FDA Table 17

Patients With Adverse Events by Female-Specific FDA Medical Query (Narrow) and Preferred Term, Female Safety Population, Pooled Analyses

FMQ (Narrow)                   A: Drug X   B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  Preferred Term                (N=134)     (N=134)        (N=132)                 (N=268)           
—————————————————————————————————————————————————————————————————————————————————————————————————————
Abnormal Uterine Bleeding                                                                            
  dcd A.1.1.1.1                13 (9.7%)   10 (7.5%)      10 (7.6%)           -2.2 (-8.9 - 4.5)      
  dcd A.1.1.1.2                10 (7.5%)    9 (6.7%)      14 (10.6%)          -0.7 (-6.9 - 5.4)      
  dcd B.1.1.1.1                6 (4.5%)     7 (5.2%)       7 (5.3%)            0.7 (-4.4 - 5.9)      
  dcd B.2.1.2.1                9 (6.7%)     8 (6.0%)       6 (4.5%)           -0.7 (-6.6 - 5.1)      
  dcd C.2.1.2.1                7 (5.2%)     8 (6.0%)      11 (8.3%)            0.7 (-4.8 - 6.2)      
  dcd D.1.1.1.1                3 (2.2%)    13 (9.7%)       9 (6.8%)            7.5 (1.9 - 13.1)      
  dcd D.1.1.4.2                13 (9.7%)    8 (6.0%)       9 (6.8%)           -3.7 (-10.2 - 2.7)     
  dcd D.2.1.5.3                9 (6.7%)    11 (8.2%)      11 (8.3%)            1.5 (-4.8 - 7.8)      
Amenorrhea                                                                                           
  dcd A.1.1.1.1                7 (5.2%)     8 (6.0%)      16 (12.1%)           0.7 (-4.8 - 6.2)      
  dcd A.1.1.1.2                12 (9.0%)   14 (10.4%)      5 (3.8%)            1.5 (-5.6 - 8.6)      
  dcd B.1.1.1.1                9 (6.7%)    14 (10.4%)      9 (6.8%)           3.7 (-3.0 - 10.4)      
  dcd B.2.1.2.1                13 (9.7%)   10 (7.5%)       8 (6.1%)           -2.2 (-8.9 - 4.5)      
  dcd C.2.1.2.1                6 (4.5%)     6 (4.5%)       9 (6.8%)            0.0 (-5.0 - 5.0)      
  dcd D.1.1.1.1                11 (8.2%)    6 (4.5%)       8 (6.1%)           -3.7 (-9.6 - 2.1)      
  dcd D.1.1.4.2                8 (6.0%)     3 (2.2%)       4 (3.0%)           -3.7 (-8.5 - 1.0)      
  dcd D.2.1.5.3                7 (5.2%)    13 (9.7%)       9 (6.8%)           4.5 (-1.8 - 10.7)      
Bacterial Vaginosis                                                                                  
  dcd A.1.1.1.1                8 (6.0%)     9 (6.7%)       5 (3.8%)            0.7 (-5.1 - 6.6)      
  dcd A.1.1.1.2                6 (4.5%)     9 (6.7%)       8 (6.1%)            2.2 (-3.3 - 7.7)      
  dcd B.1.1.1.1                10 (7.5%)    9 (6.7%)       6 (4.5%)           -0.7 (-6.9 - 5.4)      
  dcd B.2.1.2.1                9 (6.7%)    10 (7.5%)       5 (3.8%)            0.7 (-5.4 - 6.9)      
  dcd C.2.1.2.1                7 (5.2%)    12 (9.0%)       5 (3.8%)            3.7 (-2.4 - 9.9)      
  dcd D.1.1.1.1                8 (6.0%)    11 (8.2%)       7 (5.3%)            2.2 (-3.9 - 8.4)      
  dcd D.1.1.4.2                8 (6.0%)     7 (5.2%)      12 (9.1%)           -0.7 (-6.2 - 4.8)      
  dcd D.2.1.5.3                7 (5.2%)    11 (8.2%)       9 (6.8%)            3.0 (-3.0 - 9.0)      
Decreased Menstrual Bleeding                                                                         
  dcd A.1.1.1.1                12 (9.0%)   13 (9.7%)       9 (6.8%)            0.7 (-6.2 - 7.7)      
  dcd A.1.1.1.2                10 (7.5%)   11 (8.2%)       7 (5.3%)            0.7 (-5.7 - 7.2)      
  dcd B.1.1.1.1                6 (4.5%)     6 (4.5%)       8 (6.1%)            0.0 (-5.0 - 5.0)      
  dcd B.2.1.2.1                5 (3.7%)    12 (9.0%)       6 (4.5%)           5.2 (-0.6 - 11.0)      
  dcd C.2.1.2.1                8 (6.0%)    13 (9.7%)       8 (6.1%)           3.7 (-2.7 - 10.2)      
  dcd D.1.1.1.1                8 (6.0%)     6 (4.5%)      11 (8.3%)           -1.5 (-6.8 - 3.8)      
  dcd D.1.1.4.2                9 (6.7%)     8 (6.0%)       8 (6.1%)           -0.7 (-6.6 - 5.1)      
  dcd D.2.1.5.3                11 (8.2%)   12 (9.0%)      12 (9.1%)            0.7 (-6.0 - 7.5)

