salmonMSE conditioning model"

In salmonMSE: Management Strategy Evaluation for Salmon Species

---

title: "salmonMSE conditioning model" date: "r Sys.Date()" output: html_document: highlight: rstudio df_print: paged

---

library(ggplot2)
library(salmonMSE)
knitr::opts_chunk$set(
  collapse = TRUE, echo = FALSE, message = FALSE,
  fig.width = 6, fig.height = 4.5, out.width = "650px", comment = "#>"
)
theme_set(theme_bw())

NAME {.tabset}

Summary

data.frame(
  Parameter = c("Historical years", "Age classes", "MCMC iterations"),
  Value = c(d$Ldyr, d$Nages, length(report))
)

df_pars <- rstan::summary(stanfit)$summary %>%
  round(3) %>%
  as.data.frame()
df_pars[, c("mean", "sd", "2.5%", "50%", "97.5%", "n_eff", "Rhat")]

Legend

knitr::kable(make_CM_table(fit), row.names = FALSE)

MCMC

pars_core <- c("cr", "log_so", "moadd", "log_FbasePT", "log_FbaseT", "lp")
CM_trace(stanfit, pars_core)

pars_cov <- c("^b")
CM_trace(stanfit, pars_cov)

pars_vul <- c("^logit_vul")
CM_trace(stanfit, pars_cov)

pars_var <- c("lnE_sd", "wt_sd", "wto_sd", "fanomalyPT_sd", "fanomalyT_sd", "sd_matt")
CM_trace(stanfit, pars_var)

CM_pairs(stanfit, pars_core)

CM_pairs(stanfit, pars_cov)

CM_pairs(stanfit, pars_vul)

CM_pairs(stanfit, pars_var)

CM_wt(stanfit, year1)

CM_wto(stanfit, year1)

Data and fits {.tabset}

Hatchery and escapement

CM_data(d$hatchrelease, c(year, max(year) + 1), ylab = "Hatchery release", xlab = "Release Year")

CM_fit_esc(report, d, year)

CM_fit_pHOS(report, d, year)

CM_covariate(d[["covariate1"]], cov1_names, year1, ylab = "M covariates (age 1)")

CM_covariate(d[["covariate"]], cov_names, year1, ylab = "M covariates (age 2+)")

CWT

CM_CWTrel(d$cwtrelease, year1, rs_names)

CM_fit_CWTcatch(report, d, PT = TRUE, year1, rs_names)

CM_fit_CWTcatch(report, d, PT = FALSE, year1, rs_names)

CM_fit_CWTesc(report, d, year1, rs_names)

if (d$n_r > 1) {
  CM_maturity(report, d, year1, rs_names = rs_names, annual = TRUE)
}

State variables {.tabset}

Spawners/Broodtake

CM_ts_origin(report, year1, var = "Spawners", xlab = "Return Year")

.CM_ts(report, year1, var = "pHOScensus", ci = TRUE, ylab = "pHOScensus", xlab = "Return Year")

.CM_ts(report, year1, var = "pNOB", ci = TRUE, ylab = "pNOB", xlab = "Brood Year")

report <- lapply(report, function(i) {
  i$PNI <- i$pNOB/(i$pNOB + i$pHOSeff)
  return(i)
})
.CM_ts(report, year1, var = "PNI", ci = TRUE, ylab = "PNI", xlab = "Brood Year")

Egg production

CM_SRR(report, year1)

.CM_ts(report, year1, var = "egg", ci = TRUE, ylab = "Egg production", xlab = "Return Year")

report <- lapply(report, function(i) {
  i$Smolt <- i$N[, 1, 1]
  return(i)
})
.CM_ts(report, year1 - 1, var = "Smolt", ci = TRUE, ylab = "Smolt production", xlab = "Brood Year")

CM_Megg(report, year1, ci = TRUE, surv = FALSE)

CM_Megg(report, year1, ci = TRUE, surv = TRUE) +
  coord_cartesian(ylim = c(0, 1))

CM_prod(report, d, year1)

CM_Srep(report, d, year1)

CM_Srep(report, d, year1, type = "egg")

Juvenile abundance

CM_Njuv(report, year1, ci = FALSE)

CM_M(report, year1)

CM_surv(report, year1) +
  coord_cartesian(ylim = c(0, 1))

CM_surv2(report, year1)

CM_covariate(d[["covariate1"]], cov1_names, year1, b = rstan::extract(stanfit, "b1")[["b1"]], ylab = "Natural mortality (age 1)")

CM_covariate(d[["covariate"]], cov_names, year1, b = rstan::extract(stanfit, "b")[["b"]], ylab = "Natural mortality (age 2+)")

Preterminal fishery

FPT <- sapply(report, getElement, "FPT")
if (sum(FPT)) CM_vul(report, type = "vulPT")

if (sum(FPT)) CM_F(report, PT = TRUE, year1)

if (sum(FPT)) CM_ER(report, brood = FALSE, type = "PT", year1, r = d$r_matt)

if (sum(FPT)) CM_ER(report, brood = TRUE, type = "PT", year1, r = d$r_matt)

Return

CM_maturity(report, d, year1, r = d$r_matt, brood = FALSE, rs_names = rs_names)

CM_maturity(report, d, year1, r = d$r_matt, brood = TRUE, rs_names = rs_names)

CM_recr(report, year1, ci = TRUE)

Terminal fishery

FT <- sapply(report, getElement, "FT")
if (sum(FT)) CM_vul(report, type = "vulT")

if (sum(FT)) CM_F(report, PT = FALSE, year1)

if (sum(FT)) CM_ER(report, brood = FALSE, type = "T", year1, r = d$r_matt)

if (sum(FT)) CM_ER(report, brood = TRUE, type = "T", year1, r = d$r_matt)

Escapement

CM_esc(report, year1)

About

This report was generated on: r Sys.time()
salmonMSE version r packageVersion("salmonMSE")
r R.version.string

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.