_M.csv** – CWT recovered at hatcheries from males and expanded.
 Grouped by brood year so each line is the age distribution each brood
 comes back as. Used in *Hatchery Cohort Reconstruction by Sex.R* Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2
 spawners to hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4
 spawners to hatchery   **Hatchery Release.csv –** Number of hatchery fish
 released for every brood year. Created from CWTReleased.csv data. Used to
 calculate survival before age-2 (not necessary for this analysis) in
 *Hatchery Cohort Reconstruction.R.* Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release).
 Individuals\_Released: total individuals released   **Natural Escapement
 to Hatchery.csv** – Male and female natural-origin fish collected for
 broodstock at the hatchery. Used in the *Natural Cohort Reconstruction
 Prep.R* Variable descriptions run\_year: the year in which the adult
 returned Hatchery.Escapement: Hatchery and natural-origin fish taken to
 the hatchery   Hatchery\_to\_Hatchery: Hatchery fish to hatchery
 Natural\_to\_Hatchery: Natural origin fish to hatchery
 NaturalMales\_to\_Hatchery: Natural-origin males to hatchery
 NaturalFemales\_to\_Hatchery: Natural-origin females to hatchery   **CWT
 to SG.csv** – Age Specific escapement by brood year. Used in the
 *Sensitivity Analysis.R* Variable descriptions brood\_year: the year in
 which eggs were laid (the summer prior to release). Age1Sp: CWT Age 1
 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground  
 **HatcheryRunSizeCWT.csv –** Total estimate of hatchery fish on the
 spawning grounds every run year. From *CWT Spawning Data Prep.R* Variable
 descriptions run\_year: the year in which the adult returned TotalCWT:
 total estimate of hatchery fish on the spawning grounds
 **CWTBootstraps.Rds –** Age Specific escapement by brood year. A list with
 1000 items, each representing a bootstrapped sample. Used in *Hatchery
 Cohort reconstruction. R* Variable descriptions brood\_year: the year in
 which eggs were laid (the summer prior to release). Age1Sp: CWT Age 1
 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground  
 **CWTBootstraps\_F.Rds–** Age and sex-specific escapement by brood year. A
 list with 1000 items, each representing a bootstrapped sample. Used in
 *Hatchery Cohort reconstruction by sex.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp: CWT Age 3
 spawners to spawning ground Age4Sp: CWT Age 4 spawners to spawning ground
 Age5Sp: CWT Age 5 spawners to spawning ground   **CWTBootstraps\_M.Rds–**
 Age and sex-specific escapement by brood year. A list with 1000 items,
 each representing a bootstrapped sample. Used in *Hatchery Cohort
 reconstruction by sex.R* Variable descriptions brood\_year: the year in
 which eggs were laid (the summer prior to release). Age1Sp: CWT Age 1
 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground ## **2\. CWT Harvest Data Prep\.R** **Data input**
 **CWTReleased.csv** – coded wire batch data for winter-run Chinook salmon
 for brood year from 2000-2017. Obtained from RMIS database. Variable
 descriptions tag\_code\_or\_release\_id: the batch code. brood\_year: the
 year in which eggs were laid (the summer prior to release).
 cwt\_1st\_mark\_count: fish with CWT and Ad Clip. cwt\_2nd\_mark\_count:
 fish with CWT and No clip. non\_cwt\_1st\_mark\_count: fish with no CWT
 and Ad Clip. non\_cwt\_2nd\_mark\_count: fish with no CWT and No Clip  
 **CWTRecoveries.csv** – all recoveries of winter-run Chinook salmon for
 brood year from 1999-2018.  Obtained from RMIS database. Variable
 descriptions run\_year: the year in which tag was recovered.
 recovery\_date: the date in which tag was recovered. fishery: 10 =
 commercial fishery; 40 = recreational fishery; 46 = in-river fishery 50 =
 hatchery; 54 = spawning ground. recovery\_location\_code: recovery
 location code. sampling\_site: sampling site location code. sex: M = male
 F = female. length: length in mm. tag code: the batch code.
 estimated\_number: expanded tag value based on sampling effort.
 recovery\_location\_name: recovery location name. brood\_year: the year in
 which eggs were laid (the summer prior to release).  
 **sitearea.modified.csv** – file with the region each sampling site is
 located within Variable descriptions agency: agency that uses the code.
 sampling\_site: sampling code area.1: region by area 1 definition area.2:
 region by area 1 definition area.code: area code definition catch.area:
 catch area description   **Size\_limits.csv** – file with the size limit
 (inches) associated with each fishery type, location, and time. Variable
 descriptions run\_year: the year in which tag was recovered. fishery: 10 =
 commercial fishery; 40 = recreational fishery location = region of
 recovery. SF = San Francisco; CO = Central Oregon; KC = Klamath,
 California, KO = Klamath, Oregon, FB = Fort Bragg; NO = Northern Oregon;
 SO = Southern Oregon, MO = Monterrey Month: month of recovery limit: size
 limit (inches)   **release.mort.rate.csv** – file with the release
 mortality rate associated with each fishery type, location, and time.
 Variable descriptions run\_year: the year in which tag was recovered.
 fishery: 10 = commercial fishery; 40 = recreational fishery location =
 region of recovery. SF = San Francisco; CO = Central Oregon; KC = Klamath,
 California, KO = Klamath, Oregon, FB = Fort Bragg; NO = Northern Oregon;
 SO = Southern Oregon, MO = Monterrey Month: month of recovery
 Release.mort.rate: release mortality rate   **length.at.age.csv** – length
 of age of winter-run Chinook salmon in the ocean. From O’Farrell et al.
 2012 Appendix A Variable descriptions age: in years, run year - brood year
 (age 2 - 5) month: calendar month at age mean: mean length (inches) sd:
 standard deviation (inches)   **years with values.csv –** Supporting file
 with months and years where fishing occurred. Use as a placeholder (for
 when there is no fishing data for a cohort in a period where there is
 fishing. Variable descriptions brood\_year: the year in which eggs were
 laid. run\_year: the year in which the adult return or was harvested
 Month: calendar month Age: in years, run year - brood year (age 2 - 5)
 **Data output** **River Harvest.csv –** Age-3 and Age-4 in-river harvest
 by brood year. Used in Hatchery Cohort Reconstruction.R Variable
 descriptions brood\_year: the year in which eggs were laid. run\_year: the
 year in which the adult return or was harvested InRiver3: age-3 in-river
 harvest InRiver4: age-4 in-river harvest   **River Harvest\_M.csv –** Male
 age-3 and Age-4 in-river harvest by brood year, split by sexes based on
 observed sex ratio in CWTs Variable descriptions brood\_year: the year in
 which eggs were laid. run\_year: the year in which the adult return or was
 harvested InRiver3: age-3 in-river harvest InRiver4: age-4 in-river
 harvest   **River Harvest\_F.csv –** Female age-3 and Age-4 in-river
 harvest by brood year, split by sexes based on observed sex ratio in CWTs
 Variable descriptions brood\_year: the year in which eggs were laid.
 run\_year: the year in which the adult return or was harvested InRiver3:
 age-3 in-river harvest InRiver4: age-4 in-river harvest   **Catch
 Bootstrap.Rds** – Ocean fishery encounters (n) by brood year and month.
