Sacramento River winter-run Chinook salmon cohort reconstruction – data and code
Data files
Oct 12, 2023 version files 45.09 MB
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1._CWT_Spawning_Data_Prep.R
13.38 KB
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10._Sensitivity_Analaysis.R
24.51 KB
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2._CWT_Harvest_Data_Prep.R
20.58 KB
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3._Hatchery_Cohort_Reconstruction.R
12.54 KB
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4._Hatchery_Cohort_Reconstruction_by_Sex.R
7.61 KB
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5._Impact_rates_shared.R
8.30 KB
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6._Natural_Cohort_Reconstruction_Prep.R
10.62 KB
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7._Natural_Cohort_Reconstruction.R
16.38 KB
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8._Comparing_Vital_Rates.R
5.89 KB
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9._SRR.R
6.95 KB
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Avg_Harvestability.Rds
625.28 KB
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Avg_ReleaseMort.Rds
730.65 KB
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Catch_Bootstrap.Rds
655.79 KB
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Catch_Representation.Rds
5.72 MB
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CWT_Cohort_Reconstruction_Females.Rds
4.66 MB
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CWT_Cohort_Reconstruction_Males.Rds
3.20 MB
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CWT_Cohort_Reconstruction.Rds
8.53 MB
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CWT_Recoveries_SG.csv
252.30 KB
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CWT_to_SG.csv
802 B
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CWTBootstraps_F.Rds
316.85 KB
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CWTBootstraps_M.Rds
5.57 KB
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CWTBootstraps.Rds
244.23 KB
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CWTRecoveries.csv
528.95 KB
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CWTReleased.csv
8.25 KB
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Escapement_Numbers.csv
1.47 KB
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Escapement_to_Hatchery_F.csv
516 B
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Escapement_to_Hatchery_M.csv
592 B
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Escapement_to_Hatchery.csv
784 B
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Female_Spawners_Adjusted.Rds
232.06 KB
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Female_Spawners_UnAdjusted.Rds
86.27 KB
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Hatchery_Release.csv
270 B
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HatcheryRunSizeCWT.csv
340 B
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Impact_Bootstrap.Rds
656.04 KB
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Impact_hatchery_notshared.csv
1.55 KB
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Impact_hatchery_shared.csv
1.73 KB
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Impact_Uncertainty_CWT.csv
1.58 KB
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Impact_Uncertainty_Natural_Female.csv
2.79 KB
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Impact_Uncertainty_Natural_Male.csv
2.78 KB
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Impact_Uncertainty_Natural.csv
2.78 KB
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length.at.age.csv
438 B
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Male_Spawners_Adjusted.Rds
237.06 KB
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Maturation_Uncertainty_CWT_Sex.csv
2.46 KB
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Maturation_Uncertainty_CWT.csv
2.36 KB
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Maturation_Uncertainty_Natural_Female.csv
1.20 KB
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Maturation_Uncertainty_Natural_Male.csv
1.18 KB
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Maturation_Uncertainty_Natural.csv
1.20 KB
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Natural_Cohort_Reconstruction_Female.Rds
5.84 MB
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Natural_Cohort_Reconstruction_Male.Rds
5.78 MB
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Natural_Cohort_Reconstruction.Rds
5.84 MB
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Natural_Escapement_to_Hatchery.csv
1.32 KB
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README.docx
27.20 KB
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README.md
60.78 KB
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release.mort.rate.csv
3.96 KB
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River_Harvest_F.csv
152 B
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River_Harvest_M.csv
167 B
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River_Harvest.csv
166 B
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Scale_Readage.csv
282.07 KB
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SexRatioSG.csv
339 B
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sitearea.modified.csv
6.48 KB
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Size_limits.csv
3.55 KB
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Spawners_Adjusted.Rds
277.23 KB
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Spawners_UnAdjusted.Rds
110 KB
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Total_Escapement_to_Hatchery.csv
230 B
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years_with_values.csv
2.36 KB
Abstract
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.
README: 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