uwSurvival: Create Survival Chart and Table
In jbirstler/biostatrpts: Functions for UW-Biostatistics Report Creation

Description Usage Arguments Details Author(s) Examples

Charts survival by treatment

uwSurvival(
  survData,
  statusName,
  trxName,
  trxControl,
  timeName,
  fun = NULL,
  color = NULL,
  pTitle = "Survival by Treatment",
  yLab = "Percent of Survival Probability",
  xLab = "Days from Randomization",
  yLim = NULL,
  markCensor = FALSE,
  Legend = TRUE,
  LegendLoc = "topright",
  LegendCex = 0.8,
  printPVals = TRUE,
  pValCex = 0.6,
  abbrevN = 1,
  printSS = TRUE,
  SSinPlot = FALSE,
  SScex = 0.5,
  Ropen = FALSE,
  firstCol.name = NULL,
  GraphSSfreq = 1,
  TableSSfreq = GraphSSfreq,
  LatexFileName = "survival.tex",
  LatexCaption = NULL,
  numDec = 1,
  cexAxis = 0.7,
  confInt = FALSE,
  ...
)

`survData`	A dataframe that includes columns for treatment, patient status (living/deceased for survival, event/no event for other measurements), and the patients' survival days.
`statusName`	String of the name for the status variable in survData
`trxName`	String of the name for the treatment variable in survData
`trxControl`	String of which level is the control level in trxName
`timeName`	String of the name for the time variable in survData
`fun`	String as the function utilized for plot.survfit. Only tested for default and 'event'
`color`	Color designations. Must be equal to nlevels of trxName
`pTitle`	Title for the graph
`yLab`	Label for y-axis
`xLab`	Label for x-axis
`yLim`	Limits for the y-axis. Defaults to c(-1, 100) when SSinPlot is TRUE and defaults to c(-10, 100) when SS in Plot is FALSE
`markCensor`	(Logical) TRUE marks where censored data occurs on the curves
`Legend`	(Logical) TRUE plots legend in spot given in LegendLoc
`LegendLoc`	String of c('topright','top','topleft','left', 'center','right','bottomright','bottom','bottomleft')
`LegendCex`	Numeric magnification of the legend size
`printPVals`	(Logical) TRUE log-rank test p-value is given atop the graph
`pValCex`	Numeric magnification of the p-value print size
`abbrevN`	(integer) indicating how many letters should abbreviation of the treatments levels be when reported in margins.
`printSS`	(Logical) Prints sample size still at risk at the designated time points
`SSinPlot`	(Logical) TRUE prints sample size at risk inside graph itself in negative margins. Useful when survival is high throughout time period
`SScex`	Numeric magnification of the sample size print size
`Ropen`	(Logical) TRUE collapses data across treatment levels
`firstCol.name`	Sting for name of first column in the LaTeX tables
`GraphSSfreq`	Whole number designating how often sample size should be shown in the lower margin of the graph
`TableSSfreq`	Whole number designating how often rows of the survfit output should be printed in the LaTex table
`LatexFileName`	Vector of strings. Individually give file path and name for each LaTeX table which will be constructed for each treatment level.
`LatexCaption`	Vector of strings to be used as the caption for the LaTeX tables
`numDec`	Numeric indicating number of decimal places to be used in the x-axis for time of follow-up
`cexAxis`	Axis label magnifier
`confInt`	Should confidence interval lines be printed
`...`	Any other arguments that can be passed on to uwLatex()

Additional packages required: library(chron)

If LaTeX table does not seem to print fully in the document try using type='longtable' argument.

Only works well with layout(1)

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

death <- sample(c(0, 1), 200, replace = TRUE, prob = c(0.4, 0.6))
trt <- rep(c("ABDC", "ABGH"), c(100, 100))
time <- ceiling(runif(200, 0, 100))

sData <- data.frame(death, trt, time)
layout(1)
uwSurvival(
  survData = sData, statusName = "death", trxName = "trt", trxControl = "ABDC",
  timeName = "time", pTitle = "Survival by Treatment",
  yLab = "Percent of Survival Probability",
  xLab = "Days from Randomization", pValCex = 0.8, SScex = 0.7,
  markCensor = FALSE, Legend = TRUE, LegendLoc = "topright",
  LatexFileName = c(
    paste(getwd(), "surv1.tex", sep = ""),
    paste(getwd(), "/surv2.tex", sep = "")
  ),
  showTab = FALSE, printPVals = TRUE, printSS = TRUE,
  Ropen = FALSE, GraphSSfreq = 5, TableSSfreq = 1, firstCol.name = NULL,
  LatexCaption = NULL, SSinPlot = TRUE,
  size = "scriptsize"
)