 Unrecovered tags in harvested fish was resampled 1000 to generate 1000
 estimates of harvest, which was then divided by the proportion that was of
 legal size to estimate number encountered.. Used in *Hatchery Cohort
 Reconstruction.R* Variable descriptions brood\_year: the year in which
 eggs were laid. Remaining column variables: Month and age of ocean fishery
 encounters **Impact Bootstrap.Rds –** Ocean fishery impact (n) by brood
 year and month. Unrecovered tags in harvested fish was resampled 1000 to
 generate 1000 estimates of fishery impact (including drop-off mortality
 and release mortality). *Used in Hatchery Cohort Reconstruction.R*
 Variable descriptions brood\_year: the year in which eggs were laid.
 Remaining column variables: Month and age of ocean fishery encounters
 **Catch Representation.Rds** – The proportion of harvest for each fishery
 type and region for every month of fishing. 1000 resampled values. Used
 later in this script when calculating the average harvestability and
 release mortality based on spatial and fishery type distribution. Variable
 descriptions brood\_year: the year in which eggs were laid. run\_year: the
 year in which the adult was harvested Month: calendar month Age: in years,
 run year - brood year (age 2 - 5) Tags\_Collected: Total tags collected
 Catch\_Sample: resampled catch Harvested\_Sample: resampled harvest
 Release\_Sample: release mortality from resampled harvest Drop\_Sample:
 drop mortality from resampled harvest Impact\_Sample: release mortality
 from resampled harvest Catch\_Sample\_Total: total catch samples from the
 time period Remaining columns: proportion of catches during the time
 period by region.fishery type   **Avg Harvestability.Rds** – the
 proportion that cohort was harvestable during a given month, based on the
 spatial distribution of catches in the ocean at the time (across cohorts).
 Used in *Impact rates shared.R* and *Natural Cohort Reconstruction.R*
 Variable descriptions brood\_year: the year in which eggs were laid.
 Remaining column variables: Month and age of ocean fishery encounters
 **Avg ReleaseMort.Rds** – the proportion that cohort was release
 mortalities during a given month, based on the spatial distribution of
 catches in the ocean at the time (across cohorts) that affected the
 release mortality rate. Used in *Impact rates shared.R* and *Natural
 Cohort Reconstruction.R* Variable descriptions brood\_year: the year in
 which eggs were laid. Remaining column variables: Month and age of ocean
 fishery encounters ## **3\. Hatchery Cohort Reconstruction\.R** **Data
 input** **CWTBootstraps.Rds –** Age Specific escapement by brood year. A
 list with 1000 items, each representing a bootstrapped sample. Created in
 *CWT Spawning Data Prep.R* Variable descriptions brood\_year: the year in
 which eggs were laid (the summer prior to release). Age1Sp: CWT Age 1
 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground  
 **Escapement to Hatchery.csv** – CWT recovered at hatcheries and expanded.
 Grouped by brood year so each line is the age distribution each brood
 comes back as. Created in *CWT Spawning Data Prep.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2 spawners to
 hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4 spawners to
 hatchery   **River Harvest.csv –** Age-3 and Age-4 in-river harvest by
 brood year. Created in *CWT Harvest Data Prep.R.* Variable descriptions
 brood\_year: the year in which eggs were laid. run\_year: the year in
 which the adult return or was harvested InRiver3: age-3 in-river harvest
 InRiver4: age-4 in-river harvest   **Hatchery Release.csv –** Number of
 hatchery fish released for every brood year. Created from CWTReleased.csv
 data. Used to calculate survival before age-2 (not necessary for this
 analysis). Variable descriptions brood\_year: the year in which eggs were
 laid (the summer prior to release). Individuals\_Released: total
 individuals released   **Catch Bootstrap.Rds** – Ocean fishery encounters
 (n) by brood year and month. Unrecovered tags in harvested fish was
 resampled 1000 to generate 1000 estimates of harvest, which was then
 divided by the proportion that was of legal size to estimate number
 encountered. From *CWT Harvest Data Prep.R.* Variable descriptions
 brood\_year: the year in which eggs were laid. Remaining column variables:
 Month and age of ocean fishery encounters **Impact Bootstrap.Rds –** Ocean
 fishery impact (n) by brood year and month. Unrecovered tags in harvested
 fish was resampled 1000 to generate 1000 estimates of fishery impact
 (including drop-off mortality and release mortality). From *CWT Harvest
 Data Prep.R.* Variable descriptions brood\_year: the year in which eggs
 were laid. Remaining column variables: Month and age of ocean fishery
 encounters **Data output** **CWT Cohort Reconstruction.Rds –** Hatchery
 cohort reconstruction full results, bootstraps. Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Individuals\_Released: total individuals released Age1Sp: CWT
 Age 1 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning
 ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4
 spawners to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground
 Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2 spawners to hatchery
 Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4 spawners to hatchery
 InRiver3: age-3 in-river harvest InRiver4: age-4 in-river harvest
 Apr3-Nov4 (Month.Age columns): fishery impact by month and age Cat3\_4 –
 Cat4\_11 (CatAge\_Month columns): Catch rate by period for both cohorts
 CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate by period for
 single cohort Age6.2 – Age2.3 (AgeAge.Month columns): Reconstructed ocean
 abundance Out\_Survival: survival from release to Age2.3 Mat4: Age-4
 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2 maturation rate
 Imp4: Age-4 impact rate Imp3: Age-3 impact rate Im3\_5 – Imp4\_11
 (ImpAge\_Month): Month specific impact rate on cohort  
 **Maturation\_Uncertainty\_CWT.csv –** Age 2, 3, and 4 maturation rates
 and their 95% confidence intervals. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release). Mat2Lower:
 lower bound of 95% confidence interval of age-2 maturation rate Mat2Mean:
 mean age-2 maturation rate Mat2Upper: upper bound of 95% confidence
 interval of age-2 maturation rate Mat3Lower: lower bound of 95% confidence
 interval of age-3 maturation rate Mat3Mean: mean age-3 maturation rate
