CMfigures: Figures for conditioning model results

In salmonMSE: Management Strategy Evaluation for Salmon Species

Figures for conditioning model results

Description

Functions used by the markdown report to generate summary figures from the age-structured conditoning model

Usage

get_report(stanfit, sims, inc_warmup = FALSE)

get_CMdata(fit)

CM_trace(stanfit, vars, inc_warmup = FALSE)

CM_pairs(stanfit, vars = c("log_so", "log_cr"), inc_warmup = FALSE)

CM_fit_esc(report, d, year)

CM_fit_pHOS(report, d, year)

CM_fit_CWTesc(report, d, year1 = 1, rs_names)

CM_fit_CWTcatch(report, d, PT = TRUE, year1 = 1, rs_names)

CM_maturity(
  report,
  d,
  year1 = 1,
  r = 1,
  brood = TRUE,
  annual = FALSE,
  rs_names
)

CM_vul(report, type = c("vulPT", "vulT"))

CM_SRR(report, year1 = 1)

CM_prod(report, d, year1 = 1, index = NULL, mean_bio = FALSE)

CM_Srep(
  report,
  d,
  year1 = 1,
  index = NULL,
  mean_bio = FALSE,
  type = c("spawner", "egg"),
  na.rm = FALSE
)

CM_M(report, year1 = 1, ci = TRUE)

CM_Megg(report, year1 = 1, ci = TRUE, surv = FALSE)

CM_Njuv(report, year1 = 1, ci = TRUE)

CM_recr(report, year1 = 1, ci = TRUE)

CM_esc(report, year1 = 1, ci = TRUE)

CM_F(report, PT = TRUE, year1 = 1, ci = TRUE)

CM_surv(report, year1 = 1, ci = TRUE)

CM_wt(stanfit, year1 = 1, ci = TRUE)

CM_surv2(report, year1 = 1, ci = TRUE, ylab = "Survival to age 2")

CM_wto(stanfit, year1 = 1, ci = TRUE)

CM_ER(
  report,
  brood = TRUE,
  type = c("PT", "T", "all"),
  year1 = 1,
  ci = TRUE,
  at_age = TRUE,
  r = 1,
  index_AEQ = NULL
)

CM_CWT_ER(
  report,
  brood = TRUE,
  type = c("PT", "T", "all"),
  year1 = 1,
  ci = TRUE,
  rs_names
)

CM_covariate(x, names, year1 = 1, b, ylab = "Covariate")

Arguments

stanfit	Output from sample_CM()
sims	Optional integer vector for subset of MCMC iterations
inc_warmup	Logical, whether to include warmup MCMC samples
fit	Output from fit_CM()
vars	Character vector for variable names (see names(stanfit@sim$samples[[1]])). Regex and partial matching supported because it is passed to the pattern argument of grepl()
report	List, output of state variables from individual MCMC samples, obtained with get_report()
d	List of data variables, obtained with get_CMdata()
year	Vector of years
year1	Numeric, first year of model
rs_names	Character vector of hatchery release strategies
PT	Logical, whether to plot preterminal catch, otherwise (plot terminal catch)
r	Integer, the release strategy for the figure (only if annual = FALSE)
brood	Logical, whether to show results by brood year or return year (FALSE)
annual	Logical, whether to show panel figure by individual year (TRUE) or a single time series figure
type	Character, indicates type of variable to plot
index	Integer vector to subset years with which to calculate reference points. Can be used to reduce computation or average biological parameters from a subset of years, see mean_bio argument. If NULL, uses all years of model.
mean_bio	Logical, whether to average the natural mortality and maturity parameters across years indicated in index
na.rm	Logical, whether to exclude replacement values (and other reference points) that are less than zero from median calculations and resulting figures
ci	Logical whether to show posterior intervals in addition to posterior median
surv	Logical, whether to plot survival (values between 0 - 1) or instantaneous mortality rates
ylab	Character y axis label
at_age	Logical, whether to make figure by individual age
index_AEQ	Optional integer vector to identify years from which to borrow natural mortality and maturity to calculate adult equivalents for incomplete brood years. Only used if at_age = FALSE.
x	Matrix of covariates by year x covariate
names	Character of covariate names
b	Matrix of fixed effect coefficients by simulation x covariate. If missing only the covariates (x) are plotted, otherwise, the dot product sum(x * b) is calculated by individual simulation and quantiles are plotted

Value

• get_report() returns the list of state variables by individual MCMC samples

• get_CMdata() returns the list of data variables used in the conditioning model

• CM_trace() returns a ggplot showing the MCMC trace plot (aka wormplot)

• CM_pairs() returns output from graphics::pairs(), a matrix of scatterplots of MCMC posterior samples

• CM_fit_esc() returns base graphics with fit to total escapement time series

• CM_fit_pHOS() returns base graphics with fit to pHOS (census) observations

• CM_fit_CWTesc() returns ggplot of fit to CWT escapement at age

• CM_fit_CWTcatch() returns ggplot of fit to CWT catch at age

• CM_maturity() returns ggplot of estimated maturity at age

• CM_vul() returns ggplot of estimated fishery vulnerability at age

• CM_SRR() returns ggplot of estimated stock-recruit relationship (density-dependent juvenile production from egg production) with average relationship and realized annual values. Years correspond to return years of egg production (predicts juvenile production of the following calendar year).

• CM_prod() returns ggplot of productivity (adults/spawner), calculated from density-dependent egg-smolt Ricker parameters, juvenile natural mortality, fecundity, and maturity. Even if egg-smolt survival function is constant, the realized productivity can vary with annual changes in natural mortality or maturity. .CM_prod() is the internal function that calculates productivity, with additional options for averaging time-varying biology.

• CM_Srep() returns ggplot of spawners or egg production at replacement, calculated from density-dependent egg-smolt Ricker parameters, juvenile natural mortality, fecundity, and maturity. Even if egg-smolt survival function is constant, the realized replacement can vary with annual changes in natural mortality or maturity. .CM_Srep() is the internal function with options for averaging time-varying biology.

• CM_M() returns ggplot of estimated natural mortality time series by age (marine stage)

• CM_Megg() returns ggplot of egg-juvenile mortality time series

• CM_Njuv() returns ggplot of juvenile abundance

• CM_recr() returns ggplot of recruitment (mature return)

• CM_esc() returns ggplot of escapement (after terminal harvest)

• CM_F() returns ggplot of instantaneous fishing mortality

• CM_surv() returns ggplot of natural survival (converting from instantaneous units of natural mortality)

• CM_wt() returns ggplot of annual deviations in egg-juvenile mortality from the Ricker function

• CM_surv2() returns ggplot of annual survival to age 2, which includes age-1 mortality (marine life stage) for both natural and hatchery origin fish. Hatchery fish experience additional mortality specified by release mortality.

• CM_wt() returns ggplot of annual deviations in age 1 natural mortality (first year in marine life stage, deviations from time series average)

• CM_ER() returns ggplot of exploitation rate either by individual age or aggregate values. Aggregate values use adult equivalents for preterminal fisheries. .CM_ER() and .CM_ERage() are the internal functions for reporting values for all simulations and years if desired.

• CM_CWT_ER() returns ggplot of CWT exploitation rate (by release strategy)

• CM_covariate() returns ggplot of mortality covariates

See Also

CM_MSY()

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