Package {BiMaUmisc}

Type: Package
Title: BiMaU Miscellaneous
Version: 0.1.0
Maintainer: Anna Felip-Badia <annafelipibadia@gmail.com>
Description: Contains a function to plot publication-ready survival curves with the Kaplan-Meier method (1958) <doi:10.2307/2281868> and a function to format p-values, which are useful for repetitive analyses. BiMaU stands for the Biostatistics and Mathematics Research Unit at the Sant Joan de Déu - Pediatric Cancer Center Barcelona https://github.com/BiMaU-PCCB.
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Depends: R (≥ 4.1.0)
Encoding: UTF-8
Imports: exams, survival (≥ 3.8-6), latex2exp, plotfunctions, graphics, utils
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-07-24 09:28:39 UTC; afelipb
Author: Anna Felip-Badia ORCID iD [aut, cre], Aleix Martín-Moral ORCID iD [aut], Sara Perez-Jaume ORCID iD [aut]
Repository: CRAN
Date/Publication: 2026-08-04 09:50:12 UTC

BiMaU Miscellaneous

Description

This package contains useful data analysis tools, such as a function to plot survival curves, a function to format p-values, and a function (work in progress) to automatically select the test to apply when assessing differences in continuous variables between groups.

Functions

show.p, survival.plot

Author(s)

Maintainer: Anna Felip-Badia annafelipibadia@gmail.com (ORCID)

Authors:

Format p-values for display

Description

Convert p-values to a compact textual representation. The function prints decimals up to the first non-zero decimal and the following one, applying standard rounding.

Usage

show.p(p, add.p = FALSE)

Arguments

p

a value or vector of the p-value(s) to be shown, where 0<p<1.

add.p

logical indicating whether the text p= (or p<, if it applies) should be added before the p-value.
The default value is FALSE.

Details

The number of decimals shown depends on the magnitude of the p-value so that two meaningful digits are displayed after the leading zeros.

Specifically:

This formatting ensures that the first non-zero decimal of the p-value and the following digit are displayed, while avoiding an excessive number of leading zeros.

If add.p = TRUE, the prefix "*p*=" (or "*p*<" when applicable) is added to the formatted value. This will ensure the p appears in cursive when calling the function in line on R markdown documents.

Value

A character vector with the formatted p-values.

Examples

show.p(0.00785)
show.p(c(0.03042, 0.1579, 0.0000025))
show.p(0.00785, add.p = TRUE)
show.p(c(0.03042, 0.1579, 0.0000025), add.p = TRUE)

Plot survival curves

Description

This function produces an elegant survival curve plot. It can automatically append the number-at-risk table and display the log-tank test p-value (obtained from a call to survdiff). Highly customizable, it offers numerous arguments to easily modify the plot's appearance.

Usage

survival.plot(data, time, status, strata = 1,
              legend = TRUE, legend.pos = "bottomleft", legend.labs = NULL,
              legend.title = NULL, legend.cex = 1,
              events = FALSE, events.pos = NULL, events.text = NULL,
              mark.time = TRUE, lwd = 3, 
              risk = TRUE, risk.text = TRUE, risk.labs = NULL, risk.cex = 1, 
              p.value = TRUE, p.value.pos = NULL,
              units = "days", xlab = NULL, times = NULL,
              yscale = 1, ylab = NULL, 
              main = "Survival curve", col = NULL, ...)

Arguments

data

name of the dataset, of class data.frame, containing at least 2 columns (follow up time, status indicator).

time

follow-up time column name. Can be specified as a character string (with quotes) or as an unquoted symbol.

status

status indicator column name. Can be specified as a character string (with quotes) or as an unquoted symbol.

strata

strata indicator column name. Can be specified as a character string (with quotes) or as an unquoted symbol. Up to four categories. Must be a factor.
The default value is 1, this is, there are no groups.

legend

logical indicating whether a legend should be added to the plot. If strata is set to 1, this argument is ignored.
The default value is TRUE.

legend.pos

this argument can be a single keyword from the list in legend, such as "bottomleft" or "topright", which places the legend on the inside of the plot frame at the given location. In this case, this argument is passed to match.arg. Otherwise, a 2-dimensional numerical vector indicating the x-y coordinates can be indicated. If legend is set to FALSE, this argument is ignored.
The default value is "bottomleft".

legend.labs

a character vector of length \geq2 to appear as the legend labels. If legend is set to FALSE, this argument is ignored.
The default value, NULL, indicates that the levels of strata are to be used as the legend labels.

legend.title

title for the legend. If legend is set to FALSE, this argument is ignored.
The default value, NULL, indicates on title should be added.

legend.cex

legend's character expansion factor. A numerical value giving the amount by which the legend text should be magnified relative to the default. If legend is set to FALSE, this argument is ignored.
The default value is 1.

events

logical indicating whether the number of events should be added to the text in the legend. If strata is set to 1, the total number of events is added directly to the plot instead. If legend is set to FALSE and strata is not 1, this argument is ignored.
The default value is FALSE.