 Mat3Upper: upper bound of 95% confidence interval of age-3 maturation rate
 Mat4Lower: lower bound of 95% confidence interval of age-4 maturation rate
 Mat4Mean: mean age-4 maturation rate Mat4Upper: upper bound of 95%
 confidence interval of age-4 maturation rate Source: Origin and data
 source   **Impact\_Uncertainty\_CWT.csv –** Age 3 and 4 ocean fishery
 impact and their 95% confidence intervals. Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Imp 3Lower: lower bound of 95% confidence interval of age-3
 impact rate Imp3Mean: mean age-3 impact rate Imp3Upper: upper bound of 95%
 confidence interval of age-3 impact rate Imp4Lower: lower bound of 95%
 confidence interval of age-4 impact rate Imp4Mean: mean age-4 impact rate
 Imp4Upper: upper bound of 95% confidence interval of age-4 impact rate ##
 **4\. Impact rates shared\.R** **Data input** **CWT Cohort
 Reconstruction.Rds –** Hatchery cohort reconstruction full results,
 bootstraps. From *Hatchery Cohort Reconstruction.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Individuals\_Released: total individuals released Age1Sp: CWT
 Age 1 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning
 ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4
 spawners to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground
 Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2 spawners to hatchery
 Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4 spawners to hatchery
 InRiver3: age-3 in-river harvest InRiver4: age-4 in-river harvest
 Apr3-Nov4 (Month.Age columns): fishery impact by month and age Cat3\_4 –
 Cat4\_11 (CatAge\_Month columns): Catch rate by period for both cohorts
 CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate by period for
 single cohort Age6.2 – Age2.3 (AgeAge.Month columns): Reconstructed ocean
 abundance Out\_Survival: survival from release to Age2.3 Mat4: Age-4
 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2 maturation rate
 Imp4: Age-4 impact rate Imp3: Age-3 impact rate Imp3\_5 – Imp4\_11
 (ImpAge\_Month): Month specific impact rate on cohort   **Avg
 Harvestability.Rds** – the proportion that cohort was harvestable during a
 given month, based on the spatial distribution of catches in the ocean at
 the time (across cohorts). From *CWT Harvest Data Prep.R* Variable
 descriptions brood\_year: the year in which eggs were laid. Remaining
 column variables: Month and age of ocean fishery encounters **Avg
 ReleaseMort.Rds** – the proportion that cohort was release mortalities
 during a given month, based on the spatial distribution of catches in the
 ocean at the time (across cohorts) that affected the release mortality
 rate. From *CWT Harvest Data Prep.R* Variable descriptions brood\_year:
 the year in which eggs were laid. Remaining column variables: Month and
 age of ocean fishery encounters **Data output:**
 **Impact\_hatchery\_shared.csv** – Age 3 and Age 4 impact rates with 95%
 CI based on age aggregated data. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release). Imp2Lower:
 lower bound of 95% confidence interval of age-2 impact rate Imp2Mean: mean
 age-2 impact rate Imp2Upper: upper bound of 95% confidence interval of
 age-2 impact rate Imp3Lower: lower bound of 95% confidence interval of
 age-3 impact rate Imp3Mean: mean age-3 impact rate Imp3Upper: upper bound
 of 95% confidence interval of age-3 impact rate Imp4Lower: lower bound of
 95% confidence interval of age-4 impact rate Imp4Mean: mean age-4 impact
 rate Imp4Upper: upper bound of 95% confidence interval of age-4 impact
 rate   **Impact\_hatchery\_notshared.csv** – Age 3 and Age 4 impact rates
 with 95% CI based on age aggregated data. Is equivalent to
 Maturation\_Uncertainty\_CWT.csv. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release). Imp2Lower:
 lower bound of 95% confidence interval of age-2 impact rate Imp2Mean: mean
 age-2 impact rate Imp2Upper: upper bound of 95% confidence interval of
 age-2 impact rate Imp3Lower: lower bound of 95% confidence interval of
 age-3 impact rate Imp3Mean: mean age-3 impact rate Imp3Upper: upper bound
 of 95% confidence interval of age-3 impact rate Imp4Lower: lower bound of
 95% confidence interval of age-4 impact rate Imp4Mean: mean age-4 impact
 rate Imp4Upper: upper bound of 95% confidence interval of age-4 impact
 rate ## **5\. Hatchery Cohort Reconstruction by sex\.R** **Data input**
 **CWTBootstraps\_F.Rds–** Age and sex-specific escapement by brood year. A
 list with 1000 items, each representing a bootstrapped sample. From *CWT
 Spawning Data Prep.R* Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Age2Sp: CWT Age 2 spawners
 to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp:
 CWT Age 4 spawners to spawning ground Age5Sp: CWT Age 5 spawners to
 spawning ground   **CWTBootstraps\_M.Rds–** Age and sex-specific
 escapement by brood year. A list with 1000 items, each representing a
 bootstrapped sample. From *CWT Spawning Data Prep.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age1Sp: CWT Age 1 spawners to spawning ground Age2Sp: CWT Age 2
 spawners to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground
 Age4Sp: CWT Age 4 spawners to spawning ground   **Escapement to
 Hatchery\_F.csv** – CWT recovered at hatcheries from females and expanded.
 Grouped by brood year so each line is the age distribution each brood
 comes back as. From *CWT Spawning Data Prep.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age2Hat: Age 2 spawners to hatchery Age3Hat: Age 3 spawners to
 hatchery Age4Hat: Age 4 spawners to hatchery   **Escapement to
 Hatchery\_M.csv** – CWT recovered at hatcheries from males and expanded.
 Grouped by brood year so each line is the age distribution each brood
 comes back as. From *CWT Spawning Data Prep.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2 spawners to
 hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4 spawners to
 hatchery   **River Harvest\_M.csv –** Male age-3 and Age-4 in-river
 harvest by brood year, split by sexes based on observed sex ratio in CWTs.
 From *CWT Harvest Data Prep.R* Variable descriptions brood\_year: the year
 in which eggs were laid. run\_year: the year in which the adult return or
 was harvested InRiver3: age-3 in-river harvest InRiver4: age-4 in-river
 harvest   **River Harvest\_F.csv –** Female age-3 and Age-4 in-river
 harvest by brood year, split by sexes based on observed sex ratio in CWTs.
