uwConfBands: Confidence Bands for Hazard Ratios, Mean Differences, or Odds...
In jbirstler/biostatrpts: Functions for UW-Biostatistics Report Creation

Description Usage Arguments Details Value Author(s) See Also Examples

This function is meant the creation of 95% confidence intervals for subsets of a data set. Confidence intervals can be for hazard ratios, mean differences, or odds ratios.

uwConfBands(
  fullData,
  trxName,
  trxLevels,
  factVarNames,
  factFigNames = NULL,
  estimate = c("hazard", "mean", "proportion"),
  pTitle = NULL,
  coxMethod = c("breslow", "efron"),
  timeName = NULL,
  statusName = NULL,
  metricName = NULL,
  printPVals = TRUE,
  interactPVals = FALSE,
  xLim = NULL,
  xLog = TRUE,
  xDetailed = TRUE,
  leftMarWidth = 2,
  lineWidth = 6,
  pointSize = 1.3,
  LatexFileName = NULL,
  ...
)

`fullData`	Name of the data frame loaded into R.
`trxName`	String of name of treatment factor in fullData
`trxLevels`	Vector of strings giving the two levels of trxName to be used for the figure and table
`factVarNames`	Vector of strings giving all of the variable names in fullData that will be indivdually subsetted on.
`factFigNames`	Vector of strings giving all of the names that will be used in the figure. Used when factVarNames are not actually how you want the variables represented in the figure. There is positional matching between this and factVarNames
`estimate`	String indicating which statistic should be estimated from the data. 'hazard', 'mean', or 'proportion' first letter is sufficient
`pTitle`	String to be used as the Figure's title
`coxMethod`	Method for coxph() in handling ties. Defaults to breslow'
`timeName`	Only used if estimate='h'. String giving the variable name that is gives the survival time
`statusName`	Used if estimate='h' or estimate='p'. String giving the variable name that indicates whether or not the outcome of interest occurred. This should be logical or 0's and 1's.
`metricName`	Only used if estimate='m'. String giving the variable name that the differences in means between treatment levels should be calculated for.
`printPVals`	(logical) TRUE to have p-values printed
`interactPVals`	(logical) TRUE reports interaction p-values, FALSE is regular treatment comparison p-values
`xLim`	Specifies the limits of the x-axis. If null, each method based on estimate has it's own default
`xLog`	Only used if estimate='h'. Logic for type of x-axis to be printed. TRUE = log scale x-axis. FALSE = unit scale x-axis.
`xDetailed`	Only used if estimate='h'. Logic for type of x-axis printed. TRUE has multiple default tick locations. FALSE has default locations based on axis(1)
`leftMarWidth`	Sets the width of the left margin where the subset indications will be printed
`lineWidth`	Sets the width of the lines used for the confidence bands
`pointSize`	The cex for the square box representing the point estimates
`LatexFileName`	A vector of strings giving the folder and file(ending in .tex) for the LaTeX table to be saved. The default is NULL, which will not save the table only print the matrix.
`...`	Any other arguement that can be passed to uwLatex()

Additional LaTeX Packages Required if LtxTranspose=TRUE: usepackagemultirow usepackagelongtable if type='longtable' Special functions Required: uwLatex()

Output is a figure and a LaTeX table. If LatexFileName is null, the matrix of data is printed

University of Wisconsin-Madison Biostatistics and Medical Informatics Department and Frontier Science, Scott Hetzel M.S.

uwLatex()

data(colon, package = "survival") # from library(survival)
colon$sex.f <- factor(colon$sex, levels = c(0, 1), labels = c("Female", "Male"))
colon$surg.f <- factor(colon$surg,
  levels = c(0, 1),
  labels = c("Short", "Long")
)
colon$differ.f <- factor(colon$differ,
  levels = c(1, 2, 3),
  labels = c("Well", "Moderate", "Poor")
)



uwConfBands(
  fullDat = colon,
  trxName = "rx",
  trxLevels = c("Obs", "Lev"),
  factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
  factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
  estimate = "m",
  metricName = "nodes",
  printPVals = FALSE,
  LatexFileName = NULL
)


uwConfBands(
  fullDat = colon,
  trxName = "rx",
  trxLevels = c("Obs", "Lev"),
  factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
  factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
  estimate = "p",
  statusName = "status",
  printPVals = TRUE,
  LatexFileName = NULL
)

layout(matrix(c(1, 1, 1, 1, 2, 2, 2, 2), nrow = 2, byrow = TRUE))
uwConfBands(
  fullDat = colon,
  trxName = "rx",
  trxLevels = c("Obs", "Lev"),
  factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
  factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
  estimate = "h",
  statusName = "status",
  timeName = "time",
  xLim = c(0.25, 5),
  xLog = TRUE,
  printPVals = TRUE,
  interactPVals = TRUE,
  LatexFileName = NULL
)

uwConfBands(
  fullDat = colon,
  trxName = "rx",
  trxLevels = c("Obs", "Lev"),
  factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
  factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
  estimate = "h",
  statusName = "status",
  timeName = "time",
  xLim = c(0, 2),
  xLog = FALSE,
  xDetailed = FALSE,
  printPVals = TRUE,
  interactPVals = TRUE,
  LatexFileName = NULL
)