R: Create Table One Describing Baseline Characteristics

TOne {DescTools}

R Documentation

Create Table One Describing Baseline Characteristics

Description

Create a table summarizing continuous, categorical and dichotomous variables, optionally stratified by one or more variables, while performing adequate statistical tests.

Usage

TOne(x, grp = NA, add.length = TRUE, colnames = NULL, vnames = NULL, total = TRUE,
     align = "\\l", FUN = NULL, NUMTEST = NULL, numtestlab = NULL, intref = "high")

Arguments

`x`	a data.frame containing all the variables to be included in the table.
`grp`	the grouping variable.
`add.length`	logical. If set to `TRUE` (default), a row with the lengths of the group will be inserted as first row of the table.
`colnames`	a vector of columnnames for the result table.
`vnames`	a vector of variablenames to be placed in the first column instead of the real names.
`total`	logical, `TRUE` if totals should be added.
`align`	the character on whose position the strings will be aligned. Left alignment can be requested by setting `sep = "\\l"`, right alignment by `"\\r"` and center alignment by `"\\c"`. Mind the backslashes, as if they are omitted, strings would be aligned to the character l, r or c respectively. Default value is `"\\l"`, thus left alignment.
`FUN`	the function to be used as location and dispersion measure (typically `mean`/`sd` or alternatively `median`/`IQR`). See examples.
`NUMTEST`	the function to be used to compare location (default `kruskal.test`). Must be defined as function with arguments `(x, g)`, generating something similar to a p.value. (See examples.)
`numtestlab`	string, describing the test for numeric variables. Default is "Kruskal-Wallis test". Alternative could be "ANOVA".
`intref`	one out of `"high"` (default) or `"low"`, defining which value of a dichotomous numeric or logical variable should be reported. Usually this will be `1` or `TRUE`. Setting it to `"low"` will report the lower value `0` or `FALSE`.

Details

There are three types of variables currently implemented: numeric, factor and variables with only two levels.

Value

a character matrix

Author(s)

Andri Signorell <andri@signorell.net>

Examples

opt <- DescToolsOptions()

# define some special formats for count data, percentages and numeric results
# (those will be supported by TOne)
Fmt(abs=as.fmt(digits=0, big.mark="'"))
Fmt(per=as.fmt(digits=1, fmt="%"))
Fmt(num=as.fmt(digits=1, big.mark="'"))

TOne(x = d.pizza[, c("temperature","delivery_min","driver","wine_ordered")],
     grp=d.pizza$quality)

# define median/IQR as describing functions for the numeric variables
TOne(iris[, -5], iris[, 5],
  FUN = function(x) gettextf("%s / %s",
         Format(median(x, na.rm=TRUE), digits=1),
         Format(IQR(x, na.rm=TRUE), digits=3))
)

# replace kruskal.test by ANOVA and report the p.value
TOne(x = iris[, -5], grp = iris[, 5],
     FUN = function(x) gettextf("%s / %s",
            Format(mean(x, na.rm=TRUE), digits=1),
            Format(sd(x, na.rm=TRUE), digits=3)),
     NUMTEST = function(x, g)
            Format(summary(aov(x ~ g))[[1]][1, "Pr(>F)"], fmt="p"),
     numtestlab = "ANOVA"
)

# dichotomous integer or logical values can be reported by the high or low value
x <- sample(x = c(0,1), size = 100, prob = c(0.3, 0.7), replace = TRUE)
y <- sample(x = c(0,1), size = 100, prob = c(0.3, 0.7), replace = TRUE)==1
z <- factor(sample(x = c(0,1), size = 100, prob = c(0.3, 0.7), replace = TRUE))
g <- sample(x = letters[1:4], size = 100, replace = TRUE)
d.set <- data.frame(x=x, y=y, z=z, g=g)

TOne(d.set[1:3], d.set$g, intref = "low")
TOne(d.set[1:3], d.set$g, intref = "high")

# intref would not control factors, use relevel to change reported value
TOne(data.frame(z=relevel(z, "1")), g)
TOne(data.frame(z=z), g)



options(opt)

## Not run:   --  Send the whole stuff to Word

wrd <- GetNewWrd()
ToWrd(TOne(x = d.pizza[, c("temperature","delivery_min","driver","wine_ordered")],
           grp=d.pizza$quality))
           
## End(Not run)

[Package DescTools version 0.99.24 Index]