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Analysis Results Plotting

Source: R/class_analysis_results.R
plot.AnalysisResults.Rd

Plots the conditional power together with the likelihood function.

Usage

# S3 method for class 'AnalysisResults'
plot(
  x,
  y,
  ...,
  type = 1L,
  nPlanned = NA_real_,
  allocationRatioPlanned = NA_real_,
  main = NA_character_,
  xlab = NA_character_,
  ylab = NA_character_,
  legendTitle = NA_character_,
  palette = "Set1",
  legendPosition = NA_integer_,
  showSource = FALSE,
  grid = 1,
  plotSettings = NULL
)

Arguments

x

The analysis results at given stage, obtained from getAnalysisResults().

y

Not available for this kind of plot (is only defined to be compatible to the generic plot function).

...

Optional plot arguments. Furthermore the following arguments can be defined:

  • thetaRange: A range of assumed effect sizes if testing means or a survival design was specified. Additionally, if testing means was selected, assumedStDev (assumed standard deviation) can be specified (default is 1).

  • piTreatmentRange: A range of assumed rates pi1 to calculate the conditional power. Additionally, if a two-sample comparison was selected, pi2 can be specified (default is the value from getAnalysisResults()).

  • directionUpper: Specifies the direction of the alternative, only applicable for one-sided testing; default is TRUE which means that larger values of the test statistics yield smaller p-values.

  • thetaH0: The null hypothesis value, default is 0 for the normal and the binary case, it is 1 for the survival case. For testing a rate in one sample, a value thetaH0 in (0, 1) has to be specified for defining the null hypothesis H0: pi = thetaH0.

type

The plot type (default = 1). Note that at the moment only one type (the conditional power plot) is available.

nPlanned

The additional (i.e., "new" and not cumulative) sample size planned for each of the subsequent stages. The argument must be a vector with length equal to the number of remaining stages and contain the combined sample size from both treatment groups if two groups are considered. For survival outcomes, it should contain the planned number of additional events. For multi-arm designs, it is the per-comparison (combined) sample size. For enrichment designs, it is the (combined) sample size for the considered sub-population.

allocationRatioPlanned

The planned allocation ratio n1 / n2 for a two treatment groups design, default is 1. For multi-arm designs, it is the allocation ratio relating the active arm(s) to the control. For simulating means and rates for a two treatment groups design, it can be a vector of length kMax, the number of stages. It can be a vector of length kMax, too, for multi-arm and enrichment designs. In these cases, a change of allocating subjects to treatment groups over the stages can be assessed. Note that internally allocationRatioPlanned is treated as a vector of length kMax, not a scalar.

main

The main title, default is "Dataset".

xlab

The x-axis label, default is "Stage".

ylab

The y-axis label.

legendTitle

The legend title, default is "".

palette

The palette, default is "Set1".

legendPosition

The position of the legend. By default (NA_integer_) the algorithm tries to find a suitable position. Choose one of the following values to specify the position manually:

  • -1: no legend will be shown

  • NA: the algorithm tries to find a suitable position

  • 0: legend position outside plot

  • 1: legend position left top

  • 2: legend position left center

  • 3: legend position left bottom

  • 4: legend position right top

  • 5: legend position right center

  • 6: legend position right bottom

showSource

Logical. If TRUE, the parameter names of the object will be printed which were used to create the plot; that may be, e.g., useful to check the values or to create own plots with the base R plot function. Alternatively showSource can be defined as one of the following character values:

  • "commands": returns a character vector with plot commands

  • "axes": returns a list with the axes definitions

  • "test": all plot commands will be validated with eval(parse()) and returned as character vector (function does not stop if an error occurs)

  • "validate": all plot commands will be validated with eval(parse()) and returned as character vector (function stops if an error occurs)

Note: no plot object will be returned if showSource is a character.

grid

An integer value specifying the output of multiple plots. By default (1) a list of ggplot objects will be returned. If a grid value > 1 was specified, a grid plot will be returned if the number of plots is <= specified grid value; a list of ggplot objects will be returned otherwise. If grid = 0 is specified, all plots will be created using print command and a list of ggplot objects will be returned invisible. Note that one of the following packages must be installed to create a grid plot: 'ggpubr', 'gridExtra', or 'cowplot'.

plotSettings

An object of class PlotSettings created by getPlotSettings().

Value

Returns a ggplot2 object.

Details

The conditional power is calculated only if effect size and sample size is specified.

Examples

if (FALSE) { # \dontrun{
design <- getDesignGroupSequential(kMax = 2)

dataExample <- getDataset(
    n = c(20, 30),
    means = c(50, 51),
    stDevs = c(130, 140)
)

result <- getAnalysisResults(design = design, 
    dataInput = dataExample, thetaH0 = 20, 
    nPlanned = c(30), thetaH1 = 1.5, stage = 1) 

if (require(ggplot2)) plot(result, thetaRange = c(0, 100))
} # }