 From *CWT Harvest Data Prep.R* Variable descriptions brood\_year: the year
 in which eggs were laid. run\_year: the year in which the adult return or
 was harvested InRiver3: age-3 in-river harvest InRiver4: age-4 in-river
 harvest   **Hatchery Release.csv –** Number of hatchery fish released for
 every brood year. Created from CWTReleased.csv data. Used to calculate
 survival before age-2 (not necessary for this analysis). Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Individuals\_Released: total individuals released  
 **Data output** **CWT Cohort Reconstruction\_Females.Rds -** Hatchery
 cohort reconstruction full results, bootstrapped. For females. Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Individuals\_Released: total individuals released
 Age1Sp: CWT Age 1 spawners to spawning ground Age2Sp: CWT Age 2 spawners
 to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp:
 CWT Age 4 spawners to spawning ground Age5Sp: CWT Age 5 spawners to
 spawning ground Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2
 spawners to hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4
 spawners to hatchery InRiver3: age-3 in-river harvest InRiver4: age-4
 in-river harvest Apr3-Nov4 (Month.Age columns): fishery impact by month
 and age Cat3\_4 – Cat4\_11 (CatAge\_Month columns): Catch rate by period
 for both cohorts CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate
 by period for single cohort Age6.2 – Age2.3 (AgeAge.Month columns):
 Reconstructed ocean abundance Out\_Survival: survival from release to
 Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2
 maturation rate Imp4: Age-4 impact rate Imp3: Age-3 impact rate Imp3\_5 –
 Imp4\_11 (ImpAge\_Month): Month specific impact rate on cohort   **CWT
 Cohort Reconstruction\_Males.Rds -** Hatchery cohort reconstruction full
 results, bootstrapped. For males. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release).
 Individuals\_Released: total individuals released Age1Sp: CWT Age 1
 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2
 spawners to hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4
 spawners to hatchery InRiver3: age-3 in-river harvest InRiver4: age-4
 in-river harvest Apr3-Nov4 (Month.Age columns): fishery impact by month
 and age Cat3\_4 – Cat4\_11 (CatAge\_Month columns): Catch rate by period
 for both cohorts CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate
 by period for single cohort Age6.2 – Age2.3 (AgeAge.Month columns):
 Reconstructed ocean abundance Out\_Survival: survival from release to
 Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2
 maturation rate Imp4: Age-4 impact rate Imp3: Age-3 impact rate Im3\_5 –
 Imp4\_11 (ImpAge\_Month): Month specific impact rate on cohort  
 **Maturation\_Uncertainty\_CWT\_Sex.csv –** Age 2, 3, and 4 maturation
 rates and their 95% confidence intervals, by sex. Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Mat2Lower: lower bound of 95% confidence interval of age-2
 maturation rate Mat2Mean: mean age-2 maturation rate Mat2Upper: upper
 bound of 95% confidence interval of age-2 maturation rate Mat3Lower: lower
 bound of 95% confidence interval of age-3 maturation rate Mat3Mean: mean
 age-3 maturation rate Mat3Upper: upper bound of 95% confidence interval of
 age-3 maturation rate Mat4Lower: lower bound of 95% confidence interval of
 age-4 maturation rate Mat4Mean: mean age-4 maturation rate Mat4Upper:
 upper bound of 95% confidence interval of age-4 maturation rate Sex: male
 or female ## **6\. Natural Cohort Reconstruction Prep\.R** **Data input**
 **Scale Readage.csv –** scale aging by CDFW for winter-run from 2005-2018
 for natural and hatchery-origin fish. Variable descriptions Year: run year
 Sample Number: sample ID from spawning ground survey Age: age in years
 from CWT run year - brood year (age 2 - 5) Readage: age from scale reading
 Recovery Date: recovery date Fork Length (mm): Fork length in mm Sex: M =
 male; F = female CWT Code: coded-wire tag code if present   **Escapement
 Numbers.csv –** total estimate of spawners on spawning ground each year.
 Estimated number of females. Reported ratio of females. Variable
 descriptions run\_year: the year in which the adult return Annual: total
 escapement Females: Female Escapement Males: Male Escapement RatioF:
 proportion female Fry: subsequent fry   **Natural Escapement to
 Hatchery.csv** – Male and female natural-origin fish collected for
 broodstock at the hatchery. From *CWT Spawning Data Prep.R* Variable
 descriptions run\_year: the year in which the adult returned
 Hatchery.Escapement: Hatchery and natural-origin fish taken to the
 hatchery   Hatchery\_to\_Hatchery: Hatchery fish to hatchery
 Natural\_to\_Hatchery: Natural origin fish to hatchery
 NaturalMales\_to\_Hatchery: Natural-origin males to hatchery
 NaturalFemales\_to\_Hatchery: Natural-origin females to hatchery  
 **HatcheryRunSizeCWT.csv –** Total estimate of hatchery fish on the
 spawning grounds every run year. From *CWT Spawning Data Prep.R* Variable
 descriptions run\_year: the year in which the adult returned TotalCWT:
 total estimate of hatchery fish on the spawning grounds **Data output:**
 **Spawners Unadjusted.Rds –** total run size proportion by age proportions
 from scale data. No aging corrections made. For *Natural Cohort
 Reconstruction.R* Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Age2Sp: CWT Age 2 spawners
 to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp:
 CWT Age 4 spawners to spawning ground **Female Spawners Unadjusted.Rds–**
 total female run size proportion by age proportions from female scale
 data. No aging corrections made. For *Natural Cohort Reconstruction.R*
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground **Male Spawners Unadjusted.Rds–** total male run size
 proportion by age proportions from male scale data. No aging corrections
 made. For *Natural Cohort Reconstruction.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp: CWT Age 3
 spawners to spawning ground Age4Sp: CWT Age 4 spawners to spawning ground
 **Spawners Adjusted.Rds –** total run size proportion by age proportions
 from scale data with Kimura Chikuni adjustments. For *Natural Cohort
 Reconstruction.R* Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Age2Sp: CWT Age 2 spawners
 to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground  Age4Sp:
 CWT Age 4 spawners to spawning ground **Female Spawners Adjusted.Rds –**
 total female run size proportion by age proportions from female scale data
 with Kimura Chikuni adjustments. For *Natural Cohort Reconstruction.R*
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground **Male Spawners Adjusted.Rds –** total male run size
 proportion by age proportions from male scale data with Kimura Chikuni
