Absolute accrual plots — accrual_plot

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

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().

Value

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

ggplot object

Details

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

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"))