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Figures for conditioning model results

Source: R/CM_int.R, R/CMfun.R
CMfigures.Rd

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"))

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

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 years of egg production (assumes juvenile production for the following brood year).

  • CM_prod() returns ggplot of realized productivity in the absence of fishery harvest, annual values are based on natural mortality and maturity at age

  • CM_Srep() returns ggplot of realized spawner or egg production at replacement, annual values are based on natural mortality and maturity at age

  • 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