Help for package summarySCI

Title:

Produces Publication-Ready Summary Tables and Plots

Version:

1.0.0

Description:

Produces tables with descriptive statistics for continuous, categorical and dichotomous variables. It is largely based on the package 'gtsummary'; Sjoberg DD et al. (2021) <doi:10.32614/RJ-2021-053>. The tables can be accompanied by matching boxplots, line plots and stacked barplots, also over time.

License:

LGPL-3

Encoding:

UTF-8

RoxygenNote:

7.3.2

Depends:

R (≥ 4.1)

Imports:

Hmisc, cardx, dplyr, gtsummary (≥ 2.3.0), forcats, labelled, purrr, rlang, tidyr, flextable, officer, graphics, grDevices, stats, utils, tools

Suggests:

broom (≥ 1.0.8), knitr, survival, testthat (≥ 3.0.0), rmarkdown

VignetteBuilder:

knitr

URL:

https://sakk-statistics.github.io/summarySCI/, https://github.com/SAKK-Statistics/summarySCI

BugReports:

https://github.com/SAKK-Statistics/summarySCI/issues

Config/testthat/edition:

NeedsCompilation:

Packaged:

2026-11-13 15:02:39 UTC; charlottemi

Author:

Sämi Schär [aut], Charlotte Micheloud [cre, aut], Tudor Jumuga [aut]

Maintainer:

Charlotte Micheloud <Charlotte.Micheloud@swisscancerinstitute.ch>

Repository:

CRAN

Date/Publication:

2026-11-13 16:10:08 UTC

Convert a character vector to a factor with natural level order

Description

Convert a character vector to a factor with natural level order

Usage

as_natural_factor(x)

Arguments

x

A character vector.

Value

A factor; the "label" attribute is kept.

Boxplot over time

Description

Generates boxplots over time for one or multiple sub-groups.

Usage

boxplotSCI(
  data,
  var,
  order = NULL,
  visit = NULL,
  group = NULL,
  group_names = NULL,
  group_names_short = NULL,
  main = "",
  xlab = NULL,
  ylab = "Variable",
  ylim = NULL,
  y_ticks = NULL,
  col = NULL,
  cex_lab = 1,
  cex_axis = 1,
  cex_n_patients = 0.7,
  boxwex = NULL,
  shift = NULL,
  mar_custom = NULL,
  xlab_line = NULL,
  ylab_line = 3,
  xlab_position = NULL,
  lines = NULL,
  lty = NULL,
  col_lines = NULL,
  legend_position = "topright",
  legend_offset = c(0, 0),
  legend_cex = 1,
  legend_bty = "n",
  risk_table = NULL,
  missing_nr = 0,
  color_time = FALSE,
  stat_footnote = FALSE,
  ...
)

Arguments

data

A data frame or tibble containing the data to be plotted.

var

Name of the column in data indicating the measurement to be plotted. Supports bare or quoted column names.

order

Name of the column in data containing the time points of interest. The time points can be either numeric, character, or a factor. If the time points are factors, the factor levels must be in the correct chronological order for plotting. If left empty, the function will assume a single time point. If character, they need to be able to be ordered by numerical logic.

visit

Name of the column in data containing descriptive labels for the time points. Optional.

group

Name of the column in data containing the grouping variables (e.g., treatment arms). If left empty, the function will assume a single group.

group_names

A character vector containing the names of the groups to be displayed in the legend. The order must match levels(factor(data$group)). Default is NULL, which falls back to the group names found in the data.

group_names_short

A character vector containing short names or abbreviations for the groups, to be displayed below the x-axis near the patient counts. Optional. Defaults to group_names.

main

Title of the plot. Defaults to "" (no title).

xlab

A label for the x-axis. Default is "Time" if there are multiple time points, otherwise defaults to "Group".

ylab

A label for the y-axis. Default is "Variable".

ylim

The y-axis limits of the plot as a numeric vector of length 2. Default is NULL, which adds a 10% padding buffer above and below the data range.

y_ticks

A numeric vector specifying the explicit tick positions on the y-axis. Default is NULL, which places about 5 ticks at round values within the y-axis limits, as in the other plots of the package.

col

A character vector of hex colors or color names to use for the boxes. Default is NULL, which automatically applies the SCI color palette.

cex_lab

A numeric value specifying the font size of the main axis labels. Default is 1.

cex_axis

A numeric value specifying the font size of the axis tick marks. Default is 1.

cex_n_patients

A numeric value specifying the font size of the sample size labels and numbers displayed beneath the horizontal axis. Default is 0.7.

boxwex

Scale factor for the width of the boxes. Default is NULL, which scales the box flexibly to the size of total timepoints and groups.

shift

A numeric value indicating the distance between adjacent boxes within a timepoint cluster. Default is NULL, which dynamically sets spacing to boxwex * 1.15.

mar_custom

A numeric vector indicating the plot margins to be used in the form c(bottom, left, top, right). Default is NULL, which dynamically calculates spacing so that stacked sample-size rows are never clipped.

xlab_line

A numeric value indicating the margin line offset for the x-axis label. Default is NULL, which calculates an adaptive offset based on the number of groups.

ylab_line

A numeric value indicating the margin line offset for the y-axis label. Default is 3.0.

xlab_position

Horizontal position coordinate adjustment for the sample size group headers down the left-hand margin. Default is NULL, which auto-aligns them.

lines

A numeric vector indicating the vertical coordinates where horizontal reference lines will be plotted. Optional.

lty

A numeric vector of length 1 or of the same length as lines indicating the line type to be plotted. Default is 1 (solid).

col_lines

A character vector of length 1 or of the same length as lines indicating the color of the reference lines. Default is "grey".

legend_position

Position of the legend box. Options include standard base R keywords (e.g., "topright", "topleft", "bottom") or manual numeric coordinate pairs c(x, y). Default is "topright".

legend_offset

A numeric vector of length 2 specifying an inset to nudge the legend position away from plot elements. Default is c(0, 0).

legend_cex

A numeric value specifying the font and element scaling size inside the legend box. Default is 1.

legend_bty

The type of box border to be drawn around the legend. Allowed values are "n" (transparent/no border, the default) and "o" (standard box frame).

risk_table

A logical toggle switch enabling the patient numbers (non-missing observations of var) beneath the x-axis: one row per group over time, or one number under each box for a single time point. Default is NULL, which shows them over time but not for a single time point; TRUE shows them in both cases, FALSE in neither.

missing_nr

A numeric or character value indicating how zero-count patient sizes on the x-axis should be displayed. Default is 0. Can also be set to NA.

color_time

A logical toggle switch enabling legacy timepoint colorization. Supports legacy use, where, for a single timepoint, multiple groups were used as "timepoint" variable. If set to TRUE, it treats timepoints as individual categories,applying sequential coloring and rendering a matching tracking legend. Default is FALSE.

stat_footnote

Show what the plot displays as a footnote in the bottom-right corner, beneath the x-axis title: TRUE for the default text (e.g. the definition of box and whiskers), a character string for a text of your own, or FALSE (the default) for none.

...

Further graphical parameters passed on to bxp(), which draws the boxes for boxplot(), e.g. lwd, border, outline = FALSE (no points for outliers) or range (the whisker length, see above; 0 for whiskers to the minimum and maximum).

Details

The box spans the first to the third quartile with the median inside, computed as in the summary tables (summaryTable(), summaryByVisit(): quantile(type = 2)), so that a boxplot and a "median_IQR" table show the same numbers. (boxplot() itself draws Tukey's hinges, which can differ slightly.) The whiskers reach the most extreme values within range (1.5 by default) times the box length from the box; values beyond are drawn as points.

Examples

library(summarySCI)
data("hemoglobin_data")
boxplotSCI(data = hemoglobin_data,
                 var = hb,
                  order = visit_nr,
                  group = Arm,
                  group_names = c("Treatment (Arm A)", "Control (Arm B)"),
                  group_names_short = c("A", "B"),
                  # Title
                  main = "Hemoglobin over time",
                  # Col of boxes
                  col = c("lightblue", "orange"),
                  # X axis label
                  xlab = "Visits",
                  # X axis position
                  xlab_position = 0,
                  # Y axis label
                  ylab = "Score",
                  lines = c(90, 120, 160),
                  # Col of lines
                  col_lines = c("red", "grey", "red"),
                  # Type of lines
                  lty = c(2, 3, 2)
)

Digits for the categorical statistics

Description

Counts (n, N) are shown without decimals; digits_cat is used for the percentages only. The digits are returned in the order of the statistics in stat_fmt, as gtsummary expects.

Usage

cat_digits(stat_fmt, digits_cat)

Arguments

stat_fmt

Statistic string, e.g. "{n} ({p}%)".

digits_cat

Digits for percentages.

Value

Integer vector, one value per statistic.

Resolve a column-name argument

Description

Turns the argument of a plotting function into column name(s). Accepts quoted names ("x", c("x", "y")), a variable holding such names, and bare names (x): a bare name does not evaluate to a character vector, so it is deparsed instead.

Usage

col_names(sub, val_fun)

Arguments

sub

The unevaluated argument, i.e. substitute(arg).

val_fun

A function evaluating the argument, i.e. function() arg.

