FDA Table 35

Patients With Adverse Events by System Organ Class, Safety Population, Pooled Analysis (or Trial X)

gtsummary Table Setup

# Load Libraries & Data
library(cardinal)

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

# Output Table
make_table_35(df = adae, denominator = adsl, return_ard = FALSE)

Function Details

`make_table_35()`

Required variables:

df: The variables specified by id_var, arm_var, saffl_var, and soc_var.
denominator (if specified): USUBJID and the variables specified by arm_var and saffl_var
If both the ARD (return_ard = TRUE) and an overall column (lbl_overall not missing) are requested, a list of two ARDs will be returned: one for the table by groups, and the other for the overall column.

Argument	Description	Default
`df`	(`data.frame`) Dataset (typically ADSL) required to build table.	No default
`return_ard`	(`flag`) Whether an ARD should be returned.	`TRUE`
`denominator`	(`character`) Alternative dataset used only to calculate column counts.	`NULL`
`id_var`	(`character`) Identifier variable used to count the participants within each flag.	`"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"`
`soc_var`	(`character`) SOC variable from `adae` to include in the table.	`"ARBODSYS"`
`na_level`	(`character`) String to represent missing values.	`"<Missing>"`
`lbl_overall`	(`character`) String to represent the label of an overall column.	`NULL`

Source code for this function is available here.

ARD Setup

# Load Libraries & Data
library(cardinal)

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

# Create Table and ARD
result <- make_table_35(df = adae, denominator = adsl)

# Output ARD
result$ard

$tbl_hierarchical

{cards} data frame: 72 x 13

   group1 group1_level variable variable_level   context stat_name stat_label  stat stat_fmt fmt_fn warning error gts_column
1    <NA>                   ARM      A: Drug X categori…         n          n   134      134      0                   stat_1
2    <NA>                   ARM      A: Drug X categori…         N          N   400      400      0                   stat_1
3    <NA>                   ARM      A: Drug X categori…         p          % 0.335     33.5   <fn>                   stat_1
4    <NA>                   ARM      B: Place… categori…         n          n   134      134      0                   stat_2
5    <NA>                   ARM      B: Place… categori…         N          N   400      400      0                   stat_2
6    <NA>                   ARM      B: Place… categori…         p          % 0.335     33.5   <fn>                   stat_2
7    <NA>                   ARM      C: Combi… categori…         n          n   132      132      0                   stat_3
8    <NA>                   ARM      C: Combi… categori…         N          N   400      400      0                   stat_3
9    <NA>                   ARM      C: Combi… categori…         p          %  0.33     33.0   <fn>                   stat_3
10    ARM    A: Drug X AEBODSYS         cl A.1 hierarch…         n          n    78       78   <fn>                   stat_1

ℹ 62 more rows

ℹ Use `print(n = ...)` to see more rows

rtables Table Setup

# Load Libraries & Data
library(random.cdisc.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_35_rtables(df = adae, alt_counts_df = adsl, risk_diff = risk_diff)

                             A: Drug X    B: Placebo   C: Combination   Risk Difference (%) (95% CI)
Body System or Organ Class    (N=134)      (N=134)        (N=132)                 (N=268)           
————————————————————————————————————————————————————————————————————————————————————————————————————
cl A.1                       78 (58.2%)   75 (56.0%)     89 (67.4%)          -2.2 (-14.1 - 9.6)     
cl B.2                       79 (59.0%)   74 (55.2%)     85 (64.4%)          -3.7 (-15.6 - 8.1)     
cl D.1                       79 (59.0%)   67 (50.0%)     80 (60.6%)          -9.0 (-20.8 - 2.9)     
cl D.2                       47 (35.1%)   58 (43.3%)     57 (43.2%)          8.2 (-3.4 - 19.9)      
cl B.1                       47 (35.1%)   49 (36.6%)     43 (32.6%)          1.5 (-10.0 - 13.0)     
cl C.2                       35 (26.1%)   48 (35.8%)     55 (41.7%)          9.7 (-1.3 - 20.7)      
cl C.1                       43 (32.1%)   46 (34.3%)     43 (32.6%)          2.2 (-9.0 - 13.5)

Function Details

`make_table_35_rtables()`

Required variables:

df: USUBJID and the variables specified by arm_var, saffl_var and soc_var.
alt_counts_df (if specified): USUBJID and the variables specified by arm_var and saffl_var.

