FDA Table 7

Deaths, Safety Population, Pooled Analyses

                                  A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
Deaths                             (N=134)      (N=134)        (N=132)                 (N=268)           
—————————————————————————————————————————————————————————————————————————————————————————————————————————
Total deaths                      24 (17.9%)   19 (14.2%)     20 (15.2%)          -3.7 (-12.5 - 5.0)     
  ADVERSE EVENT                   8 (33.3%)    6 (31.6%)      10 (50.0%)          -1.5 (-6.8 - 3.8)      
  DISEASE PROGRESSION             8 (33.3%)    5 (26.3%)      6 (30.0%)           -2.2 (-7.4 - 2.9)      
  LOST TO FOLLOW UP                2 (8.3%)     1 (5.3%)       1 (5.0%)           -0.7 (-3.3 - 1.8)      
  MISSING                          2 (8.3%)    3 (15.8%)       1 (5.0%)            0.7 (-2.5 - 4.0)      
  Post-study reporting of death    1 (4.2%)     1 (5.3%)       1 (5.0%)            0.0 (-2.1 - 2.1)      
  SUICIDE                          2 (8.3%)    2 (10.5%)       1 (5.0%)            0.0 (-2.9 - 2.9)      
  UNKNOWN                          1 (4.2%)     1 (5.3%)          0                0.0 (-2.1 - 2.1)      
Treatment-emergent deaths         12 (9.0%)    15 (11.2%)     16 (12.1%)           2.2 (-5.0 - 9.4)      
  ADVERSE EVENT                   3 (25.0%)    5 (33.3%)      9 (56.2%)            1.5 (-2.6 - 5.6)      
  DISEASE PROGRESSION             3 (25.0%)    5 (33.3%)      4 (25.0%)            1.5 (-2.6 - 5.6)      
  LOST TO FOLLOW UP                1 (8.3%)        0              0               -0.7 (-2.2 - 0.7)      
  MISSING                         2 (16.7%)     1 (6.7%)       1 (6.2%)           -0.7 (-3.3 - 1.8)      
  Post-study reporting of death       0         1 (6.7%)       1 (6.2%)            0.7 (-0.7 - 2.2)      
  SUICIDE                         2 (16.7%)    2 (13.3%)       1 (6.2%)            0.0 (-2.9 - 2.9)      
  UNKNOWN                          1 (8.3%)     1 (6.7%)          0                0.0 (-2.1 - 2.1)      
Nontreatment-emergent deaths      12 (9.0%)     4 (3.0%)       4 (3.0%)          -6.0 (-11.6 - -0.3)     
  ADVERSE EVENT                   5 (41.7%)    1 (25.0%)      1 (25.0%)           -3.0 (-6.5 - 0.5)      
  DISEASE PROGRESSION             5 (41.7%)        0          2 (50.0%)           -3.7 (-6.9 - -0.5)     
  LOST TO FOLLOW UP                1 (8.3%)    1 (25.0%)      1 (25.0%)            0.0 (-2.1 - 2.1)      
  MISSING                             0        2 (50.0%)          0                1.5 (-0.6 - 3.5)      
  Post-study reporting of death    1 (8.3%)        0              0               -0.7 (-2.2 - 0.7)      
# Load Libraries & Data
library(cardinal)

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Pre-Processing - Ensure all required variables are present in adae
set.seed(1)
adae$TRTEMFL <- ifelse(adae$USUBJID %in% sample(adsl$USUBJID, size = as.integer(nrow(adsl) / 3)), "N", "Y")

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_07(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

make_table_07()

Required variables:

  • adae: USUBJID, TRTEMFL, DTHFL, DTHCAUS, and the variables specified by arm_var and saffl_var.
  • alt_counts_df (if specified): USUBJID and the variables specified by arm_var and saffl_var.
Argument Description Default
adae (data.frame) Dataset (typically ADAE) required to build table. No default
alt_counts_df (character) Alternative dataset (typically ADSL) used only to calculate column counts. NULL
show_colcounts (flag) Whether column counts should be printed. TRUE
arm_var (character) Arm variable used to split table into columns. "ARM"
saffl_var (character) Flag variable used to indicate inclusion in safety population. "SAFFL"
lbl_overall (character) If specified, an overall column will be added to the table with the given value as the column label. NULL
risk_diff

(named list) List of settings to apply to add a risk difference column to the table. See tern::add_riskdiff() for more details. List should contain the following elements:

  • arm_x: (required) the name of reference arm.

  • arm_y: (required) the name of the arm to compare to the reference arm.

  • col_label: (optional) label to use for the risk difference column. Defaults to "Risk Difference (%) (95% CI)".

  • pct: (optional) whether the output should be returned as percentages. Defaults to TRUE.

 NULL
prune_0 (flag) Whether all-zero rows should be removed from the table. TRUE
na_level (character) String to represent missing values. "MISSING"
annotations (named list of character) List of annotations to add to the table. Valid annotation types are title, subtitles, main_footer, and prov_footer. Each name-value pair should use the annotation type as name and the desired string as value. NULL

Source code for this function is available here.