Value

A character vector, or NULL if the argument is NULL.

Digits for the continuous statistics

Description

digits_cont for every statistic, except the geometric SD: a factor close to 1 (e.g. 1.13), which gets at least 2 decimals. The digits are returned in the order of the statistics in stat_fmt, as gtsummary expects.

Usage

cont_digits(stat_fmt, digits_cont)

Arguments

stat_fmt

Statistic string, e.g. "{geom_mean} ({geom_sd})".

digits_cont

Digits for continuous statistics.

Value

Integer vector, one value per statistic.

Robust Fisher's exact test for gtsummary::add_p()

Description

Runs stats::fisher.test(); if it fails because the FEXACT workspace is too small (tables with many levels), retries with a larger workspace and finally falls back to a Monte Carlo p-value (reproducible with set.seed()). Returns NA if the table is degenerate.

Usage

fisher_test_safe(data, variable, by, ...)

Arguments

data, variable, by

Passed by gtsummary::add_p().

Value

A data frame with columns p.value and method.

Geometric mean

Description

This function return the geometric mean. It is only defined for positive values: if x contains zeros or negative values, NA is returned with a warning (instead of silently dropping them, which log() and na.rm would otherwise do).

Usage

geom_mean(x, na.rm = TRUE)

Arguments

x

Numeric vector

na.rm

Logical; whether missing values are removed first.

Value

Geometric mean

Geometric standard deviation

Description

The standard deviation on the log scale, back-transformed: exp(sd(log(x))). It is a factor: about two thirds of log-normal values lie between the geometric mean divided and multiplied by it. Like geom_mean(), it is only defined for positive values and is NA otherwise (without a second warning), and NA for fewer than two values.

Usage

geom_sd(x, na.rm = TRUE)

Arguments

x

Numeric vector

na.rm

Logical; whether missing values are removed first.

Value

Geometric standard deviation

Get the labels from a dataset

Description

This function get the labels from a dataset

Usage

get_labels(data, vars)

Arguments

data

Dataset

vars

Variables of interest

Value

The labels

Hemoglobin data (to illustrate `boxplotSCI()` and `summaryByVisit()`)

Description

A dataset containing the hemoglobin value of 169 patients over 9 visits. Adapted from SAKK 08/14.

Usage

data(hemoglobin_data)

Format

`hemoglobin_data`

A data frame with 1307 rows and 5 columns:

ID: Patient ID
Arm: Experimental arm ("Arm A", "Arm B")
visit: Visit (character, "Cycle 1" to "Cycle 9")
visit_nr: Visit number (numeric, 1 to 9)
hb: Hemoglobin value (g/L)

Source

SAKK

Line plot of a summary statistic over time, by group

Description

Generates line plots of a central-tendency statistic over time for one or multiple sub-groups, optionally with a dispersion band (ribbon or whiskers) and a table of patient numbers beneath the horizontal axis.

Usage

lineplotSCI(
  data,
  var,
  order,
  group = NULL,
  visit = NULL,
  n_order = NULL,
  group_names = NULL,
  group_names_short = NULL,
  stat = c("median", "mean", "geomean"),
  interval = c("iqr", "range", "ci", "sd", "se", "gsd", "none"),
  interval_type = c("whiskers", "ribbon"),
  alpha = 0.05,
  dodge = 0,
  connect = TRUE,
  connect_shade = 0.15,
  main = "",
  xlab = "Time",
  ylab = "Variable",
  xlim = NULL,
  ylim = NULL,
  y_ticks = NULL,
  col = NULL,
  cex_lab = 1,
  cex_axis = 1,
  cex_n_patients = 0.7,
  risk_table = FALSE,
  missing_nr = 0,
  rotate_labels = FALSE,
  mar_custom = NULL,
  xlab_line = NULL,
  ylab_line = 3,
  xlab_position = NULL,
  lines = NULL,
  lty = 1,
  col_lines = "grey",
  legend_position = "topright",
  legend_title = NULL,
  legend_offset = c(0, 0),
  legend_cex = 1,
  legend_bty = "n",
  stat_footnote = FALSE,
  ...
)

Arguments

data

A data frame or tibble containing the data to be plotted.

var

Name of the column in data indicating the measurement to be plotted. Supports bare or quoted column names.

order

Name of the column in data containing the time points of interest. The time points must be numeric or coercible to numeric, since they are used as the plotting coordinates on the x-axis. Rows with a missing time point are dropped.

group

Name of the column in data containing the grouping variable (e.g., treatment arms). Supports bare or quoted column names. Rows with a missing group are dropped. Default is NULL, which draws a single line, labelled with var (or group_names).

visit

Descriptive labels for the time points. Either the name of a column in data containing the labels (bare or quoted; the first label observed at each time point is used), or a character vector with one entry per tick position. Default is NULL, which prints the time values themselves.

n_order

A numeric value indicating the number of tick positions on the x-axis. Default is NULL, which places one tick at each distinct value of order. Set explicitly to reserve ticks for time points with no observed data, in which case ticks are drawn at 1:n_order.

group_names

group_names_short

A character vector containing short names or abbreviations for the groups, to be displayed below the x-axis near the patient counts. Optional. Defaults to group_names.

stat

The summary statistic plotted as the point estimate: "median" (the default), "mean" or "geomean" (geometric mean, for positive values: as in the tables, groups and time points with a value of zero or below are left out, with a warning).

interval

The quantity spanned by the error band around the point estimate. One of "iqr" (the default, 25th to 75th percentile, computed as in the summary tables, i.e. quantile(type = 2)), "range" (observed minimum to maximum), "ci" (a two-sided confidence interval at level 1 - alpha), "sd" (point estimate +/- one standard deviation), "se" (point estimate +/- one standard error), "gsd" (geometric mean divided and multiplied by the geometric standard deviation, exp(sd(log(x))); only with stat = "geomean"), or "none" to plot point estimates alone. With stat = "geomean", only "gsd", "iqr", "range" and "none" are available.

interval_type

The style in which the error band is drawn. Either "whiskers" (the default; vertical bars with caps) or "ribbon" (a shaded polygon with a dashed border). Ignored when interval is "none".

alpha

The two-sided significance level used when interval = "ci". Default is 0.05, giving 95% confidence intervals. For stat = "mean" the interval is the usual t-interval; for stat = "median" it is the distribution-free interval based on the binomial order statistics, which is undefined for very small cells and returned as NA there.

dodge

A numeric value giving the total horizontal offset applied across groups, in x-axis units, so that overlapping error bars remain readable. Default is 0 (all groups drawn at the same x position).

connect

A logical toggle switch controlling whether the point estimates within a group are joined by a line. Default is TRUE.

connect_shade

A numeric value between 0 and 1 giving how much lighter the connecting lines are drawn than the point estimates. The color is mixed with white rather than made transparent, so the lines stay opaque where they cross error bars or a ribbon. Default is 0.15 (15% lighter); 0 draws the lines in the group color.

main

Title of the plot. Defaults to "" (no title).

xlab

A label for the x-axis. Default is "Time".

ylab

A label for the y-axis. Default is "Variable".

xlim

The x-axis limits of the plot as a numeric vector of length 2. Default is NULL, which spans all tick positions and observed time points.

ylim

The y-axis limits of the plot as a numeric vector of length 2. Default is NULL, which adds a 10% padding buffer above and below the data range (band included, where one is drawn).

y_ticks

A numeric vector specifying the explicit tick positions on the y-axis. Default is NULL, which falls back to automatic tick placement.

col

A character vector of hex colors or color names to use for the groups. Recycled if shorter than the number of groups. Default is NULL, which automatically applies the SCI color palette.

cex_lab

A numeric value specifying the font size of the main axis labels. Default is 1.

cex_axis

A numeric value specifying the font size of the axis tick marks. Default is 1.

cex_n_patients

A numeric value specifying the font size of the sample size labels and numbers displayed beneath the horizontal axis. Default is 0.7.

risk_table

A logical toggle switch enabling the table of patient numbers (non-missing observations of var per group and time point) beneath the x-axis. Default is FALSE.

missing_nr

A numeric or character value indicating how zero-count patient sizes on the x-axis should be displayed. Default is 0. Can also be set to NA, which leaves the cell blank.

rotate_labels

A logical toggle switch rotating the x-axis tick labels by 90 degrees. Default is FALSE. Bottom margin and label offsets are adjusted accordingly.

mar_custom

xlab_line

A numeric value indicating the margin line offset for the x-axis label. Default is NULL, which calculates an adaptive offset based on the number of groups and on rotate_labels.

ylab_line

A numeric value indicating the margin line offset for the y-axis label. Default is 3.0.

xlab_position

Horizontal position coordinate adjustment for the sample size group headers down the left-hand margin. Default is NULL, which auto-aligns them just outside the plot region.

lines

A numeric vector indicating the vertical coordinates where horizontal reference lines will be plotted. Optional.

lty

A numeric vector of length 1 or of the same length as lines indicating the line type to be plotted. Default is 1 (solid).

col_lines

A character vector of length 1 or of the same length as lines indicating the color of the reference lines. Default is "grey".

legend_position

Position of the legend box. Options include standard base R keywords (e.g., "topright", "topleft", "bottom") or manual numeric coordinate pairs c(x, y). Default is "topright". NULL removes the legend.

legend_title

Title of the legend box. Default is NULL (no title).

legend_offset

A numeric vector of length 2 specifying an inset to nudge the legend position away from plot elements. Default is c(0, 0). Ignored when legend_position is given as coordinates.

legend_cex

A numeric value specifying the font and element scaling size inside the legend box. Default is 1.

legend_bty

The type of box border to be drawn around the legend. Allowed values are "n" (transparent/no border, the default) and "o" (standard box frame).

stat_footnote

Show what the plot displays as a footnote in the bottom-right corner, beneath the x-axis title: TRUE for the default text (e.g. "Median (Q1, Q3)"), a character string for a text of your own, or FALSE (the default) for none.

