plot.reproFitTT: Plotting method for 'reproFitTT' objects

In morse: Modelling Reproduction and Survival Data in Ecotoxicology

Plotting method for reproFitTT objects

Description

This is the generic plot S3 method for the reproFitTT class. It plots the concentration-effect fit under target time reproduction analysis.

Usage

## S3 method for class 'reproFitTT'
plot(
  x,
  xlab = "Concentration",
  ylab = "Nb of offspring per ind/day",
  main = NULL,
  fitcol = "orange",
  fitlty = 1,
  fitlwd = 1,
  spaghetti = FALSE,
  cicol = "orange",
  cilty = 2,
  cilwd = 1,
  ribcol = "grey70",
  addlegend = FALSE,
  log.scale = FALSE,
  style = "ggplot",
  ...
)

Arguments

x	an object of class reproFitTT
xlab	a label for the X-axis, by default Concentration
ylab	a label for the Y-axis, by default Nb of offspring per ind/day
main	main title for the plot
fitcol	color of the fitted curve
fitlty	line type of the fitted curve
fitlwd	width of the fitted curve
spaghetti	if TRUE, the credible interval is represented by multiple curves
cicol	color of the 95 % credible limits
cilty	line type of the 95 % credible limits
cilwd	width of the 95 % credible limits
ribcol	color of the ribbon between lower and upper credible limits. Transparent if NULL
addlegend	if TRUE, adds a default legend to the plot
log.scale	if TRUE, displays X-axis in log-scale
style	graphical backend, can be 'ggplot' or 'generic'
...	Further arguments to be passed to generic methods

Details

The fitted curve represents the estimated reproduction rate at the target time as a function of the chemical compound concentration. The function plots 95% credible intervals for the estimated reproduction rate (by default the grey area around the fitted curve). Typically a good fit is expected to display a large overlap between the two types of intervals. If spaghetti = TRUE, the credible intervals are represented by two dotted lines limiting the credible band, and a spaghetti plot is added to this band. It consists of the representation of simulated curves using parameter values sampled in the posterior distribution (10% of the MCMC chains are randomly taken for this sample).

Value

a plot of class ggplot

Note

When style = "generic", the function calls the generic function plot

When style = "ggplot", the function return an object of class ggplot, see function ggplot

morse documentation built on Sept. 30, 2024, 9:31 a.m.