Figures for conditioning model results — get

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)

CM_Srep(report, d, year1 = 1, 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
)

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
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
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_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_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 using adult equivalents

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

CM_covariate() returns ggplot of mortality covariates