plotDoseResponse.reproData: Plot dose-response from 'reproData' objects

In morse: Modelling Reproduction and Survival Data in Ecotoxicology

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.

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

See Also

pois.exact

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 documentation built on Oct. 29, 2022, 1:14 a.m.