uwCumulAccr: Cumulative Accrual Line Graphs

In jbirstler/biostatrpts: Functions for UW-Biostatistics Report Creation

Description

Cumulative accrual line graphs for the total cohort or separated by treatment level. Also available is the ability to add projected accrual lines for total cohort or separated by treatment level. Beneficial for DSMB to judge if pre-determined accrual rates are being met.

Usage

uwCumulAccr(
  accData,
  dateName,
  trxName = NULL,
  yLab = "Cumulative Number of Subjects",
  yLim = NULL,
  pTitle = NULL,
  LegendCor = NULL,
  startDate = NULL,
  currentDate = NULL,
  projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric()),
  titleCex = 1
)

Arguments

accData	Data frame which includes an accural date for each patient
dateName	(string) Variable name in accData indicating the date of accrual. Must be a variable with class type 'dates' from library(chron). Function will try to coherce non-dates variables into dates of the format 'm/d/y'.
trxName	(string) Optional string giving the name of the variable in accData that indicates treatment assignment. If used, then cumulative accrual is given separately for each treatment level. If NULL then any possible treatment levels are collapsed and treated as one large group
yLab	(string) Y label of graphic
yLim	(numeric) Limits of y axis of graphic. Default is the default of plot
pTitle	(string) Title of graphic
LegendCor	Manually enter where the legend should be placed on the graph. Must be a set of coordinates of length 2 (X,Y).
startDate	(string) Date in which the x-axis should start. Generally when accrual opened for the project. Must be in m/d/y format. Defaults to the minimum date in dateName.
currentDate	(string) Date in which the x-axis should end. Generally when report is being created. Must be in m/d/y format. Defaults to the maximum date in dateName.
projectLine	(list) List of length two with each element needing to be numeric. PatsPerTRT is the number of patients expected to be accrued in each treatment. Must be of length 1 or length equal to number of trxName levels. If length is 1 then this indicates equal accrual in each arm. Order of PatsPerTRT must match order of trxName levels. DaysPerTRT is the number of days that enrollment will be open for each treatment arm. Again if length of 1 then this is equal accrual time for each arm. If these numbers are provided, then a projected accrual line will be added to the graphic either for the total cohort or for the individual treatment arms
titleCex	(numeric) Magnification of title size

Value

a line graph

Author(s)

Scott J Hetzel MS. UW-Madison Department of Biostatistics and Medical Informatics. Contributions from Patrick Lenon. Frontier Science and Technology Research Foundation

Examples

Dates <- c(
  "03/01/2008", "09/01/2007", "07/01/2007", "12/01/2006", "08/01/2007", "08/01/2007",
  "04/01/2007", "04/01/2007", "04/01/2007", "11/01/2006", "11/01/2006", "12/01/2006",
  "12/01/2006", "10/01/2006", "01/01/2007", "11/01/2006", "12/01/2006", "02/01/2007",
  "08/01/2007", "08/01/2006", "09/01/2006", "04/01/2007", "05/01/2007", "11/01/2006",
  "10/01/2006", "03/01/2007", "10/01/2007", "07/01/2007", "03/01/2007", "04/01/2006",
  "05/01/2006", "11/01/2006", "12/01/2006", "02/01/2007", "02/01/2007", "02/01/2007",
  "04/01/2007", "05/01/2007", "07/01/2007", "08/01/2007", "11/01/2007", "10/01/2007",
  "09/01/2007", "10/01/2007", "05/01/2007", "01/01/2008", "12/01/2006", "02/01/2007",
  "03/01/2007", "04/01/2007", "04/01/2007", "05/01/2007", "07/01/2007", "02/01/2007",
  "07/01/2007", "10/01/2007", "01/01/2008"
)

Date <- chron::chron(Dates, format = c(dates = "m/d/y"))
TRT <- rep(c("A", "B"), c(30, 27))

data <- data.frame(Date, TRT)

layout(matrix(c(1, 2, 3, 4), nrow = 2, byrow = TRUE))

uwCumulAccr(
  accData = data, dateName = "Date", trxName = NULL,
  yLab = "Cumulative Number of Subjects",
  yLim = NULL,
  pTitle = "Accural over Time for Total Cohort",
  projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric())
)
# Projected accrual of 32 per arm over 750 days
uwCumulAccr(
  accData = data, dateName = "Date", trxName = NULL,
  yLab = "Cumulative Number of Subjects",
  yLim = NULL, startDate = "01/01/06",
  pTitle = "Total Cohort with equal projected accrual",
  projectLine = list(PatsPerTRT = 64, DaysPerTRT = 750)
)

uwCumulAccr(
  accData = data, dateName = "Date", trxName = "TRT",
  yLab = "Cumulative Number of Subjects",
  yLim = NULL,
  pTitle = "Accural over Time by Treatment Arm",
  projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric())
)
# Projected accrual of 30 in A and 27 in B over 700 days
uwCumulAccr(
  accData = data, dateName = "Date", trxName = "TRT",
  yLab = "Cumulative Number of Subjects",
  yLim = c(0, 70), LegendCor = c(25, 55),
  pTitle = "Accural over Time by Treatment Arm",
  projectLine = list(PatsPerTRT = c(30, 27), DaysPerTRT = 700)
)

jbirstler/biostatrpts documentation built on May 7, 2020, 12:10 a.m.