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Summarize variables in columns

Source: R/summarize_colvars.R
summarize_colvars.Rd

[Stable]

The analyze function summarize_colvars() uses the statistics function s_summary() to analyze variables that are arranged in columns. The variables to analyze should be specified in the table layout via column splits (see rtables::split_cols_by() and rtables::split_cols_by_multivar()) prior to using summarize_colvars().

The function is a minimal wrapper for rtables::analyze_colvars(), a function typically used to apply different analysis methods in rows for each column variable. To use the analysis methods as column labels, please refer to the analyze_vars_in_cols() function.

Usage 

summarize_colvars(
  lyt,
  ...,
  na_str = default_na_str(),
  .stats = c("n", "mean_sd", "median", "range", "count_fraction"),
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL
)

Arguments

lyt

(PreDataTableLayouts)
layout that analyses will be added to.

...

arguments passed to s_summary().

na_str

(string)
string used to replace all NA or empty values in the output.

.stats

(character)
statistics to select for the table.

.formats

(named character or list)
formats for the statistics. See Details in analyze_vars for more information on the "auto" setting.

.labels

(named character)
labels for the statistics (without indent).

.indent_mods

(named vector of integer)
indent modifiers for the labels. Each element of the vector should be a name-value pair with name corresponding to a statistic specified in .stats and value the indentation for that statistic's row label.

Value

A layout object suitable for passing to further layouting functions, or to rtables::build_table(). Adding this function to an rtable layout will summarize the given variables, arrange the output in columns, and add it to the table layout.

See also

rtables::split_cols_by_multivar() and analyze_colvars_functions.

Examples 

dta_test <- data.frame(
  USUBJID = rep(1:6, each = 3),
  PARAMCD = rep("lab", 6 * 3),
  AVISIT = rep(paste0("V", 1:3), 6),
  ARM = rep(LETTERS[1:3], rep(6, 3)),
  AVAL = c(9:1, rep(NA, 9)),
  CHG = c(1:9, rep(NA, 9))
)

## Default output within a `rtables` pipeline.
basic_table() %>%
  split_cols_by("ARM") %>%
  split_rows_by("AVISIT") %>%
  split_cols_by_multivar(vars = c("AVAL", "CHG")) %>%
  summarize_colvars() %>%
  build_table(dta_test)
#>                         A                             B                             C          
#>                 AVAL         CHG           AVAL               CHG           AVAL         CHG   
#> ———————————————————————————————————————————————————————————————————————————————————————————————
#> V1                                                                                             
#>   n               2           2              1                 1              0           0    
#>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing>
#>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing>
#>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing>
#> V2                                                                                             
#>   n               2           2              1                 1              0           0    
#>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing>
#>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing>
#>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing>
#> V3                                                                                             
#>   n               2           2              1                 1              0           0    
#>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing>
#>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing>
#>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>

## Selection of statistics, formats and labels also work.
basic_table() %>%
  split_cols_by("ARM") %>%
  split_rows_by("AVISIT") %>%
  split_cols_by_multivar(vars = c("AVAL", "CHG")) %>%
  summarize_colvars(
    .stats = c("n", "mean_sd"),
    .formats = c("mean_sd" = "xx.x, xx.x"),
    .labels = c(n = "n", mean_sd = "Mean, SD")
  ) %>%
  build_table(dta_test)
#>                       A                           B                            C          
#>                AVAL       CHG           AVAL             CHG           AVAL         CHG   
#> ——————————————————————————————————————————————————————————————————————————————————————————
#> V1                                                                                        
#>   n             2          2             1                1              0           0    
#>   Mean, SD   7.5, 2.1   2.5, 2.1   3.0, <Missing>   7.0, <Missing>   <Missing>   <Missing>
#> V2                                                                                        
#>   n             2          2             1                1              0           0    
#>   Mean, SD   6.5, 2.1   3.5, 2.1   2.0, <Missing>   8.0, <Missing>   <Missing>   <Missing>
#> V3                                                                                        
#>   n             2          2             1                1              0           0    
#>   Mean, SD   5.5, 2.1   4.5, 2.1   1.0, <Missing>   9.0, <Missing>   <Missing>   <Missing>

## Use arguments interpreted by `s_summary`.
basic_table() %>%
  split_cols_by("ARM") %>%
  split_rows_by("AVISIT") %>%
  split_cols_by_multivar(vars = c("AVAL", "CHG")) %>%
  summarize_colvars(na.rm = FALSE) %>%
  build_table(dta_test)
#>                         A                             B                             C          
#>                 AVAL         CHG           AVAL               CHG           AVAL         CHG   
#> ———————————————————————————————————————————————————————————————————————————————————————————————
#> V1                                                                                             
#>   n               2           2              1                 1              0           0    
#>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing>
#>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing>
#>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing>
#> V2                                                                                             
#>   n               2           2              1                 1              0           0    
#>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing>
#>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing>
#>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing>
#> V3                                                                                             
#>   n               2           2              1                 1              0           0    
#>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing>
#>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing>
#>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>