...

Further graphical parameters passed on to plot().

Value

Invisibly, a list with the group-by-time matrices centre, lower, upper (both all-NA when interval is "none") and n, the number of non-missing observations per cell.

Draw a line plot from pre-computed group-by-time summaries

Description

Drawing back end shared by lineplotSCI(), which summarises raw data, and plotByVisit(), which reads the numbers off a summaryByVisit() table.

Usage

lineplot_draw(
  centre,
  lower,
  upper,
  obs,
  xs,
  at_x = xs,
  visit = as.character(at_x),
  band = any(!is.na(lower)),
  interval_type = "whiskers",
  group_names = NULL,
  group_names_short = NULL,
  dodge = 0,
  connect = TRUE,
  connect_shade = 0.15,
  main = "",
  xlab = "Time",
  ylab = "Variable",
  xlim = NULL,
  ylim = NULL,
  y_ticks = NULL,
  col = NULL,
  cex_lab = 1,
  cex_axis = 1,
  cex_n_patients = 0.7,
  risk_table = FALSE,
  missing_nr = 0,
  rotate_labels = FALSE,
  mar_custom = NULL,
  xlab_line = NULL,
  ylab_line = 3,
  xlab_position = NULL,
  lines = NULL,
  lty = 1,
  col_lines = "grey",
  legend_position = "topright",
  legend_title = NULL,
  legend_offset = c(0, 0),
  legend_cex = 1,
  legend_bty = "n",
  stat_footnote = NULL,
  ...
)

Arguments

centre, lower, upper

Numeric group-by-time matrices with the point estimate and the interval bounds (NA where unavailable). Row names are the group names.

obs

Integer group-by-time matrix of non-missing observations.

xs

The x coordinates of the columns of centre.

at_x

The tick positions on the x-axis.

visit

band

Logical; whether an error band is drawn at all.

interval_type

The style in which the error band is drawn. Either "whiskers" (the default; vertical bars with caps) or "ribbon" (a shaded polygon with a dashed border). Ignored when interval is "none".

group_names

group_names_short

A character vector containing short names or abbreviations for the groups, to be displayed below the x-axis near the patient counts. Optional. Defaults to group_names.

dodge

A numeric value giving the total horizontal offset applied across groups, in x-axis units, so that overlapping error bars remain readable. Default is 0 (all groups drawn at the same x position).

connect

A logical toggle switch controlling whether the point estimates within a group are joined by a line. Default is TRUE.

connect_shade

main

Title of the plot. Defaults to "" (no title).

xlab

A label for the x-axis. Default is "Time".

ylab

A label for the y-axis. Default is "Variable".

xlim

The x-axis limits of the plot as a numeric vector of length 2. Default is NULL, which spans all tick positions and observed time points.

ylim

The y-axis limits of the plot as a numeric vector of length 2. Default is NULL, which adds a 10% padding buffer above and below the data range (band included, where one is drawn).

y_ticks

A numeric vector specifying the explicit tick positions on the y-axis. Default is NULL, which falls back to automatic tick placement.

col

A character vector of hex colors or color names to use for the groups. Recycled if shorter than the number of groups. Default is NULL, which automatically applies the SCI color palette.

cex_lab

A numeric value specifying the font size of the main axis labels. Default is 1.

cex_axis

A numeric value specifying the font size of the axis tick marks. Default is 1.

cex_n_patients

A numeric value specifying the font size of the sample size labels and numbers displayed beneath the horizontal axis. Default is 0.7.

risk_table

A logical toggle switch enabling the table of patient numbers (non-missing observations of var per group and time point) beneath the x-axis. Default is FALSE.

missing_nr

A numeric or character value indicating how zero-count patient sizes on the x-axis should be displayed. Default is 0. Can also be set to NA, which leaves the cell blank.

rotate_labels

A logical toggle switch rotating the x-axis tick labels by 90 degrees. Default is FALSE. Bottom margin and label offsets are adjusted accordingly.

mar_custom

xlab_line

A numeric value indicating the margin line offset for the x-axis label. Default is NULL, which calculates an adaptive offset based on the number of groups and on rotate_labels.

ylab_line

A numeric value indicating the margin line offset for the y-axis label. Default is 3.0.

xlab_position

Horizontal position coordinate adjustment for the sample size group headers down the left-hand margin. Default is NULL, which auto-aligns them just outside the plot region.

lines

A numeric vector indicating the vertical coordinates where horizontal reference lines will be plotted. Optional.

lty

A numeric vector of length 1 or of the same length as lines indicating the line type to be plotted. Default is 1 (solid).

col_lines

A character vector of length 1 or of the same length as lines indicating the color of the reference lines. Default is "grey".

legend_position

legend_title

Title of the legend box. Default is NULL (no title).

legend_offset

A numeric vector of length 2 specifying an inset to nudge the legend position away from plot elements. Default is c(0, 0). Ignored when legend_position is given as coordinates.

legend_cex

A numeric value specifying the font and element scaling size inside the legend box. Default is 1.

legend_bty

The type of box border to be drawn around the legend. Allowed values are "n" (transparent/no border, the default) and "o" (standard box frame).

stat_footnote

The text of the footnote in the bottom-right corner, or NULL for none (the callers turn TRUE into their default text).

...

Further graphical parameters passed on to plot().

Value

Invisibly, a list with centre, lower, upper and n.

Natural ordering of levels for character variables

Description

Values starting with a number are sorted numerically by that number (e.g. "3" < "10", "2 doses" < "10 doses") and come first. A leading comparison operator is taken into account: "<10%" comes just before "10%", ">90%" just after "90%" (also "<=", ">=", and the symbols for these). All other values follow alphabetically, with embedded numbers compared numerically ("Arm 2" < "Arm 10"). NA is not a level.

Usage

natural_levels(x)

Arguments

x

A character vector.

Value

Character vector of levels in natural order.

Plot a summaryByVisit table

Description

Plots one variable of a table produced by summaryByVisit() over the visits, using the numbers printed in the table rather than the raw data. Continuous variables are drawn as a line plot of the point estimate with its interval (see lineplotSCI()), categorical variables as stacked bars (see stackedbarplotSCI()).

Usage

plotByVisit(
  tbl,
  var = NULL,
  stat_cont = NULL,
  missing = FALSE,
  missing_text = "Missing",
  ...
)

Arguments

tbl

A table returned by summaryByVisit() with as_flex_table = FALSE (the default TRUE returns a flextable, from which the numbers cannot be read back).

var

The variable to be plotted, given as its label in the table (the bold header row, e.g. "Hemoglobin") or its position among the variables of the table. May be omitted if the table holds a single variable.

stat_cont

The statistic of continuous variables, as passed to summaryByVisit(). Default is NULL, which reads it from the table footnote; if the footnote is not recognised, plotByVisit() stops and asks for stat_cont rather than guess. A stat_cont that does not fit the printed cells (e.g. "mean_sd" for a median (range) table) is an error too.

missing

A logical toggle switch adding the missing-value rows of a categorical variable as a segment of their own. Default is FALSE, which leaves them out, so that percentages are relative to the non-missing observations.

missing_text

The label of the missing-value rows in the table, as passed to summaryByVisit(). Default is "Missing".

...

Further arguments controlling the appearance of the plot, as documented in lineplotSCI() (continuous variables; e.g. interval_type, risk_table, col, legend_position) or stackedbarplotSCI() (categorical variables; e.g. scale, percent_labels, risk_table). For continuous variables, xs sets the positions of the visits on the x-axis (one number per visit, e.g. the study days); by default they are evenly spaced.

Details

The statistic of continuous variables is read from the table footnote and determines the error bars:

"median_range": median with whiskers from minimum to maximum;
"median_IQR": median with whiskers from the first to the third quartile;
"mean_sd" / "mean_se": mean +/- one standard deviation / standard error;
"geomMean_sd": geometric mean divided and multiplied by the geometric standard deviation.

Since the numbers are read from the printed table, they carry its rounding (digits_cont / digits_cat). Visits appear on the x-axis in the order of the table rows.

Value

Invisibly, a list with

type: "continuous" or "categorical";
summary: the rows of tidySummaryByVisit() belonging to var;
for continuous variables, the group-by-visit matrices centre, lower, upper and n;
for categorical variables, the arrays counts and percent indexed by level, group and visit, and the group-by-visit matrix n of denominators.

