calcPercChangeMCMC: calcPercChangeMCMC

In Pacific-salmon-assess/WSP-Metrics-Pkg: WSPMetrics Package: R package to calculate and use metrics for status assessments under Canada's Wild Salmon Policy (WSP)

calcPercChangeMCMC

Description

MCMC version of trend metric calculation This function calculates the percent change in abundances based on an exponential model of population decline, as per IUCN guidelines It estimates a distribution of percent declines over the period of the time-series, and provides the probability of declines being greater than a specified threhold

Usage

calcPercChangeMCMC(
  vec.in,
  method = "jags",
  model.in = NULL,
  perc.change.bm = -25,
  na.skip = FALSE,
  out.type = "short",
  mcmc.plots = FALSE,
  convergence.check = FALSE,
  logged = TRUE
)

Arguments

vec.in	vector with numeric values
method	either "jags" (default), "rstanarm", or "rstan". For properties and discussion of strengths/limitations, refer to the MetricsCOSEWIC wiki.
model.in	if NULL, use the built in functions for each method: trend.bugs.1() for jags, ETC
perc.change.bm	benchmark for Prob(Decl>BM), default = -25
na.skip	if TRUE, skip the calculations when vec.in contains any NA
out.type	"short" or "long". "short" gives summary table of posterior plus "PercChange" and "ProbDecl" "long" also includes the full mcmc samples and the jags output object
mcmc.plots	if true, create the standard series of MCMC diagnostic plots Note that these are printed to the default device (i.e. need to external wrap the function call inside a pdf /dev.off call) To get a plot of the model fit, run this function with out.type = "long", and then use plot.trend.fit().
convergence.check	if TRUE, do an automated convergence check
logged	if TRUE, then the input is already log-transformed, and the Perc Change is calculated on the exponentiated fitted values. Default is TRUE

Pacific-salmon-assess/WSP-Metrics-Pkg documentation built on July 16, 2025, 1:46 p.m.