summary.rjtrace: Some diagnostics for fitted dose-response models
In pjbouchet/espresso: Bayesian Inference For Multi-Species Behavioural Dose-response Functions

summary.rjtrace

R Documentation

Some diagnostics for fitted dose-response models

Description

Summary method for objects of class rjtrace, as returned by trace_rjMCMC. Produces a text-based summary of: (1) effective sample sizes, (2) acceptance rates, (3) model convergence, (4) posterior model probabilities, and (5) posterior inclusion probabilities (PIPs) for contextual covariates (where appropriate).

Usage

## S3 method for class 'rjtrace'
summary(
  rj.obj,
  eff.n = TRUE,
  accept.rate = TRUE,
  convergence = TRUE,
  gelman.rubin = 1.1,
  model.ranks = TRUE,
  n.top = 10,
  southall.2019 = TRUE,
  covariate.prob = TRUE,
  ff.prob = TRUE,
  x.off = 0.1,
  rmd = FALSE,
  do.plot = TRUE
)

Arguments

`rj.obj`	Input rjMCMC object, as returned by `trace_rjMCMC`.
`eff.n`	Logical. If `TRUE`, returns estimates of the effective sample size for each model parameter.
`accept.rate`	Logical. If `TRUE`, returns the acceptance rate (calculated after burn-in) for each model parameter.
`convergence`	Logical. If `TRUE`, assesses convergence using the multivariate potential scale reduction factor (Gelman-Rubin statistic), as implemented in `gelman.diag`.
`gelman.rubin`	Threshold for determining convergence based on the Gelman-Rubin statistic. Defaults to `1.1`.
`model.ranks`	Logical. If `TRUE`, returns a summary of posterior model probabilities and associated model rankings.
`n.top`	Number of top-ranking models to display when `model.ranks = TRUE`.
`southall.2019`	Logical. Whether to produce a tile plot showing species groupings, as identified in \insertCiteSouthall2019;textualespresso. This is only relevant if real-world BRS data are being analysed (and therefore, `sim = FALSE`).
`covariate.prob`	Logical. If `TRUE`, returns a summary of posterior inclusion probabilities (PIPs).
`ff.prob`	Logical. If `TRUE`, returns a summary of posterior probabilities for each functional form (monophasic vs. biphasic).
`x.off`	Offset for probability values in tile plots.
`rmd`	Logical. This is used to create a different layout of plots when exporting results using `create_report`.
`do.plot`	Logical. If `TRUE`, returns diagnostic plots in addition to text-based summaries.

Value

A detailed summary, printed to the R console.

Author(s)

Phil J. Bouchet

References

\insertAllCited

Examples

## Not run: 
library(espresso)

# Import the example data, excluding species with sample sizes < 5
# and considering the sonar covariate
mydat <- read_data(file = NULL, min.N = 5, covariates = "sonar") 
summary(mydat)

# Configure the sampler
mydat.config <- configure_rjMCMC(dat = mydat,
                                 model.select = TRUE,
                                 covariate.select = FALSE,
                                 function.select = FALSE,
                                 n.rep = 100)
summary(mydat.config)

# Run the reversible jump MCMC
rj <- run_rjMCMC(dat = mydat.config,
                 n.chains = 2,
                 n.burn = 100,
                 n.iter = 100,
                 do.update = FALSE)
summary(rj)

## End(Not run)

pjbouchet/espresso documentation built on July 27, 2024, 12:31 p.m.