FDA Table 14

Patients With Adverse Events by System Organ Class and FDA Medical Query, Safety Population, Pooled Analyses

                                                              BROAD                                                                    NARROW                                 
Body System or Organ Class   A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)   A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
  FMQ                         (N=119)      (N=139)        (N=141)                 (N=258)               (N=490)      (N=483)        (N=562)                 (N=973)           
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
cl A.1                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI       0            0              0                0.0 (0.0 - 0.0)              0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)          78 (15.9%)   75 (15.5%)     89 (15.8%)          -0.4 (-5.0 - 4.2)      
cl B.1                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI       0            0              0                0.0 (0.0 - 0.0)              0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)          47 (9.6%)    49 (10.1%)     43 (7.7%)            0.6 (-3.2 - 4.3)      
cl B.2                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI   48 (40.3%)   54 (38.8%)     51 (36.2%)         -1.5 (-13.5 - 10.5)            0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)          49 (10.0%)   44 (9.1%)      52 (9.3%)           -0.9 (-4.6 - 2.8)      
cl C.1                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI   43 (36.1%)   46 (33.1%)     43 (30.5%)          -3.0 (-14.7 - 8.6)            0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)              0            0              0                0.0 (0.0 - 0.0)       
cl C.2                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI       0            0              0                0.0 (0.0 - 0.0)              0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)          35 (7.1%)    48 (9.9%)      55 (9.8%)            2.8 (-0.7 - 6.3)      
cl D.1                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI       0            0              0                0.0 (0.0 - 0.0)              0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)          79 (16.1%)   67 (13.9%)     80 (14.2%)          -2.3 (-6.7 - 2.2)      
cl D.2                                                                                                                                                                        
  C.1.1.1.3/B.2.2.3.1 AESI       0            0              0                0.0 (0.0 - 0.0)              0            0              0                0.0 (0.0 - 0.0)       
  <Missing>                      0            0              0                0.0 (0.0 - 0.0)          47 (9.6%)    58 (12.0%)     57 (10.1%)           2.4 (-1.5 - 6.3)

# Load Libraries & Data
library(cardinal)

adae <- random.cdisc.data::cadae

# Pre-Processing - Ensure required variables FMQ01SC and FMQ01NAM exist in adae
adae <- dplyr::rename(adae, FMQ01SC = SMQ01SC, FMQ01NAM = SMQ01NAM)
levels(adae$FMQ01SC) <- c("BROAD", "NARROW")
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW"

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_14(adae = adae, risk_diff = risk_diff)

`make_table_14()`

Required variables:

adae: USUBJID, AEBODSYS, 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"`
`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 14 subtitle: Patients With Adverse Events by System Organ Class and FDA Medical Query, Safety Population, Pooled Analyses format: html --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_14.png){fig-align="center"} ## rtables Table ```{r tbl, message=FALSE, warning=FALSE} # Load Libraries & Data library(cardinal) adae <- random.cdisc.data::cadae # Pre-Processing - Ensure required variables FMQ01SC and FMQ01NAM exist in adae adae <- dplyr::rename(adae, FMQ01SC = SMQ01SC, FMQ01NAM = SMQ01NAM) levels(adae$FMQ01SC) <- c("BROAD", "NARROW") adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "NARROW" # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional make_table_14(adae = adae, risk_diff = risk_diff) ``` ## rtables Table Setup ```{r tbl, eval=FALSE, echo=TRUE} ``` ## Function Details ### `make_table_14()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `USUBJID`, `AEBODSYS`, 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"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | `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_14.R). :::