# Load Libraries & Data
library(cardinal)

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

# Pre-Processing - Ensure required variables FMQ01SC and FMQ01NAM exist in adae
set.seed(1)
adae <- dplyr::rename(adae, FMQ01SC = SMQ01SC, FMQ01NAM = SMQ01NAM)
levels(adae$FMQ01SC) <- c("BROAD", "NARROW")
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"
adae$FMQ01NAM <- factor(adae$FMQ01NAM, levels = c(
  unique(adae$FMQ01NAM), "Abnormal Uterine Bleeding", "Amenorrhea",
  "Bacterial Vaginosis", "Decreased Menstrual Bleeding"
))
adae$FMQ01NAM[adae$SEX == "F"] <- as.factor(
  sample(c(
    "Abnormal Uterine Bleeding", "Amenorrhea",
    "Bacterial Vaginosis", "Decreased Menstrual Bleeding"
  ), sum(adae$SEX == "F"), replace = TRUE)
)

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X")
make_table_17(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)

`make_table_17()`

Required variables:

adae: adae must contain USUBJID, SEX, and the variables specified by arm_var, saffl_var, pref_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"`
`pref_var`	(`character`) Preferred term variable to use in table.	`"AEDECOD"`
`sex_scope`	(`character`) Level of `SEX` to output in table.	`"F"`
`fmq_scope`	(`character`) FMQ scope value to use in table.	`"NARROW"`
`fmqsc_var`	(`character`) FMQ scope variable to use in table.	`"FMQ01SC"`
`fmqnam_var`	(`character`) FMQ reference name variable to use in table.	`"FMQ01NAM"`
`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 17 subtitle: Patients With Adverse Events by Female-Specific FDA Medical Query (Narrow) and Preferred Term, Female Safety Population, Pooled Analyses format: html --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_17.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 # Pre-Processing - Ensure required variables FMQ01SC and FMQ01NAM exist in adae set.seed(1) adae <- dplyr::rename(adae, FMQ01SC = SMQ01SC, FMQ01NAM = SMQ01NAM) levels(adae$FMQ01SC) <- c("BROAD", "NARROW") adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW" adae$FMQ01NAM <- factor(adae$FMQ01NAM, levels = c( unique(adae$FMQ01NAM), "Abnormal Uterine Bleeding", "Amenorrhea", "Bacterial Vaginosis", "Decreased Menstrual Bleeding" )) adae$FMQ01NAM[adae$SEX == "F"] <- as.factor( sample(c( "Abnormal Uterine Bleeding", "Amenorrhea", "Bacterial Vaginosis", "Decreased Menstrual Bleeding" ), sum(adae$SEX == "F"), replace = TRUE) ) # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") make_table_17(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff) ``` ## rtables Table Setup ```{r tbl, eval=FALSE, echo=TRUE} ``` ## Function Details ### `make_table_17()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `adae` must contain `USUBJID`, `SEX`, and the variables specified by `arm_var`, `saffl_var`, `pref_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"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `pref_var` | (`character`) Preferred term variable to use in table. | `"AEDECOD"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `sex_scope` | (`character`) Level of `SEX` to output in table. | `"F"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `fmq_scope` | (`character`) FMQ scope value to use in table. | `"NARROW"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `fmqsc_var` | (`character`) FMQ scope variable to use in table. | `"FMQ01SC"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `fmqnam_var` | (`character`) FMQ reference name variable to use in table. | `"FMQ01NAM"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `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_17.R). :::