FDA Table 11

Patients with FDA Medical Query (Narrow) Leading to Treatment Discontinuation, Safety Population, Pooled Analyses

Body System or Organ Class                                 A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  FMQ (Narrow)                                              (N=134)      (N=134)        (N=132)                 (N=268)           
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Patients with at least one AE leading to discontinuation   83 (61.9%)   90 (67.2%)     88 (66.7%)          5.2 (-6.2 - 16.7)      
cl A.1                                                     53 (39.6%)   55 (41.0%)     69 (52.3%)          1.5 (-10.3 - 13.2)     
  FMQ1                                                     22 (16.4%)   21 (15.7%)     37 (28.0%)          -0.7 (-9.5 - 8.0)      
  FMQ2                                                     24 (17.9%)   31 (23.1%)     33 (25.0%)          5.2 (-4.4 - 14.9)      
  FMQ3                                                     28 (20.9%)   25 (18.7%)     31 (23.5%)          -2.2 (-11.8 - 7.3)     
cl B.1                                                     35 (26.1%)   41 (30.6%)     36 (27.3%)          4.5 (-6.3 - 15.3)      
  FMQ1                                                     12 (9.0%)    17 (12.7%)     19 (14.4%)          3.7 (-3.7 - 11.2)      
  FMQ2                                                      9 (6.7%)    21 (15.7%)     20 (15.2%)           9.0 (1.5 - 16.4)      
  FMQ3                                                     19 (14.2%)   11 (8.2%)       7 (5.3%)           -6.0 (-13.5 - 1.5)     
cl B.2                                                     36 (26.9%)   33 (24.6%)     35 (26.5%)          -2.2 (-12.7 - 8.2)     
  FMQ1                                                     16 (11.9%)   15 (11.2%)     12 (9.1%)           -0.7 (-8.4 - 6.9)      
  FMQ2                                                     17 (12.7%)   12 (9.0%)      16 (12.1%)          -3.7 (-11.2 - 3.7)     
  FMQ3                                                     11 (8.2%)    13 (9.7%)      15 (11.4%)           1.5 (-5.3 - 8.3)      
cl C.2                                                     26 (19.4%)   39 (29.1%)     43 (32.6%)          9.7 (-0.5 - 19.9)      
  FMQ1                                                     11 (8.2%)    12 (9.0%)      19 (14.4%)           0.7 (-6.0 - 7.5)      
  FMQ2                                                     11 (8.2%)    15 (11.2%)     14 (10.6%)          3.0 (-4.1 - 10.1)      
  FMQ3                                                      8 (6.0%)    14 (10.4%)     14 (10.6%)          4.5 (-2.1 - 11.0)      
cl D.1                                                     51 (38.1%)   51 (38.1%)     60 (45.5%)          0.0 (-11.6 - 11.6)     
  FMQ1                                                     22 (16.4%)   22 (16.4%)     32 (24.2%)           0.0 (-8.9 - 8.9)      
  FMQ2                                                     24 (17.9%)   25 (18.7%)     33 (25.0%)          0.7 (-8.5 - 10.0)      
  FMQ3                                                     19 (14.2%)   24 (17.9%)     26 (19.7%)          3.7 (-5.0 - 12.5)      
cl D.2                                                     35 (26.1%)   46 (34.3%)     44 (33.3%)          8.2 (-2.7 - 19.2)      
  FMQ1                                                     11 (8.2%)    23 (17.2%)     17 (12.9%)           9.0 (1.1 - 16.9)      
  FMQ2                                                     18 (13.4%)   16 (11.9%)     18 (13.6%)          -1.5 (-9.5 - 6.5)      
  FMQ3                                                     11 (8.2%)    16 (11.9%)     15 (11.4%)          3.7 (-3.5 - 10.9)

# Load Libraries & Data
library(dplyr)
library(cardinal)

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

# Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae
set.seed(1)
adae <- adae %>%
  rename(FMQ01SC = SMQ01SC) %>%
  mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT"
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_11(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

`make_table_11()`

Required variables:

adae: USUBJID, AEBODSYS, AESER, DCSREAS, and the variables specified by arm_var, saffl_var, fmqsc_var, and fmqnam_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 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"`
`fmqsc_var`	(`character`) FMQ scope variable to use in table.	`"FMQ01SC"`
`fmqnam_var`	(`character`) FMQ reference name variable to use in table.	`"FMQ01NAM"`
`fmq_scope`	(`character`) FMQ scope, can be ‘“NARROW”’ or ‘“BROAD”’.	`"NARROW"`
`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`
`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.

--- title: FDA Table 11 subtitle: Patients with FDA Medical Query (Narrow) Leading to Treatment Discontinuation, Safety Population, Pooled Analyses format: html --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_11.png){fig-align="center"} ## rtables Table ```{r tbl, message=FALSE, warning=FALSE} # Load Libraries & Data library(dplyr) library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Pre-Processing - Ensure required variables fmqsc_var and fmqnam_var exist in adae set.seed(1) adae <- adae %>% rename(FMQ01SC = SMQ01SC) %>% mutate( AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE), FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE) ) adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT" adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW" # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional make_table_11(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff) ``` ## rtables Table Setup ```{r tbl, eval=FALSE, echo=TRUE} ``` ## Function Details ### `make_table_11()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `USUBJID`, `AEBODSYS`, `AESER`, `DCSREAS`, and the variables specified by `arm_var`, `saffl_var`, `fmqsc_var`, and `fmqnam_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 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"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `fmqsc_var` | (`character`) FMQ scope variable to use in table. | `"FMQ01SC"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `fmqnam_var` | (`character`) FMQ reference name variable to use in table. | `"FMQ01NAM"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `fmq_scope` | (`character`) FMQ scope, can be '"NARROW"' or '"BROAD"'. | `"NARROW"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `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` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `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](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_11.R). :::