Argument	Description	Default
`df`	(`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`
`id_var`	(`character`) Subject identifier variable .	`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"`
`soc_var`	(`character`) SOC variable from `adae` to include in the table.	`"AEDECOD"`
`lbl_soc_var`	(`character`) Label corresponding to SOC variable `soc_var` to print in the table.	`formatters::var_labels(adae, fill = TRUE)[soc_var]`
`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 35 subtitle: Patients With Adverse Events by System Organ Class, Safety Population, Pooled Analysis (or Trial X) --- ```{r setup, echo=FALSE} ``` ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_35.png){fig-align="center" width="70%"} ## gtsummary Table <details> <summary>gtsummary Table Setup</summary> ```{r tbl1, eval=FALSE, echo=TRUE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Output Table make_table_35(df = adae, denominator = adsl, return_ard = FALSE) ``` </details> <details> <summary>Function Details</summary> ### `make_table_35()` ------------------------------------------------------------------------ Required variables: - **`df`**: The variables specified by `id_var`, `arm_var`, `saffl_var`, and `soc_var`. - **`denominator`** (if specified): `USUBJID` and the variables specified by `arm_var` and `saffl_var` - If both the ARD (`return_ard = TRUE`) and an overall column (`lbl_overall` not missing) are requested, a list of two ARDs will be returned: one for the table by groups, and the other for the overall column. +---------------+------------------------------------------------------------------------------------+---------------+ | **Argument** | **Description** | **Default** | +---------------+------------------------------------------------------------------------------------+---------------+ | `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* | +---------------+------------------------------------------------------------------------------------+---------------+ | `return_ard` | (`flag`) Whether an ARD should be returned. | `TRUE` | +---------------+------------------------------------------------------------------------------------+---------------+ | `denominator` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` | +---------------+------------------------------------------------------------------------------------+---------------+ | `id_var` | (`character`) Identifier variable used to count the participants within each flag. | `"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"` | +---------------+------------------------------------------------------------------------------------+---------------+ | `soc_var` | (`character`) SOC variable from `adae` to include in the table. | `"ARBODSYS"` | +---------------+------------------------------------------------------------------------------------+---------------+ | `na_level` | (`character`) String to represent missing values. | `"<Missing>"` | +---------------+------------------------------------------------------------------------------------+---------------+ | `lbl_overall` | (`character`) String to represent the label of an overall column. | `NULL` | +---------------+------------------------------------------------------------------------------------+---------------+ Source code for this function is available [here](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_35.R). </details> ## ARD <details> <summary>ARD Setup</summary> ```{r tbl2, echo=TRUE, message=FALSE, warning=FALSE, results='hide'} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Create Table and ARD result <- make_table_35(df = adae, denominator = adsl) # Output ARD result$ard ``` ```{r tbl2-print, echo=FALSE} withr::local_options(width = 9999) print(result$ard, columns = "all") ``` </details> ## rtables Table <details> <summary>rtables Table Setup</summary> ```{r tbl3, eval=FALSE, echo=TRUE} # Load Libraries & Data library(random.cdisc.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_35_rtables(df = adae, alt_counts_df = adsl, risk_diff = risk_diff) ``` </details> ```{r tbl3, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `make_table_35_rtables()` ------------------------------------------------------------------------ Required variables: - **`df`**: `USUBJID` and the variables specified by `arm_var`, `saffl_var` and `soc_var`. - **`alt_counts_df`** (if specified): `USUBJID` and the variables specified by `arm_var` and `saffl_var`. +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------+ | **Argument** | **Description** | **Default** | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------+ | `df` | (`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` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------+ | `id_var` | (`character`) Subject identifier variable . | `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"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------+ | `soc_var` | (`character`) SOC variable from `adae` to include in the table. | `"AEDECOD"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------+ | `lbl_soc_var` | (`character`) Label corresponding to SOC variable `soc_var` to print in the table. | `formatters::var_labels(adae, fill = TRUE)[soc_var]` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------+ | `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_35.R). </details> :::