Examples

library(summarySCI)
data("hemoglobin_data")
hb <- subset(hemoglobin_data, visit_nr <= 3)   # first 3 cycles, to keep it short
attr(hb$hb, "label") <- "Hemoglobin"           # subset() drops the label
tbl <- summaryByVisit(hb, vars = "hb",
                      group = "Arm", visit = "visit", stat_cont = "median_IQR",
                      as_flex_table = FALSE)
plotByVisit(tbl, var = "Hemoglobin", risk_table = TRUE)


# a categorical variable
hb$hb_cat <- cut(hb$hb, c(-Inf, 120, 140, Inf),
                 labels = c("< 120", "120-140", "> 140"))
tbl <- summaryByVisit(hb, vars = c("hb", "hb_cat"),
                      group = "Arm", visit = "visit", stat_cont = "median_IQR",
                      as_flex_table = FALSE)
plotByVisit(tbl, var = "hb_cat", legend_title = "Hemoglobin")

One row of patient numbers beneath the x-axis

Description

Draws the numbers n at the x positions at on margin line line, zero counts shown as missing_nr, and optionally the row label "# <label>" left of the plot, as in boxplotSCI().

Usage

risk_row(n, line, at, label = NULL, label_at = NULL, cex = 0.7, missing_nr = 0)

Arguments

n

Numbers of patients.

line

Margin line of the row.

at

x positions of the numbers.

label

Group label of the row, or NULL for none.

label_at

x position of the right end of the label.

cex

Font size.

missing_nr

Shown instead of zero counts.

Save a plot to a file

Description

Draws a plot of summarizeSCI() into a file. The format follows the file extension: .png, .jpeg/.jpg, .tiff, .pdf or .svg.

Usage

save_plot(x, file, width = 8, height = 5, res = 300)

Arguments

x

A sci_plot object, e.g. res$plots$hb.

file

Path of the file to write.

width, height

Size of the plot in inches. Default is 8 by 5.

res

Resolution in dots per inch, for the pixel formats. Default is 300.

Value

The path of the file, invisibly.

Save plots to files

Description

Writes the plots of a summarizeSCI() or summarizeByVisitSCI() result, or a single plot such as res$plots$hb, each into its own file.

Usage

save_plots(
  x,
  file_name = NULL,
  file_path = ".",
  format = "png",
  width = 8,
  height = 5,
  res = 300
)

Arguments

x

The result of summarizeSCI() or summarizeByVisitSCI() (made with type = "both" or "plot"), or a single plot, e.g. res$plots$hb.

file_name

Name(s) of the files, without extension. Either one name per plot, or a single name that prefixes the variable names when x holds several plots (e.g. "fig" gives fig_hb.png, fig_hb_cat.png). Default is NULL, which names each file after its variable (hb.png).

file_path

Folder to write the files into. Created if it does not exist. Default is the working directory.

format

File format: "png" (the default), "jpeg", "tiff", "pdf" or "svg".

width, height

Size of the plot in inches. Default is 8 by 5.

res

Resolution in dots per inch, for the pixel formats. Default is 300.

Value

The paths of the files, invisibly.

Examples

## Not run: 
save_plots(res)                                   # hb.png, hb_cat.png
save_plots(res, file_name = "fig", file_path = "figures", format = "pdf")
save_plots(res$plots$hb, file_name = "hemoglobin")  # hemoglobin.png

## End(Not run)

Save a flextable to a Word document

Description

What summaryTable(), summaryByVisit() and the wrappers do with word_output = TRUE.

Usage

save_word(ft, file_path)

Arguments

ft

A flextable.

file_path

Path of the .docx file.

Value

file_path, invisibly.

Layout of the plots

Description

Margins, lines of the patient numbers and of the x-axis title shared by boxplotSCI(), lineplotSCI() and stackedbarplotSCI(), so that plots used together line up. The blueprint is the layout of boxplotSCI().

Usage

sci_layout(n_time, n_groups, risk_table, offset = 0, footnote = FALSE)

Arguments

n_time

Number of time points; 1 for a single time point.

n_groups

Number of groups.

risk_table

Logical. Are patient numbers drawn beneath the x-axis?

offset

Lines taken by extra labels beneath the x-axis (e.g. group labels under bars, or rotated labels), by which the numbers and the x-axis title move down.

footnote

Logical. Is a footnote on the statistic drawn beneath the x-axis title? It adds the same space to every plot type.

Value

A list with mar (for par(mar = )), rows (margin lines of the rows of patient numbers, one per group over time, one for a single time point), xlab_line and note_line (the line of the footnote).

SCI color palette

Description

The default colors of all plotting functions of the package.

Usage

sci_palette(n, lines = FALSE, bars = FALSE)

Arguments

n

Number of colors.

lines

Logical. If TRUE, only the darker shades are used, since the light ones are hard to see as lines and points on a white background. Default is FALSE, for filled boxes.

bars

Logical. If TRUE, the palette of the stacked bars: the lightest shade is left out, as it is hard to tell from the white background. Default is FALSE.

Value

A character vector of n hex colors, light to dark.

Plot objects

Description

The plotting functions of the package draw with base R graphics, which produce no object to keep. The wrappers summarizeSCI() therefore store each plot as a sci_plot: the instructions to draw it, together with the numbers it shows. Printing a sci_plot draws it on the current device, and save_plot() draws it into a file of the requested size, so that the layout is always worked out for the size it is drawn at.

Usage

## S3 method for class 'sci_plot'
print(x, ...)

## S3 method for class 'sci_plot'
plot(x, ...)

Arguments

x

A sci_plot object.

...

Ignored.

Value

print() and plot() return x invisibly.

Standard error

Description

This function return the standard error

Usage

se(x)

Arguments

x

Numeric vector

Value

standard error

Draw a stacked barplot from pre-computed counts

Description

Drawing back end shared by stackedbarplotSCI(), which counts raw data, and plotByVisit(), which reads the counts off a summaryByVisit() table.

Usage

stackedbar_draw(
  counts,
  n,
  visit = dimnames(counts)[[3]],
  group_names = NULL,
  group_names_short = NULL,
  scale = "percent",
  main = "",
  xlab = NULL,
  ylab = NULL,
  ylim = NULL,
  y_ticks = NULL,
  col = NULL,
  greyscale = FALSE,
  percent_labels = TRUE,
  col_percent = NULL,
  cex_percent = NULL,
  digits = 0,
  bar_width = NULL,
  cex_lab = 1,
  cex_axis = 1,
  cex_n_patients = 0.7,
  cex_groups = NULL,
  missing_seg = NULL,
  risk_table = FALSE,
  missing_nr = 0,
  rotate_labels = FALSE,
  mar_custom = NULL,
  xlab_line = NULL,
  ylab_line = 3,
  xlab_position = NULL,
  legend_position = "top",
  legend_title = NULL,
  legend_offset = c(0, 0),
  legend_cex = 1,
  legend_bty = "n",
  stat_footnote = NULL,
  ...
)

Arguments

counts

Numeric array of counts indexed by segment, group and time point, with dimnames.

n

Numeric group-by-time matrix of denominators for the percentages.

visit

Character vector of labels for the time points, one per column of the third dimension of counts.

group_names

A character vector containing the names of the groups to be displayed on the x-axis. The order must match levels(factor(data$group)). Default is NULL, which falls back to the group names found in the data.

group_names_short

A character vector containing short names or abbreviations for the groups, displayed beneath the bars and in the table of patient numbers. Optional. Defaults to group_names.

scale

The quantity on the y-axis. Either "percent" (the default) or "count".

main

Title of the plot. Defaults to "" (no title).

xlab

A label for the x-axis. Default is NULL, which uses "Time" if there are several time points, otherwise "Group".

ylab

A label for the y-axis. Default is NULL, which uses "Percentage of patients" or "Number of patients" depending on scale.

ylim

The y-axis limits of the plot as a numeric vector of length 2. Default is NULL, which spans 0 to 100 for percentages (more if the stacks exceed 100%) and 0 to the tallest stack for counts.

y_ticks

A numeric vector specifying the explicit tick positions on the y-axis. Default is NULL, which falls back to automatic tick placement.

col

A character vector of hex colors or color names to use for the stacked segments, bottom to top. Recycled if shorter than the number of segments. The missing-value segment (see missing) is always hatched and takes no color. Default is NULL, which applies the SCI color palette without its lightest shade.

greyscale

A logical toggle switch replacing the color palette by a sequential grey ramp, for print or black-and-white reproduction. Default is FALSE. Ignored if col is supplied.

percent_labels

A logical toggle switch enabling the percentage labels printed inside the segments. Default is TRUE. Empty segments, and segments too thin to hold a label, are left unlabelled.

col_percent

A character value giving the color of the percentage labels. Default is NULL, which picks black or white per segment, whichever contrasts better with the fill.

cex_percent

A numeric value specifying the font size of the percentage labels. Default is NULL, which sizes them to fit the width of the bars (at most 0.8). A number is used as given, even if labels then overflow narrow bars.

