Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline

The analyze function count_abnormal_lab_worsen_by_baseline() creates a layout element to count patients with analysis toxicity grades which have worsened from baseline, categorized by highest (worst) grade post-baseline.

This function analyzes primary analysis variable var which indicates analysis toxicity grades. Additional analysis variables that can be supplied as a list via the variables parameter are id (defaults to USUBJID), a variable to indicate unique subject identifiers, baseline_var (defaults to BTOXGR), a variable to indicate baseline toxicity grades, and direction_var (defaults to GRADDIR), a variable to indicate toxicity grade directions of interest to include (e.g. "H" (high), "L" (low), or "B" (both)).

For the direction(s) specified in direction_var, patient counts by worst grade for patients who have worsened from baseline are calculated as follows:

1 to 4: The number of patients who have worsened from their baseline grades with worst grades 1-4, respectively.
Any: The total number of patients who have worsened from their baseline grades.

Fractions are calculated by dividing the above counts by the number of patients who's analysis toxicity grades have worsened from baseline toxicity grades during treatment.

Prior to using this function in your table layout you must use rtables::split_rows_by() to create a row split on variable direction_var.

Usage

count_abnormal_lab_worsen_by_baseline(
  lyt,
  var,
  variables = list(id = "USUBJID", baseline_var = "BTOXGR", direction_var = "GRADDR"),
  na_str = default_na_str(),
  nested = TRUE,
  ...,
  table_names = NULL,
  .stats = NULL,
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL
)

s_count_abnormal_lab_worsen_by_baseline(
  df,
  .var = "ATOXGR",
  variables = list(id = "USUBJID", baseline_var = "BTOXGR", direction_var = "GRADDR")
)

a_count_abnormal_lab_worsen_by_baseline(
  df,
  .var = "ATOXGR",
  variables = list(id = "USUBJID", baseline_var = "BTOXGR", direction_var = "GRADDR")
)

Arguments

lyt

(PreDataTableLayouts)
layout that analyses will be added to.

variables

(named list of string)
list of additional analysis variables including:

id (string)
subject variable name.
baseline_var (string)
name of the data column containing baseline toxicity variable.
direction_var (string)
see direction_var for more details.

na_str

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

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.

...

additional arguments for the lower level functions.

table_names

(character)
this can be customized in the case that the same vars are analyzed multiple times, to avoid warnings from rtables.

.stats

(character)
statistics to select for the table. Run get_stats("abnormal_by_worst_grade_worsen") to see all available statistics.

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

df

(data.frame)
data set containing all analysis variables.

.var, var

(string)
single variable name that is passed by rtables when requested by a statistics function.

Value

count_abnormal_lab_worsen_by_baseline() returns a layout object suitable for passing to further layouting functions, or to rtables::build_table(). Adding this function to an rtable layout will add formatted rows containing the statistics from s_count_abnormal_lab_worsen_by_baseline() to the table layout.

s_count_abnormal_lab_worsen_by_baseline() returns the counts and fraction of patients whose worst post-baseline lab grades are worse than their baseline grades, for post-baseline worst grades "1", "2", "3", "4" and "Any".

a_count_abnormal_lab_worsen_by_baseline() returns the corresponding list with formatted rtables::CellValue().

Functions

count_abnormal_lab_worsen_by_baseline(): Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper for rtables::analyze().
s_count_abnormal_lab_worsen_by_baseline(): Statistics function for patients whose worst post-baseline lab grades are worse than their baseline grades.
a_count_abnormal_lab_worsen_by_baseline(): Formatted analysis function which is used as afun in count_abnormal_lab_worsen_by_baseline().

Examples

library(dplyr)

# The direction variable, GRADDR, is based on metadata
adlb <- tern_ex_adlb %>%
  mutate(
    GRADDR = case_when(
      PARAMCD == "ALT" ~ "B",
      PARAMCD == "CRP" ~ "L",
      PARAMCD == "IGA" ~ "H"
    )
  ) %>%
  filter(SAFFL == "Y" & ONTRTFL == "Y" & GRADDR != "")

df <- h_adlb_worsen(
  adlb,
  worst_flag_low = c("WGRLOFL" = "Y"),
  worst_flag_high = c("WGRHIFL" = "Y"),
  direction_var = "GRADDR"
)

basic_table() %>%
  split_cols_by("ARMCD") %>%
  add_colcounts() %>%
  split_rows_by("PARAMCD") %>%
  split_rows_by("GRADDR") %>%
  count_abnormal_lab_worsen_by_baseline(
    var = "ATOXGR",
    variables = list(
      id = "USUBJID",
      baseline_var = "BTOXGR",
      direction_var = "GRADDR"
    )
  ) %>%
  append_topleft("Direction of Abnormality") %>%
  build_table(df = df, alt_counts_df = tern_ex_adsl)
#>                                ARM A           ARM B           ARM C    
#> Direction of Abnormality      (N=69)          (N=73)          (N=58)    
#> ————————————————————————————————————————————————————————————————————————
#> IGA                                                                     
#>   High                                                                  
#>     1                       6/63 (9.5%)     6/64 (9.4%)      4/50 (8%)  
#>     2                      8/64 (12.5%)     5/67 (7.5%)    8/53 (15.1%) 
#>     3                      7/66 (10.6%)     5/68 (7.4%)    9/57 (15.8%) 
#>     4                       6/68 (8.8%)     2/72 (2.8%)     3/58 (5.2%) 
#>     Any                    27/68 (39.7%)    18/72 (25%)    24/58 (41.4%)
#> ALT                                                                     
#>   High                                                                  
#>     1                      7/63 (11.1%)     6/62 (9.7%)     2/48 (4.2%) 
#>     2                       12/63 (19%)      4/67 (6%)      11/50 (22%) 
#>     3                       4/65 (6.2%)    11/71 (15.5%)   7/56 (12.5%) 
#>     4                       1/67 (1.5%)    8/71 (11.3%)      4/57 (7%)  
#>     Any                    24/67 (35.8%)   29/71 (40.8%)   24/57 (42.1%)
#>   Low                                                                   
#>     1                      12/67 (17.9%)    4/66 (6.1%)    7/52 (13.5%) 
#>     2                      9/68 (13.2%)    12/69 (17.4%)   6/55 (10.9%) 
#>     3                       6/69 (8.7%)     4/71 (5.6%)     5/56 (8.9%) 
#>     4                      7/69 (10.1%)     7/73 (9.6%)    6/58 (10.3%) 
#>     Any                    34/69 (49.3%)    27/73 (37%)    24/58 (41.4%)
#> CRP                                                                     
#>   Low                                                                   
#>     1                      11/66 (16.7%)   10/67 (14.9%)    4/47 (8.5%) 
#>     2                      8/66 (12.1%)     1/70 (1.4%)     6/50 (12%)  
#>     3                       4/68 (5.9%)    9/70 (12.9%)     5/53 (9.4%) 
#>     4                      7/69 (10.1%)     6/72 (8.3%)     4/55 (7.3%) 
#>     Any                    30/69 (43.5%)   26/72 (36.1%)   19/55 (34.5%)