bypass-length-sar

This repository holds the data and R code used in analyses to support Faulkner et al. (2019) and Faulkner et al. (2020).

Data

There are two data sets used for the analyses on bypass probabilities and there are four data sets used for the analyses on adult return probabilities (smolt-to-adult returns or SAR). These data were used in both the main paper and the formal response to comment on the paper.

• chinook_bypass_data.csv - bypass event data and covariates for Chinook
• steelhead_bypass_data.csv - bypass event data and covariates for steelhead
• chinook_ULGR_SAR_data.csv - adult return data and covariates for Chinook tagged upstream of Lower Granite Dam
• chinook_LGR_SAR_data.csv - adult return data and covariates for Chinook tagged at Lower Granite Dam
• steelhead_ULGR_SAR_data.csv - adult return data and covariates for steelhead tagged upstream of Lower Granite Dam
• steelhead_LGR_SAR_data.csv - adult return data and covariates for steelhead tagged at Lower Granite Dam
• steelhead_LGR_SAR_data.csv - adult return data and covariates for steelhead tagged at Lower Granite Dam

The following data sets were only used in the response to comment:

• annual_freshwater_variables.csv - annual summaries of freshwater variables
• ocean_indicators.csv - annual variables for ocean conditions

R Code

The following scripts were used for analyses in the main paper:

• chinook_bypass_analysis.r - model fitting and selection for bypass probabilities for Chinook
• steelhead_bypass_analysis.r - model fitting and selection for bypass probabilities for steelhead
• chinook_sar_analysis.r - model fitting and selection and simulations for adult return probabilities for Chinook
• steelhead_sar_analysis.r - model fitting and selection and simulations for adult return probabilities for steelhead

The following scripts were used for analyses and plots in the response to comment:

• chinook_power_simulations.r - simulations to produce power estimates for Chinook used in Figure 2 and Table 1
• steelhead_power_simulations.r - simulations to produce power estimates for steelhead used in Figure 2 and Table 1
• adult_return_pred_for_response_fig1.r - code to generate adult return probability predictions in Figure 1
• chinook_lgs_bypass_response_fig3.r - code to generate bypass probability predictions in Figure 3
• ocean_variable_correlations.r - code to calculate correlations among annual summary variables in Table 2

References

Faulkner, JR, BL Bellerud, DL Widener, and RW Zabel. 2019. Associations among fish length, dam passage history, and survival to adulthood in two at-risk species of Pacific salmon. Transactions of the American Fisheries Society 148:1069-1087.

Faulkner, JR, BL Bellerud, DL Widener, SG Smith and RW Zabel. Associations among fish length, dam passage history, and survival to adulthood in two at-risk species of Pacific salmon: response to comment. Transactions of the American Fisheries Society -- In Review