morse: plot.MFx – R documentation

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plot.MFx

Plotting method for MFx objects

Description

This is the generic plot S3 method for the MFx class. It plots the survival probability as a function of the multiplication factor applied or as a function of time.

Usage

## S3 method for class 'MFx'
plot(
  x,
  x_variable = "MFx",
  xlab = NULL,
  ylab = "Survival probability \n median and 95 CI",
  main = NULL,
  log_scale = FALSE,
  ncol = 3,
  ...
)

Arguments

`x`	An object of class `MFx`.
`x_variable`	A character to define the variable for the X-axis, either `"MFx"` or `"Time"`. The default is `"MFx"`.
`xlab`	A label for the X-axis, by default `NULL` and depend on the argument `x_variable`.
`ylab`	A label for the Y-axis, by default `Survival probability median and 95 CI`.
`main`	A main title for the plot.
`log_scale`	If `TRUE`, the x-axis is log-scaled. Default is `FALSE`.
`ncol`	An interger for the number of columns when several panels are plotted.
`...`	Further arguments to be passed to generic methods.

Examples

# (1) Load the data
data("propiconazole")

# (2) Create an object of class 'survData'
dataset <- survData(propiconazole)

## Not run: 
# (3) Run the survFit function with model_type SD (or IT)
out_SD <- survFit(dataset, model_type = "SD")

# (4) data to predict
data_4prediction <- data.frame(time = 1:10, conc = c(0,0.5,3,3,0,0,0.5,3,1.5,0))

# (5) estimate MF for 30% reduction of survival at time 4
MFx_SD_30.4 <- MFx(out_SD, data_predict = data_4prediction , X = 30, time_MFx = 4)

# (6) plot the object of class 'MFx'
plot(MFx_SD_30.4)

# (6bis) plot with log-scale of x-axis
plot(MFx_SD_30.4, log_scale = TRUE)

# (6ter) plot with "Time" as the x-axis
plot(MFx_SD_30.4, x_variable = "Time") 

# (7) plot when X = NULL and along a MFx_range from 5 to 10:
MFx_SD_range <- MFx(out_SD, data_predict = data_4prediction ,
                    X = NULL, time_MFx = 4, MFx_range = seq(5, 10, length.out = 50))
plot(MFx_SD_range)
plot(MFx_SD_range, x_variable = "Time", ncol = 10)

## 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