Generate report

Convenience function for creating a summary of results using R Markdown

create_report(
  outdir = getwd(),
  filename = "espresso_report",
  plot.height = 3,
  model.ranks = 1
)

Arguments

outdir	Output directory. Defaults to the current working directory.
filename	Output file name (without the file extension). Defaults to espresso_report.html.
plot.height	Height of tile plots used for comparing species groupings.
model.ranks	Used to define which models to get dose-response curves for when by.model = TRUE.

Value

An html file showing the outputs of summary.brsdata, summary.rjtrace, plot.rjtrace, and plot.dose_response.

See also

summary.brsdata summary.rjtrace plot.rjtrace plot.dose_response

Author

Phil J. Bouchet

Examples

if (FALSE) {
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,
                                 proposal.mh = list(t.ij = 10, mu.i = 10, 
                                                    mu = 7, phi = 10, sigma = 10),
                                 proposal.rj = list(dd = 20, cov = 7),
                                 prior.covariates = c(0, 30),
                                 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)
                 
# Extract results
rj.post <- trace_rjMCMC(rj)

# Generate report
create_report()
}