FDA Table 38

Patients With Adverse Events by System Organ Class, FDA Medical Query (Broad) and Preferred Term, Safety Population, Pooled Analysis (or Trial X)

Body System or Organ Class                                                                           
  FMQ (Broad)                 A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
    Dictionary-Derived Term    (N=134)      (N=134)        (N=132)                 (N=268)           
—————————————————————————————————————————————————————————————————————————————————————————————————————
cl A.1                                                                                               
  FMQ1                        32 (23.9%)   29 (21.6%)     48 (36.4%)          -2.2 (-12.3 - 7.8)     
    dcd A.1.1.1.1             17 (12.7%)   13 (9.7%)      29 (22.0%)          -3.0 (-10.5 - 4.6)     
    dcd A.1.1.1.2             20 (14.9%)   20 (14.9%)     26 (19.7%)           0.0 (-8.5 - 8.5)      
  FMQ2                        35 (26.1%)   40 (29.9%)     39 (29.5%)          3.7 (-7.0 - 14.5)      
    dcd A.1.1.1.1             24 (17.9%)   25 (18.7%)     30 (22.7%)          0.7 (-8.5 - 10.0)      
    dcd A.1.1.1.2             18 (13.4%)   18 (13.4%)     13 (9.8%)            0.0 (-8.2 - 8.2)      
  FMQ3                        37 (27.6%)   39 (29.1%)     38 (28.8%)          1.5 (-9.3 - 12.3)      
    dcd A.1.1.1.1             19 (14.2%)   18 (13.4%)     21 (15.9%)          -0.7 (-9.0 - 7.5)      
    dcd A.1.1.1.2             21 (15.7%)   23 (17.2%)     23 (17.4%)          1.5 (-7.4 - 10.4)      
cl B.1                                                                                               
  FMQ1                        19 (14.2%)   21 (15.7%)     21 (15.9%)          1.5 (-7.0 - 10.0)      
    dcd B.1.1.1.1             19 (14.2%)   21 (15.7%)     21 (15.9%)          1.5 (-7.0 - 10.0)      
  FMQ2                        14 (10.4%)   21 (15.7%)     24 (18.2%)          5.2 (-2.8 - 13.3)      
    dcd B.1.1.1.1             14 (10.4%)   21 (15.7%)     24 (18.2%)          5.2 (-2.8 - 13.3)      
  FMQ3                        21 (15.7%)   16 (11.9%)     10 (7.6%)           -3.7 (-12.0 - 4.5)     
    dcd B.1.1.1.1             21 (15.7%)   16 (11.9%)     10 (7.6%)           -3.7 (-12.0 - 4.5)     
cl B.2                                                                                               
  FMQ1                        40 (29.9%)   34 (25.4%)     39 (29.5%)          -4.5 (-15.2 - 6.2)     
    dcd B.2.1.2.1             22 (16.4%)   22 (16.4%)     20 (15.2%)           0.0 (-8.9 - 8.9)      
    dcd B.2.2.3.1             20 (14.9%)   17 (12.7%)     22 (16.7%)          -2.2 (-10.5 - 6.0)     
  FMQ2                        40 (29.9%)   37 (27.6%)     43 (32.6%)          -2.2 (-13.1 - 8.6)     
    dcd B.2.1.2.1             20 (14.9%)   15 (11.2%)     24 (18.2%)          -3.7 (-11.8 - 4.3)     
    dcd B.2.2.3.1             22 (16.4%)   25 (18.7%)     21 (15.9%)          2.2 (-6.9 - 11.3)      
  FMQ3                        31 (23.1%)   36 (26.9%)     40 (30.3%)          3.7 (-6.6 - 14.1)      
    dcd B.2.1.2.1             16 (11.9%)   17 (12.7%)     20 (15.2%)           0.7 (-7.1 - 8.6)      
    dcd B.2.2.3.1             18 (13.4%)   24 (17.9%)     23 (17.4%)          4.5 (-4.2 - 13.2)      
cl C.1                                                                                               
  FMQ1                        14 (10.4%)   19 (14.2%)     21 (15.9%)          3.7 (-4.1 - 11.6)      
    dcd C.1.1.1.3             14 (10.4%)   19 (14.2%)     21 (15.9%)          3.7 (-4.1 - 11.6)      
  FMQ2                        17 (12.7%)   22 (16.4%)     19 (14.4%)          3.7 (-4.7 - 12.2)      
    dcd C.1.1.1.3             17 (12.7%)   22 (16.4%)     19 (14.4%)          3.7 (-4.7 - 12.2)      
  FMQ3                        20 (14.9%)   16 (11.9%)     19 (14.4%)          -3.0 (-11.1 - 5.2)     
    dcd C.1.1.1.3             20 (14.9%)   16 (11.9%)     19 (14.4%)          -3.0 (-11.1 - 5.2)     
cl C.2                                                                                               
  FMQ1                        17 (12.7%)   15 (11.2%)     23 (17.4%)          -1.5 (-9.3 - 6.3)      
    dcd C.2.1.2.1             17 (12.7%)   15 (11.2%)     23 (17.4%)          -1.5 (-9.3 - 6.3)      
  FMQ2                        12 (9.0%)    19 (14.2%)     19 (14.4%)          5.2 (-2.4 - 12.9)      
    dcd C.2.1.2.1             12 (9.0%)    19 (14.2%)     19 (14.4%)          5.2 (-2.4 - 12.9)      
  FMQ3                        12 (9.0%)    16 (11.9%)     19 (14.4%)          3.0 (-4.3 - 10.3)      
    dcd C.2.1.2.1             12 (9.0%)    16 (11.9%)     19 (14.4%)          3.0 (-4.3 - 10.3)      
cl D.1                                                                                               
  FMQ1                        37 (27.6%)   30 (22.4%)     44 (33.3%)          -5.2 (-15.6 - 5.1)     
    dcd D.1.1.1.1             18 (13.4%)   17 (12.7%)     21 (15.9%)          -0.7 (-8.8 - 7.3)      
    dcd D.1.1.4.2             23 (17.2%)   15 (11.2%)     25 (18.9%)          -6.0 (-14.3 - 2.4)     
  FMQ2                        35 (26.1%)   33 (24.6%)     40 (30.3%)          -1.5 (-11.9 - 8.9)     
    dcd D.1.1.1.1             22 (16.4%)   18 (13.4%)     26 (19.7%)          -3.0 (-11.5 - 5.5)     
    dcd D.1.1.4.2             18 (13.4%)   16 (11.9%)     18 (13.6%)          -1.5 (-9.5 - 6.5)      
  FMQ3                        30 (22.4%)   28 (20.9%)     37 (28.0%)          -1.5 (-11.4 - 8.4)     
    dcd D.1.1.1.1             15 (11.2%)   13 (9.7%)      19 (14.4%)          -1.5 (-8.8 - 5.8)      
    dcd D.1.1.4.2             16 (11.9%)   18 (13.4%)     18 (13.6%)           1.5 (-6.5 - 9.5)      
cl D.2                                                                                               
  FMQ1                        17 (12.7%)   27 (20.1%)     22 (16.7%)          7.5 (-1.4 - 16.3)      
    dcd D.2.1.5.3             17 (12.7%)   27 (20.1%)     22 (16.7%)          7.5 (-1.4 - 16.3)      
  FMQ2                        25 (18.7%)   21 (15.7%)     24 (18.2%)          -3.0 (-12.0 - 6.0)     
    dcd D.2.1.5.3             25 (18.7%)   21 (15.7%)     24 (18.2%)          -3.0 (-12.0 - 6.0)     
  FMQ3                        13 (9.7%)    20 (14.9%)     19 (14.4%)          5.2 (-2.6 - 13.1)      
    dcd D.2.1.5.3             13 (9.7%)    20 (14.9%)     19 (14.4%)          5.2 (-2.6 - 13.1)

