TOne: 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, TEST = NULL, intref = "high",
     fmt = list(abs = Fmt("abs"), num  = Fmt("num"), per = Fmt("per"),
              pval = as.fmt(fmt = "*", na.form = "   ")) )

Arguments

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.

TEST

a list of functions to be used to test the variables. Must be named as "num", "cat" and "dich" and be defined as function with arguments (x, g), generating something similar to a p.value. (See examples.)

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.

fmt

format codes for absolute, numeric and percentage values, and for the p-values of the tests.

Value

a character matrix

Details

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

Examples

Run this code

# NOT RUN {
options(scipen = 8)
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
# Change tests for all the types
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)), 

     TEST = list(
       num = list(fun = function(x, g){summary(aov(x ~ g))[[1]][1, "Pr(>F)"]},
                        lbl = "ANOVA"),
               cat = list(fun = function(x, g){chisq.test(table(x, g))$p.val},
                        lbl = "Chi-Square test"),
               dich = list(fun = function(x, g){fisher.test(table(x, g))$p.val},
                         lbl = "Fisher exact test")),
       fmt = list(abs = Fmt("abs"), num  = Fmt("num"), per = Fmt("per"),
                pval = as.fmt(fmt = "*", na.form = "   ")) 
)

# 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)
)

# }