digits

A numeric value indicating the number of decimal places shown in the percentage labels. Default is 0.

bar_width

A numeric value giving the width of each bar in x-axis units. Default is NULL, which fills about 70% of each time point with the cluster of group bars.

cex_lab

A numeric value specifying the font size of the main axis labels. Default is 1.

cex_axis

A numeric value specifying the font size of the axis tick marks. Default is 1.

cex_n_patients

A numeric value specifying the font size of the table of patient numbers. Default is 0.7.

cex_groups

A numeric value specifying the font size of the group labels beneath the bars (several groups over time). Default is NULL, which uses cex_n_patients and shrinks the labels until they fit the bars. A number is used as given, even if long labels then overlap.

missing_seg

Index of the segment holding the missing values, drawn hatched instead of coloured. Default is NULL (none).

risk_table

A logical toggle switch enabling the table of patient numbers (the denominator of each bar) beneath the x-axis. Default is FALSE.

missing_nr

A numeric or character value indicating how zero-count patient sizes on the x-axis should be displayed. Default is 0. Can also be set to NA, which leaves the cell blank.

rotate_labels

A logical toggle switch rotating the x-axis tick labels by 90 degrees. Default is FALSE.

mar_custom

A numeric vector indicating the plot margins to be used in the form c(bottom, left, top, right). Default is NULL, which dynamically calculates spacing for the labels, the table of patient numbers and the legend.

xlab_line

A numeric value indicating the margin line offset for the x-axis label. Default is NULL, which calculates an adaptive offset.

ylab_line

A numeric value indicating the margin line offset for the y-axis label. Default is 3.0.

xlab_position

Horizontal position of the row labels of the table of patient numbers. Default is NULL, which aligns them just outside the plot region.

legend_position

Position of the legend box. "top" (the default) places it in one row above the bars, which keeps their full width; "right" places it outside the plot region to the right of the bars; "none" or NULL suppresses it. Other base R keywords (e.g., "topright") place it inside the plot region, and a numeric pair c(x, y) gives explicit coordinates. The margins are sized to the legend text.

legend_title

Title of the legend box. Default is NULL (no title).

legend_offset

A numeric vector of length 2 specifying an inset to nudge a keyword-placed legend. Default is c(0, 0).

legend_cex

A numeric value specifying the font and element scaling size inside the legend box. Default is 1.

legend_bty

The type of box border to be drawn around the legend. Allowed values are "n" (no border, the default) and "o" (standard box frame).

stat_footnote

The text of the footnote in the bottom-right corner, or NULL for none (the callers turn TRUE into their default text).

...

Further graphical parameters passed on to plot().

Value

Invisibly, a list with counts, n and percent.

Stacked barplot over time

Description

Generates stacked barplots of a categorical variable over time for one or multiple sub-groups. Each bar shows the distribution of the levels of var at one time point in one group, optionally with the percentages printed inside the segments and a table of patient numbers beneath the horizontal axis.

Usage

stackedbarplotSCI(
  data,
  var,
  order = NULL,
  visit = NULL,
  group = NULL,
  id = NULL,
  group_names = NULL,
  group_names_short = NULL,
  level_names = NULL,
  scale = c("percent", "count"),
  missing = FALSE,
  missing_text = "Missing",
  main = "",
  xlab = NULL,
  ylab = NULL,
  ylim = NULL,
  y_ticks = NULL,
  col = NULL,
  greyscale = FALSE,
  percent_labels = TRUE,
  col_percent = NULL,
  cex_percent = NULL,
  digits = 0,
  bar_width = NULL,
  cex_lab = 1,
  cex_axis = 1,
  cex_n_patients = 0.7,
  cex_groups = NULL,
  risk_table = FALSE,
  missing_nr = 0,
  rotate_labels = FALSE,
  mar_custom = NULL,
  xlab_line = NULL,
  ylab_line = 3,
  xlab_position = NULL,
  legend_position = "top",
  legend_title = NULL,
  legend_offset = c(0, 0),
  legend_cex = 1,
  legend_bty = "n",
  stat_footnote = FALSE,
  ...
)

Arguments

data

A data frame or tibble containing the data to be plotted.

var

Name of the column(s) in data to be stacked. A single column supports bare or quoted names; several columns are given as a character vector.

order

Name of the column in data containing the time points of interest. Numeric time points are sorted numerically; factors keep their level order; character values are sorted by the number they contain (e.g. "Visit 2" before "Visit 10"), or by order of appearance if they contain none. If left empty, a single time point is assumed and one bar is drawn per group. Rows with a missing time point are dropped.

visit

Name of the column in data containing descriptive labels for the time points (the first label observed at each time point is used). Optional.

group

Name of the column in data containing the grouping variable (e.g., treatment arms). If left empty, a single group is assumed. Rows with a missing group are dropped.

id

Name of the column in data identifying the patient. Only used when var names several Yes/No columns, as the denominator of the percentages. Default is NULL, which counts rows instead.

group_names

group_names_short

A character vector containing short names or abbreviations for the groups, displayed beneath the bars and in the table of patient numbers. Optional. Defaults to group_names.

level_names

A character vector containing the names of the stacked segments to be displayed in the legend. The order must match the levels of var (or the columns in var). Default is NULL, which uses the levels (or column names) themselves.

scale

The quantity on the y-axis. Either "percent" (the default) or "count".

missing

A logical toggle switch adding missing values of var as a segment of their own, on top of the stack, hatched in grey on white rather than coloured. Default is FALSE, which drops them. Only used when var is a single column.

missing_text

Legend text for the missing-value segment. Default is "Missing".

main

Title of the plot. Defaults to "" (no title).

xlab

A label for the x-axis. Default is NULL, which uses "Time" if there are several time points, otherwise "Group".

ylab

A label for the y-axis. Default is NULL, which uses "Percentage of patients" or "Number of patients" depending on scale.

ylim

The y-axis limits of the plot as a numeric vector of length 2. Default is NULL, which spans 0 to 100 for percentages (more if the stacks exceed 100%) and 0 to the tallest stack for counts.

y_ticks

A numeric vector specifying the explicit tick positions on the y-axis. Default is NULL, which falls back to automatic tick placement.

col

greyscale

A logical toggle switch replacing the color palette by a sequential grey ramp, for print or black-and-white reproduction. Default is FALSE. Ignored if col is supplied.

percent_labels

A logical toggle switch enabling the percentage labels printed inside the segments. Default is TRUE. Empty segments, and segments too thin to hold a label, are left unlabelled.

col_percent

A character value giving the color of the percentage labels. Default is NULL, which picks black or white per segment, whichever contrasts better with the fill.

cex_percent

digits

A numeric value indicating the number of decimal places shown in the percentage labels. Default is 0.

bar_width

A numeric value giving the width of each bar in x-axis units. Default is NULL, which fills about 70% of each time point with the cluster of group bars.

cex_lab

A numeric value specifying the font size of the main axis labels. Default is 1.

cex_axis

A numeric value specifying the font size of the axis tick marks. Default is 1.

cex_n_patients

A numeric value specifying the font size of the table of patient numbers. Default is 0.7.

cex_groups

risk_table

A logical toggle switch enabling the table of patient numbers (the denominator of each bar) beneath the x-axis. Default is FALSE.

missing_nr

A numeric or character value indicating how zero-count patient sizes on the x-axis should be displayed. Default is 0. Can also be set to NA, which leaves the cell blank.

rotate_labels

A logical toggle switch rotating the x-axis tick labels by 90 degrees. Default is FALSE.

mar_custom

xlab_line

A numeric value indicating the margin line offset for the x-axis label. Default is NULL, which calculates an adaptive offset.

ylab_line

A numeric value indicating the margin line offset for the y-axis label. Default is 3.0.

xlab_position

Horizontal position of the row labels of the table of patient numbers. Default is NULL, which aligns them just outside the plot region.

legend_position

legend_title

Title of the legend box. Default is NULL (no title).

legend_offset

A numeric vector of length 2 specifying an inset to nudge a keyword-placed legend. Default is c(0, 0).

legend_cex

A numeric value specifying the font and element scaling size inside the legend box. Default is 1.

legend_bty

The type of box border to be drawn around the legend. Allowed values are "n" (no border, the default) and "o" (standard box frame).

stat_footnote

Show what the bars display as a footnote in the bottom-right corner, beneath the x-axis title: TRUE for the default text (e.g. "\% of patients with a non-missing value"), a character string for a text of your own, or FALSE (the default) for none.

...

Further graphical parameters passed on to plot().

Details

Two layouts of the data are supported:

var names one categorical column (long format): its levels are stacked, and percentages are relative to the number of non-missing observations in the bar (or all observations if missing = TRUE).
var names several columns coded "Yes" / "No" (wide format, e.g. one column per adverse event): each column becomes one segment holding the number of "Yes" answers, and percentages are relative to the number of patients in the bar (id, or rows if id is NULL). Missing values count as "No". Since a patient may answer "Yes" to several columns, the segments can add up to more than 100%.

Value

Invisibly, a list with counts and percent, arrays indexed by segment, group and time point, and n, the group-by-time matrix of denominators.

