desctable tips

Here is collection of tips and tricks to go further with desctable

Label variables

You can define labels for variables using the .labels argument in desc_table

labels <- c(mpg   = "Miles/(US) gallon",
            cyl   = "Number of cylinders",
            disp  = "Displacement (cu.in.)",
            hp    = "Gross horsepower",
            drat  = "Rear axle ratio",
            wt    = "Weight (1000 lbs)",
            qsec  = "1/4 mile time",
            vs    = "Engine",
            am    = "Transmission",
            gear  = "Number of forward gears",
            CARBURATOR = "Number of carburetors")

mtcars %>%
  desc_table(.labels = labels) %>%
  desc_output("DT")

As you can see with CARBURATOR instead of carb, not all variables need to have a label, and unused labels are discarded.

Default statistics

desc_table chooses its own statistics this way:

• always show N = length
• show "%" = percent if there is at least a factor
• show min, max, Q1, Q3, median, mean, sd, IQR if there is at least a numeric

Defining your own default statistics

You can define your own automatic statistic function using the .auto argument in desc_table.
This function should accept one argument, the table to choose statistics for (in the case of a grouped dataframe the subtables will be passed to the function). It should return a list of statistics.
Here is the code of stats_auto, the default value of .auto

stats_auto <- function(data) {
  data %>%
    lapply(is.numeric) %>%
    unlist() %>%
    any -> numeric

  data %>%
    lapply(is.factor) %>%
    unlist() %>%
    any() -> fact

  stats <- list("Min"  = min,
                "Q1"   = ~quantile(., .25),
                "Med"  = stats::median,
                "Mean" = mean,
                "Q3"   = ~quantile(., .75),
                "Max"  = max,
                "sd"   = stats::sd,
                "IQR"  = IQR)

  if (fact & numeric)
    c(list("N" = length,
           "%" = percent),
      stats)
  else if (fact & !numeric)
    list("N" = length,
         "%" = percent)
  else if (!fact & numeric)
    stats
}

Reuse a list of defined statistics

If you often reuse the same statistics for multiple tables and you don’t want to repeat yourself, you can splice a list to desc_table using the rlang::!!! operator

stats = list(N = length,
             Mean = mean,
             SD = sd)

mtcars %>%
  desc_table(!!!stats) %>%
  desc_output("DT")

When splicing, all stats need to be explicitly named

stats2 = list(N = length,
              mean,
              sd)

mtcars %>%
  desc_table(!!!stats2) %>%
  desc_output("DT")

You can also define a “dumb” automatic function

default_stats <- function(data)
{
  list(N = length,
       mean,
       sd)
}

Default statistical tests

desc_table chooses its own statistical tests this way:

• if the variable is a factor, use fisher.test
  • if fisher.test fails, fallback on chisq.test
• if the variable is numeric, use
  • wilcoxon.test if there are two groups
  • kruskal.test if there are more than two groups

Defining your own default statistical tests

You can define your own automatic statistic function using the .auto argument in desc_tests.
This function should accept two arguments, the variable to compare and the grouping variable, and return a statistical test that accepts a formula argument and returns an object with a p.value element.
Here is the code of tests_auto, the default value of .auto

tests_auto <- function(var, grp) {
  grp <- factor(grp)

  if (nlevels(grp) < 2)
    ~no.test
  else if (is.factor(var)) {
    if (tryCatch(is.numeric(fisher.test(var ~ grp)$p.value), error = function(e) F))
      ~fisher.test
    else
      ~chisq.test
  } else if (nlevels(grp) == 2)
    ~wilcox.test
  else
    ~kruskal.test
}

You can also provide a default statistical test using the .default argument

mtcars %>%
  group_by(am) %>%
  desc_table(mean, sd) %>%
  desc_tests(.default = ~t.test) %>%
  desc_output("DT")

Note that as with named tests, it is necessary to prepend the test name with a tilde (~).

You can still choose individual tests when you define either a .auto or a .default test

mtcars %>%
  group_by(am) %>%
  desc_table(mean, sd, median, IQR) %>%
  desc_tests(.default = ~t.test, carb = ~wilcox.test) %>%
  desc_output("DT")

Note that if a .default test is provided, .auto is ignored.

Output options

You can set the number of significant digits to display with the digits argument. The p values are truncated at 1E-digits.

iris %>%
  group_by(Species) %>%
  desc_table(mean, sd) %>%
  desc_tests() %>%
  desc_output("DT", digits = 10)

Any additional argument given to desc_output will be carried to the output function

iris %>%
  group_by(Species) %>%
  desc_table(mean, sd) %>%
  desc_output("DT", filter = "top")