Formatting Functions
In tern: Create Common TLGs Used in Clinical Trials

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

`tern` Formatting Functions Overview

The tern R package provides functions to create common analyses from clinical trials in R and these functions have default formatting arguments for displaying the values in the output a specific way.

tern formatting differs compared to the formatting available in the formatters package as tern formats are capable of handling logical statements, allowing for more fine-tuning of the output displayed. Depending on what type of value is being displayed, and what that value is, the format of the output will change. Whereas when using the formatters package, the specified format is applied regardless of the value.

To see the available formatting functions available in tern see ?formatting_functions. To see the available format strings available in formatters see formatters::list_valid_format_labels().

Comparing `tern` & `formatters` Formats

The packages used in this vignette are:

library(rtables)
library(formatters)
library(tern)
library(dplyr)

The example below demonstrates the use of tern formatting in the count_abnormal() function. The example "low" category has a non-zero numerator value so both a fraction and a percentage value are displayed, while the "high" value has a numerator value of zero and so the fraction value is displayed without also displaying the redundant zero percentage value.

df2 <- data.frame(
  ID = as.character(c(1, 1, 2, 2)),
  RANGE = factor(c("NORMAL", "LOW", "HIGH", "LOW")),
  BL_RANGE = factor(c("NORMAL", "NORMAL", "HIGH", "HIGH")),
  ONTRTFL = c("", "Y", "", "Y"),
  stringsAsFactors = FALSE
)

df2 <- df2 %>%
  filter(ONTRTFL == "Y")

basic_table() %>%
  count_abnormal(
    var = "RANGE",
    abnormal = list(low = "LOW", high = "HIGH"),
    variables = list(id = "ID", baseline = "BL_RANGE"),
    exclude_base_abn = FALSE,
    .formats = list(fraction = format_fraction)
  ) %>%
  build_table(df2)

In the following example the count_abnormal() function is utilized again. This time both "low" values and "high" values have a non-zero numerator and so both show a percentage.

df2 <- data.frame(
  ID = as.character(c(1, 1, 2, 2)),
  RANGE = factor(c("NORMAL", "LOW", "HIGH", "HIGH")),
  BL_RANGE = factor(c("NORMAL", "NORMAL", "HIGH", "HIGH")),
  ONTRTFL = c("", "Y", "", "Y"),
  stringsAsFactors = FALSE
)

df2 <- df2 %>%
  filter(ONTRTFL == "Y")

basic_table() %>%
  count_abnormal(
    var = "RANGE",
    abnormal = list(low = "LOW", high = "HIGH"),
    variables = list(id = "ID", baseline = "BL_RANGE"),
    exclude_base_abn = FALSE,
    .formats = list(fraction = format_fraction)
  ) %>%
  build_table(df2)

The following example demonstrates the difference when formatters is used instead to format the output. Here we choose to use "xx / xx" as our value format. The "high" value has a zero numerator value and the "low" value has a non-zero numerator, yet both are displayed in the same format.

df2 <- data.frame(
  ID = as.character(c(1, 1, 2, 2)),
  RANGE = factor(c("NORMAL", "LOW", "HIGH", "LOW")),
  BL_RANGE = factor(c("NORMAL", "NORMAL", "HIGH", "HIGH")),
  ONTRTFL = c("", "Y", "", "Y"),
  stringsAsFactors = FALSE
)
df2 <- df2 %>%
  filter(ONTRTFL == "Y")

basic_table() %>%
  count_abnormal(
    var = "RANGE",
    abnormal = list(low = "LOW", high = "HIGH"),
    variables = list(id = "ID", baseline = "BL_RANGE"),
    exclude_base_abn = FALSE,
    .formats = list(fraction = "xx / xx")
  ) %>%
  build_table(df2)

The same concept occurs when using any of the available formats from the formatters package. The following example displays the same result using the "xx.x / xx.x" format instead. Use formatters::list_valid_format_labels() to see the full list of available formats in formatters.

df2 <- data.frame(
  ID = as.character(c(1, 1, 2, 2)),
  RANGE = factor(c("NORMAL", "LOW", "HIGH", "LOW")),
  BL_RANGE = factor(c("NORMAL", "NORMAL", "HIGH", "HIGH")),
  ONTRTFL = c("", "Y", "", "Y"),
  stringsAsFactors = FALSE
)
df2 <- df2 %>%
  filter(ONTRTFL == "Y")

basic_table() %>%
  count_abnormal(
    var = "RANGE",
    abnormal = list(low = "LOW", high = "HIGH"),
    variables = list(id = "ID", baseline = "BL_RANGE"),
    exclude_base_abn = FALSE,
    .formats = list(fraction = "xx.x / xx.x")
  ) %>%
  build_table(df2)

Formatting Function Basics

Current tern formatting functions consider some of the following aspects when setting custom behaviors:

Missing values - a custom value or string can be set to display for missing values instead of NA.
0's - if a cell value is zero, tern fraction formatting functions will exclude the accompanying percentage value.
Number of decimal places to display - the number of decimal places can be fixed if needed.
Value thresholds - a different format or value can be displayed depending on whether the value is within a certain threshold.

