accrual_plot_abs: Absolute accrual plots

In CTU-Bern/accrualPlot: Accrual Plots and Predictions for Clinical Trials

Absolute accrual plots

Description

Plot of absolute recruitment by time unit using an accrual data frame produced by accrual_create_df.

Usage

accrual_plot_abs(
  accrual_df,
  unit = c("month", "year", "week", "day"),
  target = NULL,
  overall = TRUE,
  name_overall = attr(accrual_df, "name_overall"),
  ylim = NULL,
  xlim = NULL,
  ylab = "Recruited patients",
  xlabformat = NULL,
  xlabsel = NA,
  xlabpos = NULL,
  xlabsrt = 45,
  xlabadj = c(1, 1),
  xlabcex = 1,
  col = NULL,
  legend.list = NULL,
  ...
)

gg_accrual_plot_abs(
  accrual_df,
  unit = c("month", "year", "week", "day"),
  xlabformat = NULL
)

Arguments

accrual_df	object of class 'accrual_df' or 'accrual_list' produced by accrual_create_df.
unit	time unit for which the bars should be plotted, one of "month", "year", "week" or "day".
target	adds horizontal line for target recruitment per time unit.
overall	logical, indicates that accrual_df contains a summary with all sites that should be removed from stacked barplot (only if by is not NA).
name_overall	name of the summary with all sites (if by is not NA and overall==TRUE).
ylim	limits for y-axis.
xlim	limits for x-axis.
ylab	y-axis label.
xlabformat	format of date on x-axis.
xlabsel	selection of x-labels if not all should be shown, by default all are shown up to 15 bars, with more an automated selection is done, either NA (default), NULL (show all), or a numeric vector.
xlabpos	position of the x-label.
xlabsrt	rotation of x-axis labels in degrees.
xlabadj	adjustment of x-label, numeric vector with length 1 or 2 for different adjustment in x- and y-direction.
xlabcex	size of x-axis label.
col	colors of bars in barplot, can be a vector if accrual_df is a list, default is grayscale.
legend.list	named list with options passed to legend().
...	further arguments passed to barplot() and axis().

Details

When the accrual_df includes multiple sites, the dataframe passed to ggplot includes a site variable which can be used for facetting

Value

accrual_plot_abs returns a barplot of absolute accrual by time unit (stacked if accrual_df is a list).

ggplot object

Examples

set.seed(2020)
enrollment_dates <- as.Date("2018-01-01") + sort(sample(1:100, 50, replace=TRUE))
accrual_df<-accrual_create_df(enrollment_dates)
accrual_plot_abs(accrual_df,unit="week")

#time unit
accrual_plot_abs(accrual_df,unit="day")

#include target
accrual_plot_abs(accrual_df,unit="week",target=5)

#further plot options
accrual_plot_abs(accrual_df,unit="week",ylab="No of recruited patients",
   xlabformat="%Y-%m-%d",xlabsrt=30,xlabpos=-0.8,xlabadj=c(1,0.5),
   col="pink",tck=-0.03,mgp=c(3,1.2,0))

#accrual_df with by option
set.seed(2020)
centers<-sample(c("Site 1","Site 2","Site 3"),length(enrollment_dates),replace=TRUE)
centers<-factor(centers,levels=c("Site 1","Site 2","Site 3"))
accrual_df<-accrual_create_df(enrollment_dates,by=centers)
accrual_plot_abs(accrual_df=accrual_df,unit=c("week"))

### ggplot2 approach
data(accrualdemo)
accrual_df<-accrual_create_df(accrualdemo$date)
gg_accrual_plot_abs(accrual_df, unit = "week")
gg_accrual_plot_abs(accrual_df, unit = "week") +
  ggplot2::theme_classic()

#time unit
gg_accrual_plot_abs(accrual_df, unit = "day")

#accrual_df with by option
accrual_df <- accrual_create_df(accrualdemo$date, by = accrualdemo$site)
gg_accrual_plot_abs(accrual_df = accrual_df, unit = "week")
gg_accrual_plot_abs(accrual_df = accrual_df, unit = "week") +
  ggplot2::scale_fill_discrete(type = c("black", "red", "blue", "green"))

CTU-Bern/accrualPlot documentation built on Aug. 17, 2024, 8:20 p.m.