Please contact Mark Sorel for questions about the code or data: mark.sorel@dfw.wa.gov{.email}
Secondary contact: Sarah Converse (sconver@usgs.gov{.email})
A primary challenge in conservation is optimally allocating resources to achieve desired outcomes. There are a variety of management interventions available for the conservation of imperiled salmonids in North America, and tools are needed to inform the allocation of management effort to activities such as habitat restoration and hatchery supplementation. We convened a workshop of decision makers and experts on Chinook salmon (Oncorhynchus tshawytscha) conservation in the Wenatchee River Basin of Washington State. Participants helped define candidate strategies involving habitat restoration and hatchery management. We evaluated the effects of these strategies on a variety of metrics -- including persistence and maintenance of wild genetic structure -- using simulations built on an integrated population model. Simulations indicated that restoration of natal streams would result in greater natural production than restoration of downstream habitats. However, downstream restoration would benefit fish from multiple natal streams as well as fish that spawn in downstream habitats. Reducing hatchery broodstock sizes from current targets would result in relatively small changes in natural productivity and reduce the risk of the hatchery program affecting adaptations of the wild population. Using principals of decision analysis and management modeling enabled evaluation of alternative management strategies that are most relevant to conservation decisions.
Contains scripts to run all analyses.
IPM_4_3_hatch.R Constructs the integrated population model from an Rdata object data/dat_IPM_hatch.Rdata with data and a TMB model src/IPM_non_centered_hatchery_scenarios.cpp. Then posterior samples are drawn using tmbstan.
PVA-preliminary-results-scenarios.Rmd Conducts population projection simulations assuming different habitat and hatchery management strategies. The outputs from the simulations are saved in the results folder. The script also summarizes the results of the simulations in text and figures. This Rmarkdown script can be knitted to generate the figures in the manuscript.
IPM_non_centered_hatchery_scenarios.cpp The integrated population model written in TMB.
Contains processed data and model inputs. For raw data and to see the steps for generating model inputs, see this repository.
dat_IPM_hatch.Rdata Data inputs to the integrated population model.
par_IPM_hatch.Rdata Initial parameter inputs to the model.
map_IPM_hatch.Rdata Parameters to be treated as random effects.
rand_par_IPM_hatch.Rdata Parameters to be fixed at initial values during fitting
broodstock_remova.xlsx Historical numbers of natural origin fish removed for hatchery broodstock.
proj_arrays_hatch_8_11_2022.Rdata Simulated future trajectories of environmental variables included as covariates in the population .
Contains raw and processed results
ipm_fit_non_centered_4_13_hatch_scen.Rdata The TMB integrated population model object. This is used to conducted the population projections using posterior samples of parameters, simulated environmental variables, and random draws of random effects of year.
list_of_draws.rda This file contains posterior samples from the integrated population model.
list_of_sims_8_11_22.Rdata Raw results of population projection simulations under alternative management strategies. This file is too big for GitHub but is available for download on Zenodo. The 'PVA-preliminary-results-scenarios.Rmd' file has code (line 477) to download the file from Zenodo into the correct place in the file directory.
summarized_sims_01_17_24.Rdata Processed and summarized results of population projection simulations.
2_panel_map_elev_9242021.png Map used in the manuscript.
base_4.2.2
dplyr_1.1.0
forcats_1.0.0
ggplot2_3.4.1
graphics_4.2.2
grDevices_4.2.2
here_1.0.1
lubridate_1.9.1
methods_4.2.2
purrr_1.0.1
readxl_1.4.3
stats_4.2.2
stringr_1.5.0
tibble_3.1.8
tidyr_1.3.0
tidyverse_2.0.0
TMB_1.9.3
TMBhelper_1.4.0
tmbstan_1.0.7
utils_4.2.2
viridisLite_0.4.1
Sorel MH, RW Zabel, AR Murdoch, and SJ Converse. In review. Management modeling of salmon habitat restoration and hatchery supplementation.
The Rmarkdown file located in the 'scripts' folder is the main scripts for the analysis and can be knit to generate the results in the paper. Several of the steps in that script of circumvented to save time, and results are simply read in from an Rdata file. However, those code chunks that are set to eval=FALSE, could be turned back on to re-generate the results. The IPM_4_3_hatch.R file in th 'scripts' folder draws posterior samples using tmbstan, but is very computationally and time intensive, so samples have been saved in the results and archived on Zenodo.