 adjustments. For *Natural Cohort Reconstruction.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp: CWT Age 3
 spawners to spawning ground Age4Sp: CWT Age 4 spawners to spawning ground
 ## **7\. Natural Cohort Reconstruction\.R** **Data input** **CWT Cohort
 Reconstruction.Rds –** Hatchery cohort reconstruction full results,
 bootstraps. From *Hatchery Cohort Reconstruction.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Individuals\_Released: total individuals released Age1Sp: CWT
 Age 1 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning
 ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4
 spawners to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground
 Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2 spawners to hatchery
 Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4 spawners to hatchery
 InRiver3: age-3 in-river harvest InRiver4: age-4 in-river harvest
 Apr3-Nov4 (Month.Age columns): fishery impact by month and age Cat3\_4 –
 Cat4\_11 (CatAge\_Month columns): Catch rate by period for both cohorts
 CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate by period for
 single cohort Age6.2 – Age2.3 (AgeAge.Month columns): Reconstructed ocean
 abundance Out\_Survival: survival from release to Age2.3 Mat4: Age-4
 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2 maturation rate
 Imp4: Age-4 impact rate Imp3: Age-3 impact rate Imp3\_5 – Imp4\_11
 (ImpAge\_Month): Month specific impact rate on cohort   **Avg
 Harvestability.Rds** – the proportion that cohort was harvestable during a
 given month, based on the spatial distribution of catches in the ocean at
 the time (across cohorts). From *CWT Harvest Data Prep.R* Variable
 descriptions brood\_year: the year in which eggs were laid. Remaining
 column variables: Month and age of ocean fishery encounters **Avg
 ReleaseMort.Rds** – the proportion that cohort was release mortalities
 during a given month, based on the spatial distribution of catches in the
 ocean at the time (across cohorts) that affected the release mortality
 rate. From *CWT Harvest Data Prep.R* Variable descriptions brood\_year:
 the year in which eggs were laid. Remaining column variables: Month and
 age of ocean fishery encounters **Escapement Numbers.csv –** total
 estimate of spawners on spawning ground each year. Estimated number of
 females. Reported ratio of females. Variable descriptions run\_year: the
 year in which the adult return Annual: total escapement Females: Female
 Escapement Males: Male Escapement RatioF: proportion female Fry:
 subsequent fry   **Female Spawners Unadjusted.Rds –** total female run
 size proportion by age proportions from female scale data with Kimura
 Chikuni adjustments. From *Natural Cohort Reconstruction Prep.R.* Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp:
 CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners to
 spawning ground **Male Spawners Unadjusted.Rds –** total male run size
 proportion by age proportions from male scale data with Kimura Chikuni
 adjustments. *Natural Cohort Reconstruction Prep.R.* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp: CWT Age 3
 spawners to spawning ground Age4Sp: CWT Age 4 spawners to spawning ground
 **Data output** **Natural Cohort Reconstruction.Rds–** Natural cohort
 reconstruction full results, bootstrapped. Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Fry: estimated fry equivalents Age2Sp: CWT Age 2 spawners to
 spawning ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT
 Age 4 spawners to spawning ground Age5.2 – Age2.3 (AgeAge.Month columns):
 Reconstructed ocean abundance Imp4\_11– Imp3\_4 (ImpAge\_Month): Month
 specific impact rate on cohort Imp3: Age 3 impact (N) Imp3rate: Age-3
 impact rate Out\_Survival: survival from release to Age2.3 Mat4: Age-4
 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2 maturation rate  
 **Natural Cohort Reconstruction\_Male.Rds–** Natural cohort reconstruction
 full results for males, bootstrapped. Variable descriptions brood\_year:
 the year in which eggs were laid (the summer prior to release). Fry:
 estimated fry equivalents Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground Age5.2 – Age2.3 (AgeAge.Month columns): Reconstructed
 ocean abundance Imp4\_11– Imp3\_4 (ImpAge\_Month): Month specific impact
 rate on cohort Imp3: Age 3 impact (N) Imp3rate: Age-3 impact rate
 Out\_Survival: survival from release to Age2.3 Mat4: Age-4 maturation rate
 Mat3: Age-3 maturation rate Mat2: Age-2 maturation rate   **Natural Cohort
 Reconstruction\_Female.Rds–** Natural cohort reconstruction full results
 for females, bootstrapped. Variable descriptions brood\_year: the year in
 which eggs were laid (the summer prior to release). Fry: estimated fry
 equivalents Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp: CWT Age
 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners to spawning
 ground Age5.2 – Age2.3 (AgeAge.Month columns): Reconstructed ocean
 abundance Imp4\_11– Imp3\_4 (ImpAge\_Month): Month specific impact rate on
 cohort Imp3: Age 3 impact (N) Imp3rate: Age-3 impact rate Out\_Survival:
 survival from release to Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3
 maturation rate Mat2: Age-2 maturation rate  
 **Maturation\_Uncertainty\_Natural.csv** **–** Age 2, 3, and 4
 natural-origin maturation rates and their 95% confidence intervals.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Mat2Lower: lower bound of 95% confidence
 interval of age-2 maturation rate Mat2Mean: mean age-2 maturation rate
 Mat2Upper: upper bound of 95% confidence interval of age-2 maturation rate
 Mat3Lower: lower bound of 95% confidence interval of age-3 maturation rate
 Mat3Mean: mean age-3 maturation rate Mat3Upper: upper bound of 95%
 confidence interval of age-3 maturation rate Mat4Lower: lower bound of 95%
 confidence interval of age-4 maturation rate Mat4Mean: mean age-4
 maturation rate Mat4Upper: upper bound of 95% confidence interval of age-4
 maturation rate   **Maturation\_Uncertainty\_Natural\_Male.csv** **–** Age
 2, 3, and 4 male natural-origin maturation rates and their 95% confidence
 intervals. Variable descriptions brood\_year: the year in which eggs were
 laid (the summer prior to release). Mat2Lower: lower bound of 95%
 confidence interval of age-2 maturation rate Mat2Mean: mean age-2
 maturation rate Mat2Upper: upper bound of 95% confidence interval of age-2
 maturation rate Mat3Lower: lower bound of 95% confidence interval of age-3
 maturation rate Mat3Mean: mean age-3 maturation rate Mat3Upper: upper
 bound of 95% confidence interval of age-3 maturation rate Mat4Lower: lower
 bound of 95% confidence interval of age-4 maturation rate Mat4Mean: mean
 age-4 maturation rate Mat4Upper: upper bound of 95% confidence interval of