Number of Decimal Places to Display

Two functions that set a fixed number of decimal places (specifically 1) are format_fraction_fixed_dp() and format_count_fraction_fixed_dp(). By default, formatting functions will remove trailing zeros, but these two functions will always have one decimal place in their percentage, even if the digit is a zero. See the following example:

format_fraction_fixed_dp(x = c(num = 1L, denom = 3L))
format_fraction_fixed_dp(x = c(num = 1L, denom = 2L))

format_count_fraction_fixed_dp(x = c(2, 0.6667))
format_count_fraction_fixed_dp(x = c(2, 0.25))

Value Thresholds

Functions that set custom values according to a certain threshold include format_extreme_values(), format_extreme_values_ci(), and format_fraction_threshold(). The extreme value formats work similarly to allow the user to specify the maximum number of digits to include, and very large or very small values are given a special string value. For example:

extreme_format <- format_extreme_values(digits = 2)
extreme_format(0.235)
extreme_format(0.001)
extreme_format(Inf)

The format_fraction_threshold() function allows the user to specify a lower percentage threshold, below which values are instead assigned a special string value. For example:

fraction_format <- format_fraction_threshold(0.05)
fraction_format(x = c(20, 0.1))
fraction_format(x = c(2, 0.01))

See the documentation on each function for specific details on their behavior and how to customize them.

Creating Custom Formatting Functions

If your table requires customized output that cannot be displayed using one of the pre-existing tern formatting functions, you may want to consider creating a new formatting function. When creating your own formatting function it is important to consider the aspects listed in the Formatting Function Customization section above.

In this section we will create a custom formatting function derived from the format_fraction_fixed_dp() function. First we will take a look at this function in detail and then we will customize it.

# First we will see how the format_fraction_fixed_dp code works and displays the outputs
format_fraction_fixed_dp <- function(x, ...) {
  attr(x, "label") <- NULL
  checkmate::assert_vector(x)
  checkmate::assert_count(x["num"])
  checkmate::assert_count(x["denom"])

  result <- if (x["num"] == 0) {
    paste0(x["num"], "/", x["denom"])
  } else {
    paste0(
      x["num"], "/", x["denom"],
      " (", sprintf("%.1f", round(x["num"] / x["denom"] * 100, 1)), "%)"
    )
  }
  return(result)
}

Here we see that if the numerator value is greater than 0, the fraction and percentage is displayed. If the numerator is 0, only the fraction is shown. Percent values always display 1 decimal place. Below we will create a dummy dataset and then observe the output value behavior when this formatting function is applied.

df2 <- data.frame(
  ID = as.character(c(1, 1, 2, 2)),
  RANGE = factor(c("NORMAL", "LOW", "HIGH", "LOW")),
  BL_RANGE = factor(c("NORMAL", "NORMAL", "HIGH", "HIGH")),
  ONTRTFL = c("", "Y", "", "Y"),
  stringsAsFactors = FALSE
) %>%
  filter(ONTRTFL == "Y")

basic_table() %>%
  count_abnormal(
    var = "RANGE",
    abnormal = list(low = "LOW", high = "HIGH"),
    variables = list(id = "ID", baseline = "BL_RANGE"),
    exclude_base_abn = FALSE,
    .formats = list(fraction = format_fraction_fixed_dp)
  ) %>%
  build_table(df2)

Now we will modify this function to make our custom formatting function, custom_format. We want to display 3 decimal places in the percent value, and if the numerator value is 0 we only want to display a 0 value (without the denominator).

custom_format <- function(x, ...) {
  attr(x, "label") <- NULL
  checkmate::assert_vector(x)
  checkmate::assert_count(x["num"])
  checkmate::assert_count(x["denom"])

  result <- if (x["num"] == 0) {
    paste0(x["num"]) # We remove the denominator on this line so that only a 0 is displayed
  } else {
    paste0(
      x["num"], "/", x["denom"],
      " (", sprintf("%.3f", round(x["num"] / x["denom"] * 100, 1)), "%)" # We include 3 decimal places with %.3f
    )
  }
  return(result)
}

basic_table() %>%
  count_abnormal(
    var = "RANGE",
    abnormal = list(low = "LOW", high = "HIGH"),
    variables = list(id = "ID", baseline = "BL_RANGE"),
    exclude_base_abn = FALSE,
    .formats = list(fraction = custom_format) # Here we implement our new custom_format function
  ) %>%
  build_table(df2)

Summary

Each tern analysis function has pre-specified default format functions to implement when generating output, some of which are taken from the formatters package and some of which are custom formatting functions stored in tern. These tern functions differ compared to those from formatters in that logical statements can be used to set value-dependent customized formats. If you would like to create your own custom formatting function to use with tern, be sure to carefully consider which rules you want to implement to handle different input values.