# 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$FMQ01SC[is.na(adae$FMQ01SC)] <- "BROAD"

# Select Preferred Term Variable
pref_var <- "AEDECOD"

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_38(adae = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff)

`make_table_38()`

Required variables:

adae: USUBJID, AEBODSYS, AESER, and the variables specified by arm_var, saffl_var, trtemfl_var, fmqsc_var, fmqnam_var, and pref_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`
`id_var`	(`character`) variable used as unique subject identifier.	`USUBJID`
`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"`
`trtemfl_var`	(`character`) Flag variable used to identify Treatment-emergent AE.	`"TRTEMFL"`
`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"`
`pref_var`	(`character`) Preferred term variable from `adae` to include in the table.	`"AEDECOD"`
`lbl_overall`	(`character`) If specified, an overall column will be added to the table with the given value as the column label.	`NULL`
`lbl_pref_var`	(`character`) Label corresponding to preferred term variable `pref_var` to print in the table.	`formatters::var_labels(adae, fill = TRUE)[pref_var]`
`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.

--- title: FDA Table 38 subtitle: Patients With Adverse Events by System Organ Class, FDA Medical Query (Broad) and Preferred Term, Safety Population, Pooled Analysis (or Trial X) format: html --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_38.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$FMQ01SC[is.na(adae$FMQ01SC)] <- "BROAD" # Select Preferred Term Variable pref_var <- "AEDECOD" # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional make_table_38(adae = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff) ``` ## rtables Table Setup ```{r tbl, eval=FALSE, echo=TRUE} ``` ## Function Details ### `make_table_38()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `USUBJID`, `AEBODSYS`, `AESER`, and the variables specified by `arm_var`, `saffl_var`, `trtemfl_var`, `fmqsc_var`, `fmqnam_var`, and `pref_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` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `id_var` | (`character`) variable used as unique subject identifier. | `USUBJID` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `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"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `trtemfl_var` | (`character`) Flag variable used to identify Treatment-emergent AE. | `"TRTEMFL"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `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"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `pref_var` | (`character`) Preferred term variable from `adae` to include in the table. | `"AEDECOD"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `lbl_overall` | (`character`) If specified, an overall column will be added to the table with the given value as the column label. | `NULL` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `lbl_pref_var` | (`character`) Label corresponding to preferred term variable `pref_var` to print in the table. | `formatters::var_labels(adae, fill = TRUE)[pref_var]` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `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. | `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](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_38.R). :::