 age-4 maturation rate Sex: male or female  
 **Maturation\_Uncertainty\_Natural\_Female.csv** **–** Age 2, 3, and 4
 female natural-origin maturation rates and their 95% confidence intervals.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Mat2Lower: lower bound of 95% confidence
 interval of age-2 maturation rate Mat2Mean: mean age-2 maturation rate
 Mat2Upper: upper bound of 95% confidence interval of age-2 maturation rate
 Mat3Lower: lower bound of 95% confidence interval of age-3 maturation rate
 Mat3Mean: mean age-3 maturation rate Mat3Upper: upper bound of 95%
 confidence interval of age-3 maturation rate Mat4Lower: lower bound of 95%
 confidence interval of age-4 maturation rate Mat4Mean: mean age-4
 maturation rate Mat4Upper: upper bound of 95% confidence interval of age-4
 maturation rate Sex: male or female   **Impact\_Uncertainty\_Natural.csv**
 **–** Age 3 and 4 ocean fishery impact (N and rate) and their 95%
 confidence intervals. Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Impact3Lower: lower bound of
 95% confidence interval of age-3 impact rate Impact3Mean: mean age-3
 impact rate Impact3Upper: upper bound of 95% confidence interval of age-3
 impact rate Impact4Lower: lower bound of 95% confidence interval of age-4
 impact rate Impact4Mean: mean age-4 impact rate Impact4Upper: upper bound
 of 95% confidence interval of age-4 impact rate Impactrate3Lower: lower
 bound of 95% confidence interval of age-3 impact rate Impactrate3Mean:
 mean age-3 impact rate Impactrate3Upper: upper bound of 95% confidence
 interval of age-3 impact rate Impactrate4Lower: lower bound of 95%
 confidence interval of age-4 impact rate Impactrate4Mean: mean age-4
 impact rate Impactrate4Upper: upper bound of 95% confidence interval of
 age-4 impact rate   **Impact\_ Uncertainty\_Natural \_Male.csv** **–**
 Male Age 3 and 4 ocean fishery impact (N and rate) and their 95%
 confidence intervals. Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Impact3Lower: lower bound of
 95% confidence interval of age-3 impact rate Impact3Mean: mean age-3
 impact rate Impact3Upper: upper bound of 95% confidence interval of age-3
 impact rate Impact4Lower: lower bound of 95% confidence interval of age-4
 impact rate Impact4Mean: mean age-4 impact rate Impact4Upper: upper bound
 of 95% confidence interval of age-4 impact rate Impactrate3Lower: lower
 bound of 95% confidence interval of age-3 impact rate Impactrate3Mean:
 mean age-3 impact rate Impactrate3Upper: upper bound of 95% confidence
 interval of age-3 impact rate Impactrate4Lower: lower bound of 95%
 confidence interval of age-4 impact rate Impactrate4Mean: mean age-4
 impact rate Impactrate4Upper: upper bound of 95% confidence interval of
 age-4 impact rate   **Impact\_ Uncertainty\_Natural \_Female.csv** **–**
 Female Age 3 and 4 ocean fishery impact (N and rate) and their 95%
 confidence intervals. Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Impact3Lower: lower bound of
 95% confidence interval of age-3 impact rate Impact3Mean: mean age-3
 impact rate Impact3Upper: upper bound of 95% confidence interval of age-3
 impact rate Impact4Lower: lower bound of 95% confidence interval of age-4
 impact rate Impact4Mean: mean age-4 impact rate Impact4Upper: upper bound
 of 95% confidence interval of age-4 impact rate Impactrate3Lower: lower
 bound of 95% confidence interval of age-3 impact rate Impactrate3Mean:
 mean age-3 impact rate Impactrate3Upper: upper bound of 95% confidence
 interval of age-3 impact rate Impactrate4Lower: lower bound of 95%
 confidence interval of age-4 impact rate Impactrate4Mean: mean age-4
 impact rate Impactrate4Upper: upper bound of 95% confidence interval of
 age-4 impact rate ## **8\. Comparing Vital Rates\.R** **Data input**
 **Maturation\_Uncertainty\_CWT.csv –** Age 2, 3, and 4 maturation rates
 and their 95% confidence intervals. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release). Mat2Lower:
 lower bound of 95% confidence interval of age-2 maturation rate Mat2Mean:
 mean age-2 maturation rate Mat2Upper: upper bound of 95% confidence
 interval of age-2 maturation rate Mat3Lower: lower bound of 95% confidence
 interval of age-3 maturation rate Mat3Mean: mean age-3 maturation rate
 Mat3Upper: upper bound of 95% confidence interval of age-3 maturation rate
 Mat4Lower: lower bound of 95% confidence interval of age-4 maturation rate
 Mat4Mean: mean age-4 maturation rate Mat4Upper: upper bound of 95%
 confidence interval of age-4 maturation rate Source: Origin and data
 source   **Maturation\_Uncertainty\_Natural.csv** **–** Age 2, 3, and 4
 natural-origin maturation rates and their 95% confidence intervals.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Mat2Lower: lower bound of 95% confidence
 interval of age-2 maturation rate Mat2Mean: mean age-2 maturation rate
 Mat2Upper: upper bound of 95% confidence interval of age-2 maturation rate
 Mat3Lower: lower bound of 95% confidence interval of age-3 maturation rate
 Mat3Mean: mean age-3 maturation rate Mat3Upper: upper bound of 95%
 confidence interval of age-3 maturation rate Mat4Lower: lower bound of 95%
 confidence interval of age-4 maturation rate Mat4Mean: mean age-4
 maturation rate Mat4Upper: upper bound of 95% confidence interval of age-4
 maturation rate   **Maturation\_Uncertainty\_CWT\_Sex.csv –** Age 2, 3,
 and 4 maturation rates and their 95% confidence intervals, by sex.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Mat2Lower: lower bound of 95% confidence
 interval of age-2 maturation rate Mat2Mean: mean age-2 maturation rate
 Mat2Upper: upper bound of 95% confidence interval of age-2 maturation rate
 Mat3Lower: lower bound of 95% confidence interval of age-3 maturation rate
 Mat3Mean: mean age-3 maturation rate Mat3Upper: upper bound of 95%
 confidence interval of age-3 maturation rate Mat4Lower: lower bound of 95%
 confidence interval of age-4 maturation rate Mat4Mean: mean age-4
 maturation rate Mat4Upper: upper bound of 95% confidence interval of age-4
 maturation rate Sex: male or female
 **Maturation\_Uncertainty\_Natural\_Male.csv** **–** Age 2, 3, and 4 male
 natural-origin maturation rates and their 95% confidence intervals.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Mat2Lower: lower bound of 95% confidence
 interval of age-2 maturation rate Mat2Mean: mean age-2 maturation rate
 Mat2Upper: upper bound of 95% confidence interval of age-2 maturation rate
 Mat3Lower: lower bound of 95% confidence interval of age-3 maturation rate
 Mat3Mean: mean age-3 maturation rate Mat3Upper: upper bound of 95%
 confidence interval of age-3 maturation rate Mat4Lower: lower bound of 95%
 confidence interval of age-4 maturation rate Mat4Mean: mean age-4
 maturation rate Mat4Upper: upper bound of 95% confidence interval of age-4
