FDA Table 6

Overview of Adverse Events, Safety Population, Pooled Analyses

                                                                       A: Drug X    B: Placebo    C: Combination   Risk Difference (%) (95% CI)
Event                                                                   (N=134)       (N=134)        (N=132)                 (N=268)           
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
SAE                                                                   104 (77.6%)   101 (75.4%)     99 (75.0%)          -2.2 (-12.4 - 7.9)     
  SAEs with fatal outcome                                             76 (56.7%)    70 (52.2%)      75 (56.8%)          -4.5 (-16.4 - 7.4)     
  Life-threatening SAEs                                                9 (6.7%)      13 (9.7%)      19 (14.4%)           3.0 (-3.6 - 9.5)      
  SAEs requiring hospitalization                                      24 (17.9%)    28 (20.9%)      30 (22.7%)          3.0 (-6.5 - 12.4)      
  SAEs resulting in substantial disruption of normal life functions   28 (20.9%)    21 (15.7%)      23 (17.4%)          -5.2 (-14.5 - 4.0)     
  Congenital anomaly or birth defect                                  26 (19.4%)    27 (20.1%)      20 (15.2%)          0.7 (-8.8 - 10.3)      
  Other                                                               30 (22.4%)    37 (27.6%)      32 (24.2%)          5.2 (-5.1 - 15.6)      
AE leading to permanent discontinuation of study drug                 27 (20.1%)    26 (19.4%)      30 (22.7%)          -0.7 (-10.3 - 8.8)     
AE leading to dose modification of study drug                         71 (53.0%)    86 (64.2%)      83 (62.9%)          11.2 (-0.5 - 22.9)     
  AE leading to interruption of study drug                             4 (3.0%)      4 (3.0%)        3 (2.3%)            0.0 (-4.1 - 4.1)      
  AE leading to reduction of study drug                               46 (34.3%)    46 (34.3%)      51 (38.6%)          0.0 (-11.4 - 11.4)     
  AE leading to dose delay of study drug                              20 (14.9%)    28 (20.9%)      30 (22.7%)          6.0 (-3.2 - 15.1)      
  Other                                                               34 (25.4%)    48 (35.8%)      46 (34.8%)          10.4 (-0.5 - 21.4)     
Any AE                                                                122 (91.0%)   123 (91.8%)    120 (90.9%)           0.7 (-6.0 - 7.5)      
  MILD                                                                 7 (5.2%)      9 (6.7%)        4 (3.0%)            1.5 (-4.2 - 7.2)      
  MODERATE                                                            24 (17.9%)    24 (17.9%)      23 (17.4%)           0.0 (-9.2 - 9.2)      
  SEVERE                                                              91 (67.9%)    90 (67.2%)      93 (70.5%)         -0.7 (-12.0 - 10.5)

# Load Libraries & Data
library(cardinal)

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

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_06(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

`make_table_06()`

Required variables:

adae: USUBJID, TRTEMFL, AESEV, AESER, AESDTH, AESLIFE, AESHOSP, AESDISAB, AESCONG, AESMIE, AEACN, 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.	`FALSE`
`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.

--- title: FDA Table 6 subtitle: Overview of Adverse Events, Safety Population, Pooled Analyses format: html --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_06.png){fig-align="center"} ## rtables Table ```{r tbl, message=FALSE, warning=FALSE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional make_table_06(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff) ``` ## rtables Table Setup ```{r tbl, eval=FALSE, echo=TRUE} ``` ## Function Details ### `make_table_06()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `USUBJID`, `TRTEMFL`, `AESEV`, `AESER`, `AESDTH`, `AESLIFE`, `AESHOSP`, `AESDISAB`, `AESCONG`, `AESMIE`, `AEACN`, 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()`](https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html) for more details. List should contain the following elements: | `NULL` | | | | | | | - `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`. | | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------+ | `prune_0` | (`flag`) Whether all-zero rows should be removed from the table. | `FALSE` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------+ | `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](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_06.R). :::