morse: plotDoseResponse.reproData – R documentation

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plotDoseResponse.reproData

Plot dose-response from reproData objects

Description

This is the generic plotDoseResponse S3 method for the reproData class. It plots the number of offspring per individual-days as a function of concentration at a given target time.

Usage

## S3 method for class 'reproData'
plotDoseResponse(
  x,
  xlab = "Concentration",
  ylab = "Nb of offspring per ind.day",
  main = NULL,
  ylim = NULL,
  target.time = NULL,
  style = "ggplot",
  log.scale = FALSE,
  remove.someLabels = FALSE,
  axis = TRUE,
  addlegend = TRUE,
  ...
)

Arguments

`x`	an object of class `reproData`
`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
`ylim`	Y-axis limits
`target.time`	a numeric value corresponding to some observed time points in `data`
`style`	graphical backend, can be `'ggplot'` or `'generic'`
`log.scale`	if `TRUE`, displays X-axis in log-scale
`remove.someLabels`	if `TRUE`, removes 75% of X-axis labels in `'ggplot'` style to avoid the label overlap
`axis`	if `TRUE` displays ticks and label axis
`addlegend`	if `TRUE`, adds a default legend to the plot
`...`	Further arguments to be passed to generic methods

Details

The function plots the observed values of the reproduction rate (number of reproduction outputs per individual-day) at a given time point as a function of concentration. The 95 % Poisson confidence interval is added to each reproduction rate. It is calculated using function pois.exact from package epitools. As replicates are not pooled in this plot, overlapped points are shifted on the x-axis to help the visualization of replicates.

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(zinc)

# (2) Create an object of class 'reproData'
zinc_rpr <- reproData(zinc)

# (3) Plot dose-response
plotDoseResponse(zinc_rpr)

# (4) Plot dose-response with a generic style
plotDoseResponse(zinc_rpr, style = "generic")

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