events.pos

2-dimensional numerical vector indicating the x-y coordinates where the number of events should be added to the plot. If strata is not 1 or events is set to FALSE, this argument is ignored.
The default value, NULL, indicates that the text should be placed on the bottom-left corner.

events.text

a character indicating the text to display before the number of events in the plot. If events is set to FALSE, this argument is ignored.
The default value, NULL, indicates that the text "Events" should be added when strata is set to 1 and the text "events" should be added when strata is not set to 1.

mark.time

logical indicating whether the curves should be marked at each censoring time.
The default value is TRUE.

lwd

a number indicating the line width(s). Alternatively, when strata is not set to 1, an n-dimensional numerical vector can be indicated, where n is the number of levels in strata.
The default value is 3.

risk

logical indicating whether the number-at-risk table should be appended to the plot.
The default value is TRUE.

risk.text

logical indicating whether the legend for the number-at-risk table should display text labels. When FALSE, line segments are used instead. If risk is set to FALSE or strata is set to 1, this argument is ignored.
The default value is TRUE.

risk.labs

n-dimensional character vector, where n is the number of levels in strata, indicating the text labels in the number-at-risk table. If risk.text is set to FALSE or strata is set to 1, this argument is ignored.
The default value, NULL, indicates that the levels of strata should be used.

risk.cex

number-at-risk table's character expansion factor. A numerical value giving the amount by which the number-at-risk table text should be magnified relative to the default. If risk is set to FALSE, this argument is ignored.
The default value is 1.

p.value

logical indicating whether the p-value obtained from a call to survdiff with rho equal to 0, this is the log-rank or Mantel-Haenszel test, should be displayed in the plot. The p-value will be displayed in the format specified by the show.p function. If strata is set to 1, this argument is ignored.
The default value is TRUE.

p.value.pos

2-dimensional numerical vector indicating the x-y coordinates where the number of events should be added to the plot. If strata is not 1 or events is set to FALSE, this argument is ignored.
The default value, NULL, indicates that the text should be placed on the upper-right corner.

units

character indicating the time units. Options are: "days", "weeks", "months" or "years". This argument will be used to create the default label and tick-marks for the x-axis. This argument is not case-sensitive and is passed to match.arg.
The default value is "days".

xlab

character indicating a label for the x-axis.
The default value, NULL, indicates that indicates that the text "Time (units)" should be used, where "units" is specified by the units argument.

times

numerical vector with the time points at which tick-marks are to be drawn in the x-axis.
The default value, NULL, indicates that a time vector will be automatically constructed based on the units argument:

  • If units is set to "days": from 0 to the maximum survival time rounded up to the nearest multiple of 7.

  • If units is set to "weeks": from 0 to the maximum survival time rounded up to the nearest integer.

  • If units is set to "months": from 0 to the maximum survival time rounded up to the nearest multiple of 12.

  • If units is set to "years": from 0 to the maximum survival time rounded up to the nearest integer.

yscale

a numeric value used to multiply the labels on the y-axis. A value of 100, for instance, would be used to give a percent scale. Notice only the labels are changed, not the actual plot coordinates.
The default value is 1.

ylab

character indicating a label for the y-axis.
The default value, NULL, indicates that indicates that the text "Survival" should be used. Moreover, if yscale is set to 1 (or 100) the text "(proportion)" or "(percentage)" will also be added.

main

overall title for the plot.
The default value is "Survival curve".

col

colour palette to be used.
The default value, NULL, indicates that a different colour should be used per level in strata. This is, a vector from 1 to n, where n is the number of levels in strata, will be used.

...

other graphical parameters (to be passed to plot.survfit).

Value

A customized survival curve plot displaying the requested graphical and statistical modifications.

Note

A call to par is used in this function. Notice that the arguments font.axis, font.lab, cex.lab, las and xpd are always set to 2, 2, 1.2, 1, and TRUE, respectively. Moreover, the argument mar is always modified and depends on the number of levels in strata as well as whether or not the number-at-risk table is appended.
For optimal resolution and layout alignment when using the function in an R file, adjust the plot window. For example, ideal dimensions are approximately 7 x 5” for 24” screens and 5.9 x 4.2” for 13” screens.
For optimal resolution and layout alignment when using the function in an R markdown file or similar, use fig.dim = c(7, 5) in the corresponding chunk.

Examples

lung <- survival::cancer
lung$time_y <- lung$time/365.25
lung$sex <- factor(lung$sex, levels = 1:2, labels = c("Male", "Female"))

# no strata
survival.plot(lung, time_y, status, units = "y")
# customizing
survival.plot(lung, time_y, status, units = "y",
              xlab = "Time since diagnosis (in years)",
              yscale = 100,
              main = "Overall survival", mark.col = "darkgray")

# 2 strata
survival.plot(lung, time_y, status, sex, units = "y")
# customizing
survival.plot(lung, time_y, status, sex, 
              legend.pos = "topright", legend.title = "Sex", 
              events = TRUE, risk.text = FALSE, p.value.pos = c(2.4, 0.4),
              units = "y", xlab = "Time since diagnosis (in years)", 
              main = "Overall survival", col = c("darkviolet", "darkgreen"))