superb (version 0.9.4.2)

superbPlot: superbPlot

Description

plotsuberb plots standard error or confidence interval for various descriptive statistics under various designs, sampling schemes, population size and purposes, according to the suberb framework. See c17superb for more.

Usage

superbPlot(
  data,
  BSFactor = NULL,
  WSFactor = NULL,
  factorOrder,
  variables,
  statistic = "mean",
  errorbar = "CI",
  gamma = 0.95,
  adjustments = list(purpose = "single", popSize = Inf, decorrelation = "none",
    samplingDesign = "SRS"),
  showPlot = TRUE,
  plotStyle = "bar",
  Debug = FALSE,
  Quiet = FALSE,
  preprocessfct = NULL,
  postprocessfct = NULL,
  clusterColumn = "",
  ...
)

Arguments

data

Dataframe in wide format

BSFactor

The name of the columns containing the between-subject factor(s)

WSFactor

The name of the within-subject factor(s)

factorOrder

Order of factors as shown in the graph (x axis, groups, horizontal panels, vertical panels)

variables

The dependent variable(s)

statistic

The summary statistic function to use

errorbar

The function that computes the error bar. Should be "CI" or "SE" or any function name. Defaults to "SE"

gamma

The coverage factor; necessary when errorbar == "CI". Default is 0.95.

adjustments

List of adjustments as described below: popsize: Size of the population under study. Defaults to Inf purpose: The purpose of the comparisons. Defaults to "single". Can be "single" or "difference". decorrelation: Decorrelation method for repeated measure designs. Chooses among the methods ("CM", "LM", "CA" or "none"). Defaults to "none". samplingDesign: Sampling method to obtain the sample. implemented sampling is "SRS" (Simple Randomize Sampling) and "CRS" (Cluster-Randomized Sampling). Default is adjustments = list(purpose = "single", popSize = Inf, decorrelation = "none", samplingDesign = "SRS")

showPlot

Defaults to TRUE. Set to FALSE if you want the output to be the summary statistics and intervals.

plotStyle

The type of object to plot on the graph. Can be either "bar" or "line". Defaults to "bar".

Debug

export internal information into global environment. Default is FALSE

Quiet

Default to False, a boolean to inhibit showing additional information as warnings

preprocessfct

is a transform (or vector of) to be performed first on data matrix of each group

postprocessfct

is a transform (or vector of)

clusterColumn

used in conjunction with samplingDesign = "CRS", indicates which column contains the cluster membership

...

In addition to the parameters above, superbPlot also accept a number of optional arguments that will be transmitted to the plotting function, such as pointParams (a list of ggplot2 parameters to input inside geoms; see ?geom_bar2) and errorbarParams (a list of ggplot2 parameters for geom_errorbar; see ?geom_errorbar)

Value

a plot with the correct error bars or a table of those summary statistics. The plot is a ggplot2 object with can be modified with additional declarations.

References

Examples

# NOT RUN {
# basic example using a built-in dataframe as data; 
# by default, the mean is computed and the error bar are 95% confidence intervals
superbPlot(ToothGrowth, BSFactor = c("dose", "supp"), 
  variables = "len") 

# example changing the summary statistics to the median and
# the error bar to 90% confidence intervals
superbPlot(ToothGrowth, BSFactor = c("dose", "supp"), 
  variables = "len", statistic = "median", errorbar = "CI", gamma = .90) 

# example introducing adjustments for pairwise comparisons 
# and assuming that the whole population is limited to 200 persons
superbPlot(ToothGrowth, BSFactor = c("dose", "supp"), 
  variables = "len",  
  adjustments = list( purpose = "difference", popSize = 200) )

# This example add ggplot directives to the plot produced
library(ggplot2)
superbPlot(ToothGrowth, BSFactor = c("dose", "supp"), 
  variables = "len") + 
  xlab("Dose") + ylab("Tooth Growth") +
  theme_bw()

# This example is based on repeated measures
library(lsr)
library(gridExtra)
# define shorter column names...
names(Orange) <- c("Tree","age","circ")
# turn the data into a wide format
Orange.wide <- longToWide(Orange, circ ~ age)
p1=superbPlot( Orange.wide, WSFactor = "age(7)",
  variables = c("circ_118","circ_484","circ_664","circ_1004","circ_1231","circ_1372","circ_1582"),
  adjustments = list(purpose = "difference", decorrelation = "none"), Quiet = TRUE
) + 
  xlab("Age level") + ylab("Trunk diameter (mm)") +
  coord_cartesian( ylim = c(0,250) ) + labs(title="Basic confidence intervals")
p2=superbPlot( Orange.wide, WSFactor = "age(7)",
  variables = c("circ_118","circ_484","circ_664","circ_1004","circ_1231","circ_1372","circ_1582"),
  adjustments = list(purpose = "difference", decorrelation = "CM"), Quiet = TRUE
) + 
  xlab("Age level") + ylab("Trunk diameter (mm)") +
  coord_cartesian( ylim = c(0,250) ) + labs(title="Decorrelated confidence intervals")
grid.arrange(p1,p2,ncol=2)


# }