 maturation rate   **Maturation\_Uncertainty\_Natural\_Female.csv** **–**
 Age 2, 3, and 4 female natural-origin maturation rates and their 95%
 confidence intervals. Variable descriptions brood\_year: the year in which
 eggs were laid (the summer prior to release). Mat2Lower: lower bound of
 95% confidence interval of age-2 maturation rate Mat2Mean: mean age-2
 maturation rate Mat2Upper: upper bound of 95% confidence interval of age-2
 maturation rate Mat3Lower: lower bound of 95% confidence interval of age-3
 maturation rate Mat3Mean: mean age-3 maturation rate Mat3Upper: upper
 bound of 95% confidence interval of age-3 maturation rate Mat4Lower: lower
 bound of 95% confidence interval of age-4 maturation rate Mat4Mean: mean
 age-4 maturation rate Mat4Upper: upper bound of 95% confidence interval of
 age-4 maturation rate   **Impact\_hatchery\_shared.csv** – Age 3 and Age 4
 impact rates with 95% CI based on age aggregated data. Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Imp2Lower: lower bound of 95% confidence interval of
 age-2 impact rate Imp2Mean: mean age-2 impact rate Imp2Upper: upper bound
 of 95% confidence interval of age-2 impact rate Imp3Lower: lower bound of
 95% confidence interval of age-3 impact rate Imp3Mean: mean age-3 impact
 rate Imp3Upper: upper bound of 95% confidence interval of age-3 impact
 rate Imp4Lower: lower bound of 95% confidence interval of age-4 impact
 rate Imp4Mean: mean age-4 impact rate Imp4Upper: upper bound of 95%
 confidence interval of age-4 impact rate  
 **Impact\_hatchery\_notshared.csv** – Age 3 and Age 4 impact rates with
 95% CI based on age aggregated data. Is equivalent to
 Maturation\_Uncertainty\_CWT.csv. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release). Imp2Lower:
 lower bound of 95% confidence interval of age-2 impact rate Imp2Mean: mean
 age-2 impact rate Imp2Upper: upper bound of 95% confidence interval of
 age-2 impact rate Imp3Lower: lower bound of 95% confidence interval of
 age-3 impact rate Imp3Mean: mean age-3 impact rate Imp3Upper: upper bound
 of 95% confidence interval of age-3 impact rate Imp4Lower: lower bound of
 95% confidence interval of age-4 impact rate Imp4Mean: mean age-4 impact
 rate Imp4Upper: upper bound of 95% confidence interval of age-4 impact
 rate ## **9\. SRR\.R** **Data input** **CWT Cohort Reconstruction.Rds –**
 Hatchery cohort reconstruction full results, bootstraps. Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Individuals\_Released: total individuals released
 Age1Sp: CWT Age 1 spawners to spawning ground Age2Sp: CWT Age 2 spawners
 to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp:
 CWT Age 4 spawners to spawning ground Age5Sp: CWT Age 5 spawners to
 spawning ground Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2
 spawners to hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4
 spawners to hatchery InRiver3: age-3 in-river harvest InRiver4: age-4
 in-river harvest Apr3-Nov4 (Month.Age columns): fishery impact by month
 and age Cat3\_4 – Cat4\_11 (CatAge\_Month columns): Catch rate by period
 for both cohorts CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate
 by period for single cohort Age6.2 – Age2.3 (AgeAge.Month columns):
 Reconstructed ocean abundance Out\_Survival: survival from release to
 Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2
 maturation rate Imp4: Age-4 impact rate Imp3: Age-3 impact rate Imp3\_5 –
 Imp4\_11 (ImpAge\_Month): Month specific impact rate on cohort   **CWT
 Cohort Reconstruction\_Females.Rds -** Hatchery cohort reconstruction full
 results, bootstrapped. For females. Variable descriptions brood\_year: the
 year in which eggs were laid (the summer prior to release).
 Individuals\_Released: total individuals released Age1Sp: CWT Age 1
 spawners to spawning ground Age2Sp: CWT Age 2 spawners to spawning ground
 Age3Sp: CWT Age 3 spawners to spawning ground Age4Sp: CWT Age 4 spawners
 to spawning ground Age5Sp: CWT Age 5 spawners to spawning ground Age1Hat:
 Age 1 spawners to hatchery Age2Hat: Age 2 spawners to hatchery Age3Hat:
 Age 3 spawners to hatchery Age4Hat: Age 4 spawners to hatchery InRiver3:
 age-3 in-river harvest InRiver4: age-4 in-river harvest Apr3-Nov4
 (Month.Age columns): fishery impact by month and age Cat3\_4 – Cat4\_11
 (CatAge\_Month columns): Catch rate by period for both cohorts CatU3\_4 –
 CatU4\_11 (CatUAge\_Month columns): Catch rate by period for single cohort
 Age6.2 – Age2.3 (AgeAge.Month columns): Reconstructed ocean abundance
 Out\_Survival: survival from release to Age2.3 Mat4: Age-4 maturation rate
 Mat3: Age-3 maturation rate Mat2: Age-2 maturation rate Imp4: Age-4 impact
 rate Imp3: Age-3 impact rate Imp3\_5 – Imp4\_11 (ImpAge\_Month): Month
 specific impact rate on cohort   **CWT Cohort Reconstruction\_Males.Rds
 -** Hatchery cohort reconstruction full results, bootstrapped. For males.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Individuals\_Released: total individuals
 released Age1Sp: CWT Age 1 spawners to spawning ground Age2Sp: CWT Age 2
 spawners to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground
 Age4Sp: CWT Age 4 spawners to spawning ground Age5Sp: CWT Age 5 spawners
 to spawning ground Age1Hat: Age 1 spawners to hatchery Age2Hat: Age 2
 spawners to hatchery Age3Hat: Age 3 spawners to hatchery Age4Hat: Age 4
 spawners to hatchery InRiver3: age-3 in-river harvest InRiver4: age-4
 in-river harvest Apr3-Nov4 (Month.Age columns): fishery impact by month
 and age Cat3\_4 – Cat4\_11 (CatAge\_Month columns): Catch rate by period
 for both cohorts CatU3\_4 – CatU4\_11 (CatUAge\_Month columns): Catch rate
 by period for single cohort Age6.2 – Age2.3 (AgeAge.Month columns):
 Reconstructed ocean abundance Out\_Survival: survival from release to
 Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2
 maturation rate Imp4: Age-4 impact rate Imp3: Age-3 impact rate Imp3\_5 –
 Imp4\_11 (ImpAge\_Month): Month specific impact rate on cohort   **Natural
 Cohort Reconstruction.Rds–** Natural cohort reconstruction full results,
 bootstrapped. Variable descriptions brood\_year: the year in which eggs
 were laid (the summer prior to release). Fry: estimated fry equivalents
 Age2Sp: CWT Age 2 spawners to spawning ground Age3Sp: CWT Age 3 spawners
 to spawning ground Age4Sp: CWT Age 4 spawners to spawning ground Age5.2 –
 Age2.3 (AgeAge.Month columns): Reconstructed ocean abundance Imp4\_11–
 Imp3\_4 (ImpAge\_Month): Month specific impact rate on cohort Imp3: Age 3
 impact (N) Imp3rate: Age-3 impact rate Out\_Survival: survival from
 release to Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate
 Mat2: Age-2 maturation rate   **Natural Cohort Reconstruction\_Male.Rds–**
 Natural cohort reconstruction full results for males, bootstrapped.
