doCohortCharacteristics: Generate cohort characteristics

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

Generate cohort characteristics

Description

Generate cohort characteristics

Usage

doCohortCharacteristics(
  input.d,
  marker.name,
  marker.description,
  var.names,
  is.var.continuous,
  var.descriptions,
  marker.value.labels.tolower = TRUE,
  show.missing = TRUE,
  show.missing.continuous = TRUE,
  do.droplevels = TRUE,
  show.percent = "both",
  stat.tests = NULL,
  chisq.test.simulate.p.value = FALSE,
  stat.test.column.header = "association/correlation test",
  show.test.name = TRUE,
  round.digits.p.value = 4,
  num.boot = 1000,
  missing.codes.highlight = NULL,
  missing.codes = c("N/A", "", "Unk"),
  decimal = 0,
  caption = NA,
  html.table.border = 0,
  banded.rows = FALSE,
  css.class.name.odd = "odd",
  css.class.name.even = "even",
  custom.marker.labels = NULL,
  custom.total.label = NULL,
  split.table = 200,
  ...
)

Arguments

input.d	The data.frame containing the data
marker.name	The variable that you want to split into different columns
marker.description	The description for the variable(s) to split
var.names	The variables that you want the statistics for
is.var.continuous	Vector of length equal to the length of var.names with 1 indicating a continuous variable and 0 otherwise (this should be inferred in the function)
var.descriptions	Vector of strings to describe the variables as they are to appear in the table
marker.value.labels.tolower	Indicator as to whether to put marker value labels to lower case
show.missing	an indicator to whether to show missing values
show.missing.continuous	if set to FALSE and show.missing == FALSE, will not show the number of missing cases for continuous variables. Otherwise, it shows the number of missing for continuous variables even if show.missing == FALSE.
do.droplevels	drop categories of unobserved levels set to TRUE
show.percent	defaults to "both" which shows both rows and columns other possible values: "column", "row".
stat.tests	statistical test to perform. NULL indicates do not do test for all variables, NA indicates do not do test for specified variable. Tests: chisq, fisher, ttest, wilcox, kendall, spearman, pearson, kruskal, confusionMarkerAsRef, confusionVarAsRef
chisq.test.simulate.p.value	Whether to simulate p-value for chi-square test. this parameter is ignored if chi-square is not used. Default value=FALSE
stat.test.column.header	The name to show on the header defaults to "association/correlation test"
show.test.name	logical; if TRUE (default), the name of each test is prepended to the p-value
round.digits.p.value	The number of digits to round the P values
num.boot	the number of bootstrap samples for any bootstrap method that may be used
missing.codes.highlight	default to NULL this indicates whether we wanted the missing values broken down down or lumped together.
missing.codes	a vector to indicate how missing values are coded, default is c("N/A", "", "Unk")
decimal	number of decimal places to show for aggregate numbers such as proportions or averages; default to 0
caption	caption to use for the Table
html.table.border	the border type to use for html tables
banded.rows	If TRUE, rows have alternating shading colour
css.class.name.odd	Used to set the row colour for odd rows
css.class.name.even	Used to set the row colour for even rows
custom.marker.labels	labels of marker to show; default NULL means using existing value label of the marker
custom.total.label	label of the "Total" column; default NULL means show "Total"
split.table	number of chars per row before table is split.
...	additional arguments to pander

Value

A table with statistics reported for multiple variables, such as mean, median, and range for continuous variables and proportions and percentages for categorical variables. Relevant association and correlation tests are performed as well.

Author(s)

Aline Talhouk

Examples

dcc <- doCohortCharacteristics( input.d = mtcars, marker.name = "cyl",
marker.description = "cylinders", var.names = c("disp", "hp"),
var.descriptions = c("displacement", "horsepower"), is.var.continuous =
c(TRUE, TRUE), caption = "Some mtcars summaries")
htmlTable::htmlTable(dcc$result.table.html)

TalhoukLab/biostatUtil documentation built on April 14, 2025, 4:15 a.m.