Examples

library(summarySCI)
data("hemoglobin_data")
hemoglobin_data$hb_cat <- cut(hemoglobin_data$hb, c(-Inf, 120, 140, Inf),
                              labels = c("< 120", "120-140", "> 140"))
stackedbarplotSCI(data = hemoglobin_data,
                  var = hb_cat,
                  order = visit_nr,
                  visit = visit,
                  group = Arm,
                  group_names_short = c("A", "B"),
                  legend_title = "Hemoglobin",
                  risk_table = TRUE)

# Several Yes/No columns, one bar per arm
set.seed(14)
ae <- data.frame(id = 1:50,
                 arm = sample(c("Arm A", "Arm B"), 50, replace = TRUE),
                 fatigue = sample(c("Yes", "No"), 50, replace = TRUE),
                 nausea  = sample(c("Yes", "No"), 50, replace = TRUE))
stackedbarplotSCI(ae, var = c("fatigue", "nausea"), group = arm, id = id,
                  scale = "count", legend_title = "Adverse events")

Summarize data by visit as a table and plots

Description

Produces the table of summaryByVisit() and one plot per variable (or either of them alone, see type), the plots over the visits: a line plot or boxplots (boxplotSCI()) for continuous variables, and stacked barplots for categorical ones. The type of each plot follows the type the variable has in the table.

Usage

summarizeByVisitSCI(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  stat_cat = "n_percent",
  visit = "visit",
  order = NULL,
  visitgroup = NULL,
  missing = TRUE,
  missing_percent = TRUE,
  missing_text = "Missing",
  continuous_as_categorical = NULL,
  type = c("both", "table", "plot"),
  plot_cont = c("lineplot", "boxplot"),
  plot_args = list(),
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryByVisit_", format(Sys.Date(), "%Y%m%d"), ".docx"),
  ...
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Variables to include in the summary table. Need to be specified with quotes, e.g. "age" or c("age", "response"). Default to all variables present in the data except group.

group

A single column from data. Need to be specified with quotes, e.g. "treatment". Summary statistics will be stratified according to this variable. Default to NULL. A maximum of 3 groups are currently supported. Character variables and a character group are shown in natural order (e.g. "2" before "10"); factors keep their level order.

labels

A list containing the labels that should be used for the variables in the table, either named by variable (e.g. list(age = "Age (years)")) or unnamed in the order of vars. If NULL, labels are automatically taken from the dataset. If no label present, the variable name is taken.

stat_cont

Summary statistic to display for continuous variables. Options include "median_IQR", "median_range" (default), "mean_sd", "mean_se" and "geomMean_sd".

stat_cat

Summary statistic to display for categorical variables. Options include "n", "n_N" and "n_percent" (default).

visit

Name of the stratum for which summary statistics are displayed by line. Typically, this would be "visit".

order

A numerical variable defining the visit order. If NULL (default), visits are sorted naturally (e.g. "Visit 2" before "Visit 10"); if visit is a factor, its level order is used instead.

visitgroup

A grouping variable for the stratum for which summary statistics are displayed by line. Must be an ordered factor. Typically, this would be a visit group such as e.g., baseline, follow-up etc.

missing

Logical. If TRUE (default), the missing values are shown (only for categorical variables).

missing_percent

Indicates whether percentages for missings are shown (TRUE, default) or not (FALSE) for categorical variables. If "both", then both options are displayed next to each other.

missing_text

String indicating text shown on missing row. Default to "Missing".

continuous_as_categorical

A subset (vector) of continuous vars to be treated as categrical. Default is NULL.

type

What to produce: "both" (the default) the table and a plot per variable, "table" the table alone, or "plot" the plots alone. The table is built in every case, since it decides the type of each plot.

plot_cont

The plot for continuous variables: "lineplot" (the default) or "boxplot".

plot_args

A named list of further arguments for the plotting functions, e.g. list(risk_table = TRUE, dodge = 0.1). Each plot receives the arguments its function has, as in lineplotSCI(), boxplotSCI() and stackedbarplotSCI(), except those that compute the numbers (such as stat or interval), which come from the table; an argument no plot uses gives a warning. For example, stat_footnote = TRUE adds a footnote saying what each plot shows: for the line plot the statistic of stat_cont (e.g. "Median (Q1, Q3)").

as_flex_table

Logical. If TRUE (default) the gtsummary object is converted to a flextable object. Useful when rendering to Word.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Character string. Specify the path of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx". Default to "SummaryByVisit_YYYYMMDD.docx" (today's date) in the working directory.

...

Further arguments passed on to summaryByVisit(), e.g. digits_cont, add_n or overall.

Details

The line plots and stacked bars are drawn from the numbers printed in the table, as plotByVisit() does, so that they show exactly what the table shows (with its rounding):

stat_cont sets what the line plot shows: "median_range" the median with minimum and maximum, "median_IQR" the median with the quartiles, "mean_sd" / "mean_se" the mean +/- one standard deviation / standard error, and "geomMean_sd" the geometric mean divided and multiplied by the geometric standard deviation;
the variable labels become the axis or legend titles, the column headers the group names, and the N columns the numbers of the risk table;
missing / missing_percent decide whether missing values form a segment of their own (as they are counted in the table's percentages), and stat_cat = "n" shows counts instead of percentages;
continuous_as_categorical variables are plotted as stacked bars, and with overall = TRUE the overall column is plotted as one more group.

Boxplots show more than the table holds, and are drawn from the data: from the rows the table summarizes, with the box at the quartiles of the table (see boxplotSCI()).

The visits appear in the order of the table. If order is given, its values also set the spacing of the visits in the line plots.

Value

An object of class summarizeByVisitSCI (and summarizeSCI), a list with table and plots; see summarizeSCI().

Examples

library(summarySCI)
data("hemoglobin_data")
hb <- subset(hemoglobin_data, visit_nr <= 2)   # first 2 cycles, to keep it short
res <- summarizeByVisitSCI(hb, vars = "hb",
                           group = "Arm", visit = "visit", order = "visit_nr",
                           stat_cont = "median_IQR")
res$plots$hb


# a categorical variable
hb$hb_cat <- cut(hb$hb, c(-Inf, 120, 140, Inf),
                 labels = c("< 120", "120-140", "> 140"))
res <- summarizeByVisitSCI(hb, vars = c("hb", "hb_cat"),
                           group = "Arm", visit = "visit", order = "visit_nr",
                           stat_cont = "median_IQR")
res$plots$hb_cat

Summarize data as a table and plots

Description

Produces the summary table of summaryTable() and one plot per variable, or either of them alone (see type): a boxplot for continuous variables (boxplotSCI()) and a stacked barplot for categorical and dichotomous ones (stackedbarplotSCI()). The type of each plot follows the type the variable has in the table, so that table and plots always agree.

Usage

summarizeSCI(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  stat_cat = "n_percent",
  missing = TRUE,
  missing_percent = TRUE,
  missing_text = "Missing",
  type = c("both", "table", "plot"),
  plot_args = list(),
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryTable_", format(Sys.Date(), "%Y%m%d"), ".docx"),
  ...
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Variables to include in the summary table. Need to be specified with quotes, e.g. "age" or c("age", "response"). Default to all variables present in the data except group.

group

A single column from data. Need to be specified with quotes, e.g. "treatment". Summary statistics will be stratified according to this variable. Default to NULL.

labels

A list containing the labels that should be used for the variables in the table. If NULL, labels are automatically taken from the dataset. If no label present, the variable name is taken.

stat_cont

Summary statistic to display for continuous variables. Options include "median_IQR", "median_range" (default), "mean_sd", "mean_se" and "geomMean_sd". "geomMean_sd" shows the geometric mean with the geometric standard deviation, exp(sd(log(x))), both NA if a value is zero or negative. The geometric SD is a factor close to 1 and is shown with at least 2 decimals.

stat_cat

Summary statistic to display for categorical variables. Options include "n_percent" (default) and "n", and "n_N".

missing

Logical. If TRUE (default), the missing values are shown.

missing_percent

Indicates whether percentages for missings are shown (TRUE, default) or not (FALSE) for categorical variables. If "both", then both options are displayed next to each other.

missing_text

String indicating text shown on missing row. Default to "Missing".

type

plot_args

A named list of further arguments for the plotting functions, e.g. list(risk_table = TRUE, col = c("grey", "black")). Each plot receives the arguments its function has, as in boxplotSCI() and stackedbarplotSCI(); an argument no plot uses gives a warning. For example, stat_footnote = TRUE adds a footnote saying what each plot shows (the box and whiskers, or the denominator of the percentages).

as_flex_table

Logical. If TRUE (default) the gtsummary object is converted to a flextable object. Useful when rendering to Word.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Character string. Specify the path of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx".

...

Further arguments passed on to summaryTable(), e.g. test, ci, overall or digits_cont.

Details

The plots are drawn from the same rows as the table, and the box of the boxplot spans the quartiles as the table computes them (see boxplotSCI()). The settings of the table carry over to the plots: the variable labels become the axis or legend titles, missing / missing_percent decide whether missing values form a segment of their own (as they are counted in the table's percentages), and stat_cat = "n" shows counts instead of percentages. Options that only concern the plots go into plot_args.