 Variable descriptions brood\_year: the year in which eggs were laid (the
 summer prior to release). Fry: estimated fry equivalents Age2Sp: CWT Age 2
 spawners to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground
 Age4Sp: CWT Age 4 spawners to spawning ground Age5.2 – Age2.3
 (AgeAge.Month columns): Reconstructed ocean abundance Imp4\_11– Imp3\_4
 (ImpAge\_Month): Month specific impact rate on cohort Imp3: Age 3 impact
 (N) Imp3rate: Age-3 impact rate Out\_Survival: survival from release to
 Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2
 maturation rate   **Natural Cohort Reconstruction\_Female.Rds–** Natural
 cohort reconstruction full results for females, bootstrapped. Variable
 descriptions brood\_year: the year in which eggs were laid (the summer
 prior to release). Fry: estimated fry equivalents Age2Sp: CWT Age 2
 spawners to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground
 Age4Sp: CWT Age 4 spawners to spawning ground Age5.2 – Age2.3
 (AgeAge.Month columns): Reconstructed ocean abundance Imp4\_11– Imp3\_4
 (ImpAge\_Month): Month specific impact rate on cohort Imp3: Age 3 impact
 (N) Imp3rate: Age-3 impact rate Out\_Survival: survival from release to
 Age2.3 Mat4: Age-4 maturation rate Mat3: Age-3 maturation rate Mat2: Age-2
 maturation rate ## **10\. Sensitivity Analysis\.R** **Data input**
 **CWTReleased.csv** – coded wire batch data for winter-run Chinook salmon
 for brood year from 2000-2017. Obtained from RMIS database. Variable
 descriptions tag\_code\_or\_release\_id: the batch code. brood\_year: the
 year in which eggs were laid (the summer prior to release).
 cwt\_1st\_mark\_count: fish with CWT and Ad Clip. cwt\_2nd\_mark\_count:
 fish with CWT and No clip. non\_cwt\_1st\_mark\_count: fish with no CWT
 and Ad Clip. non\_cwt\_2nd\_mark\_count: fish with no CWT and No Clip  
 **CWTRecoveries.csv** – all recoveries of winter-run Chinook salmon for
 brood year from 1999-2018.  Obtained from RMIS database. Variable
 descriptions run\_year: the year in which tag was recovered.
 recovery\_date: the date in which tag was recovered. fishery: 10 =
 commercial fishery; 40 = recreational fishery; 46 = in-river fishery 50 =
 hatchery; 54 = spawning ground. recovery\_location\_code: recovery
 location code. sampling\_site: sampling site location code. sex: M = male
 F = female. length: length in mm. tag code: the batch code.
 estimated\_number: expanded tag value based on sampling effort.
 recovery\_location\_name: recovery location name. brood\_year: the year in
 which eggs were laid (the summer prior to release).  
 **sitearea.modified.csv** – file with the region each sampling site is
 located within Variable descriptions agency: agency that uses the code.
 sampling\_site: sampling code area.1: region by area 1 definition area.2:
 region by area 1 definition area.code: area code definition catch.area:
 catch area description   **Size\_limits.csv** – file with the size limit
 (inches) associated with each fishery type, location, and time. Variable
 descriptions run\_year: the year in which tag was recovered. fishery: 10 =
 commercial fishery; 40 = recreational fishery location = region of
 recovery. SF = San Francisco; CO = Central Oregon; KC = Klamath,
 California, KO = Klamath, Oregon, FB = Fort Bragg; NO = Northern Oregon;
 SO = Southern Oregon, MO = Monterrey Month: month of recovery limit: size
 limit (inches)   **release.mort.rate.csv** – file with the release
 mortality rate associated with each fishery type, location, and time.
 Variable descriptions run\_year: the year in which tag was recovered.
 fishery: 10 = commercial fishery; 40 = recreational fishery location =
 region of recovery. SF = San Francisco; CO = Central Oregon; KC = Klamath,
 California, KO = Klamath, Oregon, FB = Fort Bragg; NO = Northern Oregon;
 SO = Southern Oregon, MO = Monterrey Month: month of recovery
 Release.mort.rate: release mortality rate   **length.at.age.csv** – length
 of age of winter-run Chinook salmon in the ocean. From O’Farrell et al.
 2012 Appendix A Variable descriptions age: in years, run year - brood year
 (age 2 - 5) month: calendar month at age mean: mean length (inches) sd:
 standard deviation (inches)   **CWT to SG.csv** – Age Specific escapement
 by brood year. Created in *CWT Spawning Data Prep.R* Variable descriptions
 brood\_year: the year in which eggs were laid (the summer prior to
 release). Age1Sp: CWT Age 1 spawners to spawning ground Age2Sp: CWT Age 2
 spawners to spawning ground Age3Sp: CWT Age 3 spawners to spawning ground
 Age4Sp: CWT Age 4 spawners to spawning ground Age5Sp: CWT Age 5 spawners
 to spawning ground   **Escapement to Hatchery.csv** – CWT recovered at
 hatcheries and expanded. Grouped by brood year so each line is the age
 distribution each brood comes back as. Created in *CWT Spawning Data
 Prep.R* Variable descriptions brood\_year: the year in which eggs were
 laid (the summer prior to release). Age1Hat: Age 1 spawners to hatchery
 Age2Hat: Age 2 spawners to hatchery Age3Hat: Age 3 spawners to hatchery
 Age4Hat: Age 4 spawners to hatchery   **River Harvest.csv –** Age-3 and
 Age-4 in-river harvest by brood year. Created in *CWT Harvest Data
 Prep.R.* Variable descriptions brood\_year: the year in which eggs were
 laid. run\_year: the year in which the adult return or was harvested
 InRiver3: age-3 in-river harvest InRiver4: age-4 in-river harvest