set_custom_summaries: Set custom summaries to be performed within a descriptive...

In Tplyr: A Traceability Focused Grammar of Clinical Data Summary

Set custom summaries to be performed within a descriptive statistics layer

Description

This function allows a user to define custom summaries to be performed in a call to dplyr::summarize(). A custom summary by the same name as a default summary will override the default. This allows the user to override the default behavior of summaries built into 'Tplyr', while also adding new desired summary functions.

Usage

set_custom_summaries(e, ...)

Arguments

e	desc layer on which the summaries should be bound
...	Named parameters containing syntax to be used in a call to dplyr::summarize()

Details

When programming the logic of the summary function, use the variable name .var to within your summary functions. This allows you apply the summary function to each variable when multiple target variables are declared.

An important, yet not immediately obvious, part of using set_custom_summaries is to understand the link between the named parameters you set in set_custom_summaries and the names called in f_str objects within set_format_strings. In f_str, after you supply the string format you'd like your numbers to take, you specify the summaries that fill those strings.

When you go to set your format strings, the name you use to declare a summary in set_custom_summaries is the same name that you use in your f_str call. This is necessary because set_format_strings needs some means of putting two summaries in the same value, and setting a row label for the summary being performed.

Review the examples to see this put into practice. Note the relationship between the name created in set_custom_summaries and the name used in set_format_strings within the f_str call

Value

Binds a variable custom_summaries to the specified layer

Examples

#Load in pipe
library(magrittr)

tplyr_table(iris, Species) %>%
  add_layer(
    group_desc(Sepal.Length, by = "Sepal Length") %>%
      set_custom_summaries(
        geometric_mean = exp(sum(log(.var[.var > 0]),
                                     na.rm=TRUE) / length(.var))
      ) %>%
      set_format_strings(
        'Geometric Mean' = f_str('xx.xx', geometric_mean)
      )
  ) %>%
  build()

Tplyr documentation built on May 29, 2024, 10:37 a.m.