Value

An object of class summarizeSCI, a list with

table: the table, a flextable or (with as_flex_table = FALSE) a gtsummary object; NULL with type = "plot". With word_output = TRUE it is also saved to file_path, as summaryTable() does;
plots: a named list with one plot per variable, e.g. res$plots$hb; empty with type = "table". Printing a plot draws it; save_plots() writes them to files.

Printing the result shows the table and lists the plots.

Examples

library(summarySCI)
data("hemoglobin_data")
d <- hemoglobin_data[hemoglobin_data$visit_nr == 2, ]
d$hb_cat <- cut(d$hb, c(-Inf, 120, 140, Inf),
                labels = c("< 120", "120-140", "> 140"))
res <- summarizeSCI(d, vars = c("hb", "hb_cat"), group = "Arm")
res$table
res$plots$hb
res$plots$hb_cat


# the plots alone
plots <- summarizeSCI(d, vars = c("hb", "hb_cat"), group = "Arm",
                      type = "plot")$plots

## Not run: 
save_plots(res, file_name = "fig", file_path = "figures")

## End(Not run)

Creates publication-ready summary tables for data grouped, by visit

Description

Creates publication-ready summary tables for data grouped, by visit

Usage

summaryByVisit(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  stat_cat = "n_percent",
  visit = "visit",
  order = NULL,
  visitgroup = NULL,
  digits_cont = 1,
  digits_cat = 0,
  missing_percent = TRUE,
  missing = TRUE,
  missing_text = "Missing",
  add_n = TRUE,
  overall = FALSE,
  continuous_as_categorical = NULL,
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryByVisit_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Variables to include in the summary table. Need to be specified with quotes, e.g. "age" or c("age", "response"). Default to all variables present in the data except group.

group

labels

stat_cont

Summary statistic to display for continuous variables. Options include "median_IQR", "median_range" (default), "mean_sd", "mean_se" and "geomMean_sd".

stat_cat

Summary statistic to display for categorical variables. Options include "n", "n_N" and "n_percent" (default).

visit

Name of the stratum for which summary statistics are displayed by line. Typically, this would be "visit".

order

A numerical variable defining the visit order. If NULL (default), visits are sorted naturally (e.g. "Visit 2" before "Visit 10"); if visit is a factor, its level order is used instead.

visitgroup

A grouping variable for the stratum for which summary statistics are displayed by line. Must be an ordered factor. Typically, this would be a visit group such as e.g., baseline, follow-up etc.

digits_cont

Digits for summary statistics and CI of continuous variables. Default to 1.

digits_cat

Digits for summary statistics and CI of categorical variables. Default to 0.

missing_percent

Indicates whether percentages for missings are shown (TRUE, default) or not (FALSE) for categorical variables. If "both", then both options are displayed next to each other.

missing

Logical. If TRUE (default), the missing values are shown (only for categorical variables).

missing_text

String indicating text shown on missing row. Default to "Missing".

add_n

Logical. If TRUE, an additional column with the total number of non-missing observations for each variable is added. Default to TRUE.

overall

Logical. If TRUE, an additional column with the total is added to the table. Ignored, if no groups are defined. Default to FALSE.

continuous_as_categorical

A subset (vector) of continuous vars to be treated as categrical. Default is NULL.

as_flex_table

Logical. If TRUE (default) the gtsummary object is converted to a flextable object. Useful when rendering to Word.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Value

A table of class "flextable" or c("tbl_strata_nested_stack", "tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.

Examples

data("hemoglobin_data")
hb <- subset(hemoglobin_data, visit_nr <= 3)   # first 3 cycles, to keep it short

# Hemoglobin by visit and arm, with an overall column
summaryByVisit(data = hb, vars = "hb", visit = "visit",
               group = "Arm", overall = TRUE,
               labels = list(hb = "Hemoglobin (g/L)"))

Creates publication-ready summary tables for categorical data grouped, by visit

Description

Creates publication-ready summary tables for categorical data grouped, by visit

Usage

summaryByVisitCategorical(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cat = "n_percent",
  visit = "visit",
  order = NULL,
  visitgroup = NULL,
  digits_cat = 0,
  missing_percent = TRUE,
  missing = TRUE,
  missing_text = "Missing",
  add_n = TRUE,
  overall = FALSE,
  as_flex_table = FALSE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryByVisit_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Continuous variables to include in the summary table. Need to be specified with quotes, e.g. "grade" or c("grade", "stage"). Default to all variables present in the data except group.

group

labels

A list containing the labels that should be used for the variables in the table. If NULL, labels are automatically taken from the dataset. If no label present, the variable name is taken.

stat_cat

Summary statistic to display for categorical variables. Options include "n", "n_N" and "n_percent" (default).

visit

Name of the stratum for which summary statistics are displayed by line. Typically, this would be "visit".

order

A numerical variable defining the visit order.

visitgroup

A grouping variable for the stratum for which summary statistics are displayed by line. Must be an ordered factor. Typically, this would be a visit group such as e.g., baseline, follow-up etc.

digits_cat

Digits for summary statistics of categorical variables. Default to 0.

missing_percent

Indicates whether percentages for missings are shown (TRUE, default) or not (FALSE) for categorical variables. If "both", then both options are displayed next to each other.

missing

Logical. If TRUE (default), the missing values are shown.

missing_text

String indicating text shown on missing row. Default to "Missing".

add_n

Logical. If TRUE, an additional column with the total number of non-missing observations for each variable is added. Default to TRUE.

overall

Logical. If TRUE, an additional column with the total is added to the table. Ignored, if no groups are defined. Default to FALSE.

as_flex_table

Logical. If TRUE, the gtsummary object is converted to a flextable object. Useful when rendering to Word. Default to FALSE.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Character string. Specify the path of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx".

Value

A table of class "flextable" or c("tbl_strata_nested_stack", "tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.

Creates publication-ready summary tables for continuous data grouped, by visit

Description

Creates publication-ready summary tables for continuous data grouped, by visit

Usage

summaryByVisitContinuous(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  visit = "visit",
  order = NULL,
  visitgroup = NULL,
  digits_cont = 1,
  add_n = TRUE,
  overall = FALSE,
  as_flex_table = FALSE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryByVisit_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Continuous variables to include in the summary table. Need to be specified with quotes, e.g. "age" or c("age", "response"). Default to all variables present in the data except group.

group

labels

A list containing the labels that should be used for the variables in the table. If NULL, labels are automatically taken from the dataset. If no label present, the variable name is taken.

stat_cont

visit

Name of the stratum for which summary statistics are displayed by line. Typically, this would be "visit".

order

A numerical variable defining the visit order.

visitgroup

A grouping variable for the stratum for which summary statistics are displayed by line. Must be an ordered factor. Typically, this would be a visit group such as e.g., baseline, follow-up etc.

digits_cont

Digits for summary statistics and CI of continuous variables. Default to 1.

add_n

Logical. If TRUE, an additional column with the total number of non-missing observations for each variable is added. Default to TRUE.

overall

Logical. If TRUE, an additional column with the total is added to the table. Ignored, if no groups are defined. Default to FALSE.

as_flex_table

Logical. If TRUE, the gtsummary object is converted to a flextable object. Useful when rendering to Word. Default to FALSE.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Character string. Specify the path of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx".

Value

A table of class "flextable" or c("tbl_strata_nested_stack", "tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.

summaryLevels

Description

Collapses factor levels from multiple columns into one and creates summary table.

Usage

summaryLevels(
  data,
  vars = NULL,
  group = NULL,
  label = NULL,
  levels = NULL,
  stat_cat = "n_percent",
  test = FALSE,
  test_cat = "fisher.test",
  ci = FALSE,
  ci_cat = "clopper.pearson",
  conf_level = 0.95,
  digits_cat = 0,
  overall = FALSE,
  add_n = TRUE,
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryLevels_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Variables to include in the summary table. Need to be specified with quotes, e.g. "score" or c("score", "age_cat"). Default to all variables present in the data except group.

group

A single column from data. Need to be specified with quotes, e.g. "treatment". Summary statistics will be stratified according to this variable. Any number of groups (at least two) is possible. Rows with a missing value in group are removed. Default to NULL.

label

A label for the new variable to be created. If no label present, the variable name is taken.

levels

= A vector containing the values indicating presence of the factor level. Included by default are "1", "yes", "Yes". All variables in vars must be binary (e.g. 0/1, yes/no, TRUE/FALSE), unless levels is given; otherwise an error is returned.

stat_cat

Summary statistic to display for categorical variables. Options include "n_percent" (default) and "n", and "n_N".

test

Logical. Indicates whether p-values are displayed (TRUE) or not (FALSE). Default to FALSE

test_cat

Test type used to calculated the p-value for categorical variables. Only used if test = TRUE. Options include "fisher.test" (default), "chisq.test", "chisq.test.no.correct". If NULL, the function decides itself: "chisq.test.no.correct" for categorical variables with all expected cell counts >=5, and "fisher.test" for categorical variables with any expected cell count <5.

ci

Logical. Indicates whether CI are displayed (TRUE) or not (FALSE). Default to FALSE.

ci_cat

Confidence interval method for categorical variables. Options include "clopper.pearson" (default), "wilson", "wilson.no.correct", "wald", "wald.no.correct", "agresti.coull" and "jeffreys". If NULL, no CI will be displayed.

conf_level

Numeric. Confidence level. Default to 0.95.

digits_cat

Numeric. Digits for summary statistics and CI of categorical variables. Default to 0.

overall

Logical. If TRUE, an additional column with the total is added at the end of the table. Default to FALSE.

add_n

Logical. If TRUE (default), a column with the number of patients is added before each group column (and before the Overall column). As missing values are treated as absent, N is the number of patients in each group.

as_flex_table

Logical. If TRUE (default) the gtsummary object is converted to a flextable object. Useful when rendering to Word.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Character string. Specify the path of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx".

