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Summary numeric variables in columns

Source: R/analyze_vars_in_cols.R
analyze_vars_in_cols.Rd

[Experimental]

Layout-creating function which can be used for creating column-wise summary tables. This function sets the analysis methods as column labels and is a wrapper for rtables::analyze_colvars(). It was designed principally for PK tables.

Usage 

analyze_vars_in_cols(
  lyt,
  vars,
  ...,
  .stats = c("n", "mean", "sd", "se", "cv", "geom_cv"),
  .labels = c(n = "n", mean = "Mean", sd = "SD", se = "SE", cv = "CV (%)", geom_cv =
    "CV % Geometric Mean"),
  row_labels = NULL,
  do_summarize_row_groups = FALSE,
  split_col_vars = TRUE,
  imp_rule = NULL,
  avalcat_var = "AVALCAT1",
  cache = FALSE,
  .indent_mods = NULL,
  nested = TRUE,
  na_level = NULL,
  .formats = NULL,
  .aligns = NULL
)

Arguments

lyt

(layout)
input layout where analyses will be added to.

vars

(character)
variable names for the primary analysis variable to be iterated over.

...

additional arguments for the lower level functions.

.stats

(character)
statistics to select for the table.

.labels

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

row_labels

(character)
as this function works in columns space, usual .labels character vector applies on the column space. You can change the row labels by defining this parameter to a named character vector with names corresponding to the split values. It defaults to NULL and if it contains only one string, it will duplicate that as a row label.

do_summarize_row_groups

(flag)
defaults to FALSE and applies the analysis to the current label rows. This is a wrapper of rtables::summarize_row_groups() and it can accept labelstr to define row labels. This behavior is not supported as we never need to overload row labels.

split_col_vars

(flag)
defaults to TRUE and puts the analysis results onto the columns. This option allows you to add multiple instances of this functions, also in a nested fashion, without adding more splits. This split must happen only one time on a single layout.

imp_rule

(character)
imputation rule setting. Defaults to NULL for no imputation rule. Can also be "1/3" to implement 1/3 imputation rule or "1/2" to implement 1/2 imputation rule. In order to use an imputation rule, the avalcat_var argument must be specified. See imputation_rule() for more details on imputation.

avalcat_var

(character)
if imp_rule is not NULL, name of variable that indicates whether a row in the data corresponds to an analysis value in category "BLQ", "LTR", "<PCLLOQ", or none of the above (defaults to "AVALCAT1"). Variable must be present in the data and should match the variable used to calculate the n_blq statistic (if included in .stats).

cache

(flag)
whether to store computed values in a temporary caching environment. This will speed up calculations in large tables, but should be set to FALSE if the same rtable layout is used for multiple tables with different data. Defaults to FALSE.

.indent_mods

(named integer)
indent modifiers for the labels. Defaults to 0, which corresponds to the unmodified default behavior. Can be negative.

nested

(flag)
whether this layout instruction should be applied within the existing layout structure if possible (TRUE, the default) or as a new top-level element (FALSE). Ignored if it would nest a split. underneath analyses, which is not allowed.

na_level

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

.formats

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

.aligns

(character)
alignment for table contents (not including labels). When NULL, "center" is applied. See formatters::list_valid_aligns() for a list of all currently supported alignments.

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.

Note

This is an experimental implementation of rtables::summarize_row_groups() and rtables::analyze_colvars() that may be subjected to changes as rtables extends its support to more complex analysis pipelines on the column space. For the same reasons, we encourage to read the examples carefully and file issues for cases that differ from them.

Here labelstr behaves differently than usual. If it is not defined (default as NULL), row labels are assigned automatically to the split values in case of rtables::analyze_colvars (do_summarize_row_groups = FALSE, the default), and to the group label for do_summarize_row_groups = TRUE.

See also

analyze_vars(), rtables::analyze_colvars().

Examples 

library(dplyr)

# Data preparation
adpp <- tern_ex_adpp %>% h_pkparam_sort()

lyt <- basic_table() %>%
  split_rows_by(var = "STRATA1", label_pos = "topleft") %>%
  split_rows_by(
    var = "SEX",
    label_pos = "topleft",
    child_label = "hidden"
  ) %>% # Removes duplicated labels
  analyze_vars_in_cols(vars = "AGE")
result <- build_table(lyt = lyt, df = adpp)
result
#> STRATA1                                                         
#>   SEX      n    Mean    SD    SE    CV (%)   CV % Geometric Mean
#> ————————————————————————————————————————————————————————————————
#> A                                                               
#>   F       81    38.8   5.4    0.6    13.8           14.3        
#>   M       81    38.9   5.9    0.7    15.1           14.9        
#> B                                                               
#>   F       90    36.0   6.4    0.7    17.7           17.9        
#>   M       81    36.4   6.5    0.7    17.9           17.8        
#> C                                                               
#>   F       117   34.1   6.2    0.6    18.2           18.3        
#>   M       72    33.2   11.5   1.4    34.6           31.6        

