Dose-response curves

Plot dose_response curve objects produced by compile_rjMCMC.

# S3 method for dose_response
plot(
  dr.object,
  overlay = FALSE,
  do.facet = TRUE,
  facet.title = TRUE,
  colour.by = NULL,
  colour = NULL,
  colour.median = NULL,
  fill.alpha = 0.3,
  order.by = "response",
  show.pmed = TRUE,
  rotate.y = FALSE,
  all.credint = FALSE,
  scientific.name = FALSE,
  common.name = FALSE,
  overwrite.abbrev = TRUE,
  outline.outer = FALSE,
  do.save = FALSE,
  file.format = "pdf",
  ...
)

Arguments

dr.object	Input object of class dose_response, as returned by compile_rjMCMC.
overlay	Logical. If TRUE, all curves will be overlaid on the same plot.
do.facet	Logical. If TRUE, plots will be faceted by species (or species group).
colour.by	Curves can be coloured by species group (colour.by = "group") or by individual species (colour.by = "species"), or can use a single colour scheme (the default, colour.by = NULL).
colour	Used to overwrite the colour.by argument, if desired.
colour.median	Colour to use for the posterior median. Overwrites the colour.by argument.
fill.alpha	Opacity applied to the credible intervals. Ranges from 0 (transparent) to 1 (fully opaque).
order.by	How should plots be arranged? Use order.by = "species" to arrange plots by species (groups) names in alphabetical order, or order.by = "response", to arrange plots by response thresholds (from most to least sensitive species (groups), as determined by the estimated posterior medians for μ). Only relevant when overlay = FALSE.
show.pmed	Logical. If TRUE, the values of posterior medians are added to facet labels. Only relevant when overlay = FALSE.
rotate.y	Logical. If TRUE, y-axis labels are rotated clockwise by 90 degrees.
all.credint	Logical. If TRUE, plot all credible intervals. If FALSE, only plot the outermost interval.
scientific.name	Logical. If TRUE, use species' scientific names in plot titles.
common.name	Logical. If TRUE, use species' common names in plot titles.
overwrite.abbrev	Logical. If TRUE, overwrites abbreviated names for species grouped a priori using create_groups.
outline.outer	Logical. If TRUE, outline the outermost credible interval bounds.
do.save	Logical. Whether to save plots on disk.
file.format	Character. File format for output plots on disk. Can be one of png, jpeg, tiff or pdf. Only used when do.save = TRUE.
...	Additional arguments as passed to gg.save.

See also

compile_rjMCMC

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,
                                 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)
# Burn and thin
rj.trace <- trace_rjMCMC(rj.dat = rj)

# Get dose-response functions
doseR <- compile_rjMCMC(rj.trace)

# Plot dose-response curves
plot(dr.object = doseR, colour.by = "group")
}