DecisionPlot: DecisionPlot: 2D contour plot of breath-test variables

In dmenne/d13cbreath: Reads and Evaluates Gastric Emptying 13C Breath Test Data

Description

Creates a 2D percentile plot of a pair of breath test variables. By default, the green central regions contains 50 determined using a highest-density-interval (HDI) method.

Usage

DecisionPlot(con = NULL, pars = dbGetQuery(con,
  "SELECT * from BreathTestParameter")[, -1], methods = "Maes",
  parameters = c("t50", "tlag"), prob = c(0.01, 0.05, 0.25, 0.5),
  main = "Breath test parameters", kde.package = c("ash", "ks"),
  brewerPalette = "RdYlGn", outlierFak = 3, showColors = NULL,
  showPoints = TRUE, showDateLabels = TRUE)

Arguments

con	connection to sqlite database; if missing, uses default database.
pars	all parameters in the form as read from table BreathTestParameters.
methods	if one entry is given, e.g ExpBeta, BluckCoward, WN, MaesPop, it is combined with both parameters; if two are given, method and parameters are paired.
parameters	two parameter names, e.g. c("t50","tlag").
prob	quantile probabilities; color for these is determined by Brewer palette, default RdYlGn.
main	title for graph
kde.package	package to use for HDI 2D kernel smoothing
brewerPalette	color palette name from RBrewerColor to use
outlierFak	the multiples of standard deviations to use for outlier removal. Note outliers removed from computation. It cannot be ruled out the data point you are focussing on has been removed. If in doubt, try higher values, i.e. wider ranges to include.
showColors	e.g. c("green","blue","red","orange") to show all marked items.
showPoints	should data points contributing to decision be shown?
showDateLabels	If TRUE, the record date of the showPointss records are added as label.

Value

None; as a side effect, a plot using standard graphics is generated. Note that the image may contain aliasing lines when Cairo is avaialable on your system. https://groups.google.com/forum/?fromgroups#!topic/shiny-discuss/ysac9FqOQLI

Author(s)

Dieter Menne, [e-mail]

Examples

databasePath = CreateSimulatedBreathTestDatabase()
con = OpenSqliteConnection(databasePath)
opt = par(mfrow=c(2,2))
DecisionPlot(con, showColors="red", main="Method ash")
# DecisionPlot(con, showColors=c("orange","blue"),main= "Method ks", kde.package="ks")
DecisionPlot(con, method="BluckCowardPop",showColors=c("red"), main= "BluckCoward Population" )
# For Wagner-Nelson, there is no lag, we must use it from a different source
DecisionPlot(con, method=c("MaesPop","Maes"),parameters=c("t50","t50"),
 showColors=c("green","blue"),showPoints=FALSE,
   main="No points, Spectral", brewerPalette = "Spectral")
par(opt)
dbDisconnect(con)

dmenne/d13cbreath documentation built on March 1, 2020, 3:41 a.m.