morse: plot.reproFitTT – R documentation

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plot.reproFitTT

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).

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

Examples

# (1) Load the data
data(cadmium1)

# (2) Create an object of class "reproData"
dataset <- reproData(cadmium1)

## Not run: 
# (3) Run the reproFitTT function with the log-logistic gamma-Poisson model
out <- reproFitTT(dataset, stoc.part = "gammapoisson",
                  ecx = c(5, 10, 15, 20, 30, 50, 80), quiet = TRUE)


# (4) Plot the fitted curve with generic style
plot(out, xlab = expression("Concentration in" ~ mu~g.L^{-1}),
     fitcol = "blue", cicol = "lightblue",
     main = "Log-logistic response to concentration")

## End(Not run)

morse

Modelling Tools for Reproduction and Survival Data in Ecotoxicology

v3.3.1

GPL (>= 2)

Authors

Virgile Baudrot [aut], Sandrine Charles [aut], Marie Laure Delignette-Muller [aut], Wandrille Duchemin [ctb], Benoit Goussen [ctb], Nils Kehrein [ctb], Guillaume Kon-Kam-King [ctb], Christelle Lopes [ctb], Philippe Ruiz [aut], Alexander Singer [ctb], Philippe Veber [aut]

Initial release