Value

A table of class "flextable" or c("tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.

Examples

# Site of progression: one column per site, more than one site possible
progression <- data.frame(
  arm   = rep(c("A", "B"), each = 5),
  liver = c("absent", "present", "absent", "present", "absent",
            "absent", "present", "absent", "present", "absent"),
  lung  = c("absent", "absent", "present", "absent", "absent",
            "absent", "absent", "absent", "absent", "absent"),
  brain = c("present", "absent", "present", "present", "present",
            "present", "present", "present", "present", "present")
)

summaryLevels(data = progression,
              vars = c("liver", "lung", "brain"),
              label = "Site of progression",
              levels = "present")

# By arm, with an overall column
summaryLevels(data = progression,
              vars = c("liver", "lung", "brain"),
              group = "arm",
              overall = TRUE,
              label = "Site of progression",
              levels = "present")

Creates publication-ready summary tables

Description

Creates publication-ready summary tables based on the gtsummary package.

Usage

summaryTable(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  stat_cat = "n_percent",
  continuous_as = "continuous",
  dichotomous_as = "dichotomous",
  continuous_as_categorical = NULL,
  dichotomous_as_categorical = NULL,
  ref_level = NULL,
  test = FALSE,
  test_cont = NULL,
  test_cat = "fisher.test",
  ci = FALSE,
  ci_cont = "wilcox.test",
  ci_cat = "clopper.pearson",
  conf_level = 0.95,
  digits_cont = 1,
  digits_cat = 0,
  missing = TRUE,
  missing_percent = TRUE,
  missing_text = "Missing",
  overall = FALSE,
  add_n = TRUE,
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryTable_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Variables to include in the summary table. Need to be specified with quotes, e.g. "age" or c("age", "response"). Default to all variables present in the data except group.

group

A single column from data. Need to be specified with quotes, e.g. "treatment". Summary statistics will be stratified according to this variable. Default to NULL.

labels

A list containing the labels that should be used for the variables in the table. If NULL, labels are automatically taken from the dataset. If no label present, the variable name is taken.

stat_cont

stat_cat

Summary statistic to display for categorical variables. Options include "n_percent" (default) and "n", and "n_N".

continuous_as

Type for all the continuous variables. Can either be "continuous" (default) or "categorical".

dichotomous_as

Type for the dichotomous variables. Can either be "categorical" (one row per level) or "dichotomous" (only one row with reference level (see argument ref_level), only works if the variable does not contain missing values, or if missing = "FALSE" or missing_percent = FALSE.

continuous_as_categorical

A subset (vector) of continuous vars to be treated as categorical. Default is NULL.

dichotomous_as_categorical

A subset (vector) of dichotomous vars to be treated as categorical. Default is NULL.

ref_level

Specifies the reference level of a variable to display on a single row. Default is the first appearing level. The syntax is as follows: ref_level = list(varname ~ "level to show").

test

Logical. Indicates whether p-values are displayed (TRUE) or not (FALSE). Default to FALSE

test_cont

Test type used to calculate the p-value for continuous variables. Only used if test = TRUE. Options include "t.test", "oneway.test", "kruskal.test" (default for more than two groups), "wilcox.test" (default for two groups).

test_cat

Test type used to calculated the p-value for categorical variables. Only used if test = TRUE. Options include "fisher.test" (default), "chisq.test", "chisq.test.no.correct". For "fisher.test", if the exact algorithm runs out of workspace (FEXACT error, e.g. for variables with many levels), the workspace is increased and, if still insufficient, a Monte Carlo p-value (B = 100,000) is reported instead; this is indicated in the table footnote. It varies slightly between runs unless set.seed() is called before. If NULL, the function decides itself: "chisq.test.no.correct" for categorical variables with all expected cell counts >=5, and "fisher.test" for categorical variables with any expected cell count <5.

ci

Logical. Indicates whether CI are displayed (TRUE) or not (FALSE). Default to FALSE.

ci_cont

Confidence interval method for continuous variables. Only used if ci = TRUE. Options include "t.test" and "wilcox.test" (default).

ci_cat

Confidence interval method for categorical variables. Options include "clopper.pearson" (default) "wilson", "wilson.no.correct", "wald", "wald.no.correct", "agresti.coull" and "jeffreys". If NULL, no CI will be displayed.

conf_level

Numeric. Confidence level. Default to 0.95.

digits_cont

Numeric. Digits for summary statistics and CI of continuous variables. Default to 1.

digits_cat

Numeric. Digits for summary statistics and CI of categorical variables. Default to 0.

missing

Logical. If TRUE (default), the missing values are shown.

missing_percent

Indicates whether percentages for missings are shown (TRUE, default) or not (FALSE) for categorical variables. If "both", then both options are displayed next to each other.

missing_text

String indicating text shown on missing row. Default to "Missing".

overall

Logical. If TRUE, an additional column with the total is added to the table. Default to FALSE.

add_n

Logical. If TRUE (default), an additional column with the total number of non-missing observations for each variable is added.

as_flex_table

Logical. If TRUE (default) the gtsummary object is converted to a flextable object. Useful when rendering to Word.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_path

Character string. Specify the path of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx".

Details

Character variables (and a character group) are converted to factors with natural level order: values starting with a number are sorted numerically (e.g. "3", "10", "more than 10"), other values alphabetically with embedded numbers compared numerically (e.g. "Arm 2" before "Arm 10"). To control the order fully, supply a factor with the desired levels.

Value

A table of class "flextable" or c("tbl_summary", "gtsummary"). Optionally returns a .docx file in the specified folder.

Examples


library(survival)
data("cancer")
summaryTable(data = cancer,vars = c("inst", "time","age", "ph.ecog"),
             labels = list(inst = "Institution code",
                           time = "Time",
                           age = "Age",
                           ph.ecog = "ECOG score"))

Read the numbers off a summaryByVisit table

Description

Converts a table produced by summaryByVisit() into a data frame with one row per variable, visit, group and (for categorical variables) level, holding the parsed numbers. This is the parser behind plotByVisit().

Usage

tidySummaryByVisit(tbl, stat_cont = NULL)

Arguments

tbl

A table returned by summaryByVisit() with as_flex_table = FALSE (the default TRUE returns a flextable, from which the numbers cannot be read back).

stat_cont

Value

A data frame with columns variable (the label of the header row), var_type, visitgroup, visit, visit_id (position of the visit within the variable), group, level (NA for continuous variables), stat (the cell as printed), n (the number of non-missing observations shown in the table's N column), and the parsed numbers centre, lower, upper (continuous) and count (categorical).

Convert a gtsummary table to a flextable

Description

The conversion summaryTable() applies when as_flex_table = TRUE: a flextable fitted to the page width, with an outer border if requested.

Usage

to_flextable(tbl, border = TRUE)

Arguments

tbl

A gtsummary table.

border

Logical. Draw a border around header and body.

Value

A flextable.

Package {summarySCI}

Convert a character vector to a factor with natural level order

Description

Usage

Arguments

Value

Boxplot over time

Description

Usage

Arguments

Details

Examples

Digits for the categorical statistics

Description

Usage

Arguments

Value

Resolve a column-name argument

Description

Usage

Arguments

Value

Digits for the continuous statistics

Description

Usage

Arguments

Value

Robust Fisher's exact test for gtsummary::add_p()

Description

Usage

Arguments

Value

Geometric mean

Description

Usage

Arguments

Value

Geometric standard deviation

Description

Usage

Arguments

Value

Get the labels from a dataset

Description

Usage

Arguments

Value

Hemoglobin data (to illustrate boxplotSCI() and summaryByVisit())

Description

Usage

Format

hemoglobin_data

Source

Line plot of a summary statistic over time, by group

Description

Usage

Arguments

Value

Draw a line plot from pre-computed group-by-time summaries

Description

Usage

Arguments

Value

Natural ordering of levels for character variables

Description

Usage

Arguments

Value

Plot a summaryByVisit table

Description

Usage

Arguments

Details

Value

Examples

One row of patient numbers beneath the x-axis

Description

Usage

Arguments

Save a plot to a file

Hemoglobin data (to illustrate `boxplotSCI()` and `summaryByVisit()`)

`hemoglobin_data`