# By selecting just some statistics and ad-hoc labels
lyt <- basic_table() %>%
  split_rows_by(var = "ARM", label_pos = "topleft") %>%
  split_rows_by(
    var = "SEX",
    label_pos = "topleft",
    child_labels = "hidden",
    split_fun = drop_split_levels
  ) %>%
  analyze_vars_in_cols(
    vars = "AGE",
    .stats = c("n", "cv", "geom_mean"),
    .labels = c(
      n = "aN",
      cv = "aCV",
      geom_mean = "aGeomMean"
    )
  )
result <- build_table(lyt = lyt, df = adpp)
result
#> ARM                                    
#>   SEX            aN    aCV    aGeomMean
#> ———————————————————————————————————————
#> A: Drug X                              
#> B: Placebo                             
#> C: Combination                         
#>   F              288   17.6     35.5   
#>   M              234   23.4     35.3   

# Changing row labels
lyt <- basic_table() %>%
  analyze_vars_in_cols(
    vars = "AGE",
    row_labels = "some custom label"
  )
result <- build_table(lyt, df = adpp)
result
#>                      n    Mean   SD    SE    CV (%)   CV % Geometric Mean
#> —————————————————————————————————————————————————————————————————————————
#> some custom label   522   36.1   7.4   0.3    20.4           20.6        

# Pharmacokinetic parameters
lyt <- basic_table() %>%
  split_rows_by(
    var = "TLG_DISPLAY",
    split_label = "PK Parameter",
    label_pos = "topleft",
    child_label = "hidden"
  ) %>%
  analyze_vars_in_cols(
    vars = "AVAL"
  )
result <- build_table(lyt, df = adpp)
result
#> PK Parameter   n    Mean     SD    SE    CV (%)   CV % Geometric Mean
#> —————————————————————————————————————————————————————————————————————
#> Cmax           58   29.7    5.6    0.7    19.0           19.3        
#> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3        
#> CL obs         58    5.1    1.0    0.1    20.6           22.7        
#> Ae             58    1.5    0.3    0.0    21.3           24.1        
#> Fe             58   15.7    3.6    0.5    22.7           24.0        
#> CLR            58    0.0    0.0    0.0    19.9           22.2        
#> Rmax           58    9.6    2.0    0.3    21.1           21.6        
#> Tonset         58    3.0    0.7    0.1    22.4           23.3        
#> RENALCLD       58    0.0    0.0    0.0    19.0           19.4        

# Multiple calls (summarize label and analyze underneath)
lyt <- basic_table() %>%
  split_rows_by(
    var = "TLG_DISPLAY",
    split_label = "PK Parameter",
    label_pos = "topleft"
  ) %>%
  analyze_vars_in_cols(
    vars = "AVAL",
    do_summarize_row_groups = TRUE # does a summarize level
  ) %>%
  split_rows_by("SEX",
    child_label = "hidden",
    label_pos = "topleft"
  ) %>%
  analyze_vars_in_cols(
    vars = "AVAL",
    split_col_vars = FALSE # avoids re-splitting the columns
  )
result <- build_table(lyt, df = adpp)
result
#> PK Parameter                                                         
#>   SEX          n    Mean     SD    SE    CV (%)   CV % Geometric Mean
#> —————————————————————————————————————————————————————————————————————
#> Cmax           58   29.7    5.6    0.7    19.0           19.3        
#>   F            32   30.1    6.1    1.1    20.4           21.0        
#>   M            26   29.2    5.0    1.0    17.2           17.2        
#> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3        
#>   F            32   209.5   43.3   7.7    20.7           21.6        
#>   M            26   205.0   20.9   4.1    10.2           10.4        
#> CL obs         58    5.1    1.0    0.1    20.6           22.7        
#>   F            32    5.1    1.1    0.2    20.8           23.2        
#>   M            26    5.1    1.1    0.2    20.7           22.5        
#> Ae             58    1.5    0.3    0.0    21.3           24.1        
#>   F            32    1.5    0.3    0.1    19.3           20.8        
#>   M            26    1.5    0.4    0.1    23.9           27.9        
#> Fe             58   15.7    3.6    0.5    22.7           24.0        
#>   F            32   16.3    3.4    0.6    20.9           22.3        
#>   M            26   15.0    3.7    0.7    24.7           25.6        
#> CLR            58    0.0    0.0    0.0    19.9           22.2        
#>   F            32    0.0    0.0    0.0    20.5           24.8        
#>   M            26    0.0    0.0    0.0    19.5           18.9        
#> Rmax           58    9.6    2.0    0.3    21.1           21.6        
#>   F            32    9.6    2.2    0.4    22.4           23.5        
#>   M            26    9.6    1.9    0.4    19.7           19.5        
#> Tonset         58    3.0    0.7    0.1    22.4           23.3        
#>   F            32    3.0    0.7    0.1    24.7           25.9        
#>   M            26    3.0    0.6    0.1    19.8           20.0        
#> RENALCLD       58    0.0    0.0    0.0    19.0           19.4        
#>   F            32    0.0    0.0    0.0    19.6           20.4        
#>   M            26    0.0    0.0    0.0    18.0           17.6