FDA Table 9

Patients With Serious Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analyses

System Organ Class           A: Drug X    B: Placebo    C: Combination   Risk Difference (%) (95% CI)
  Dictionary-Derived Term     (N=134)       (N=134)        (N=132)                 (N=268)           
—————————————————————————————————————————————————————————————————————————————————————————————————————
Any SAE                     104 (77.6%)   101 (75.4%)     99 (75.0%)          -2.2 (-12.4 - 7.9)     
cl A                        48 (35.8%)    48 (35.8%)      50 (37.9%)          0.0 (-11.5 - 11.5)     
  dcd A.1.1.1.2             48 (35.8%)    48 (35.8%)      50 (37.9%)          0.0 (-11.5 - 11.5)     
cl B                        79 (59.0%)    78 (58.2%)      76 (57.6%)         -0.7 (-12.5 - 11.0)     
  dcd B.1.1.1.1             47 (35.1%)    49 (36.6%)      43 (32.6%)          1.5 (-10.0 - 13.0)     
  dcd B.2.2.3.1             48 (35.8%)    54 (40.3%)      51 (38.6%)          4.5 (-7.1 - 16.1)      
cl D                        50 (37.3%)    42 (31.3%)      51 (38.6%)          -6.0 (-17.3 - 5.4)     
  dcd D.1.1.1.1             50 (37.3%)    42 (31.3%)      51 (38.6%)          -6.0 (-17.3 - 5.4)

# Load Libraries & Data
library(cardinal)

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

# Select Preferred Term Variable
pref_var <- "AEDECOD"

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_09(adae = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff)

`make_table_09()`

Required variables:

adae: USUBJID, AESER, AESOC, and the variables specified by pref_var, arm_var, and saffl_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 (typically ADSL) 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 from `adae` to include in the table.	`"AEDECOD"`
`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]`
`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.	`TRUE`
`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.

Primary System Organ Class Dictionary-Derived Term	A: Drug X (N=134)	B: Placebo (N=134)	C: Combination (N=132)
Any SAE	104 (77.6%)	101 (75.4%)	99 (75.0%)
cl A	48 (35.8%)	48 (35.8%)	50 (37.9%)
dcd A.1.1.1.2	48 (35.8%)	48 (35.8%)	50 (37.9%)
cl B	79 (59.0%)	78 (58.2%)	76 (57.6%)
dcd B.1.1.1.1	47 (35.1%)	49 (36.6%)	43 (32.6%)
dcd B.2.2.3.1	48 (35.8%)	54 (40.3%)	51 (38.6%)
cl D	50 (37.3%)	42 (31.3%)	51 (38.6%)
dcd D.1.1.1.1	50 (37.3%)	42 (31.3%)	51 (38.6%)

# Load Libraries & Data
library(cardinal)

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

# Output Table
make_table_09_gtsum(adae = adae, alt_counts_df = adsl)

`make_table_09_gtsum()`

Required variables:

adae: SAFFL, USUBJID, AESER, AESOC, and the variables specified by pref_var and arm_var.
alt_counts_df (if specified): SAFFL, USUBJID, and the variable specified by arm_var.

Argument	Description	Default
`adae`	(`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`
`arm_var`	(`character`) Arm variable used to split table into columns.	`"ARM"`
`saffl_var`	(`character`) Safety population flag variable from `adae` to include in the table.	`"SAFFL"`
`ser_var`	(`character`) Serious Event variable from `adae` to include in the table.	`"AESER"`
`pref_var`	(`character`) Preferred term variable from `adae` to include in the table.	`"AEDECOD"`
`soc_var`	(`character`) Preferred term variable from `adae` to include in the table.	`"AESOC"`
`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]`
`lbl_soc_var`	(`character`) Label corresponding to system organ class 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`
`prune_0`	(`flag`) Whether all-zero rows should be removed from the table.	`TRUE`
`annotations`	(named `list` of `character`) List of annotations to add to the table. Valid annotation types are `title`, `subtitles`, and a list of characters called `footnotes`. Each name-value pair should use the annotation type as name and the desired string as value.	`NULL`
`risk_diff`	(`list` of `character` vectors) List of character vectors. Each vector must be of length 2 and contain the name of treatment arms to calculate risk difference and its 95% CI for. Those names must exist in the `arm_var` column of the dataset specified in `adae`.	`NULL`

Source code for this function is available here.

# A tibble: 9 × 4
  row_label1            `var1_A: Drug X` `var1_B: Placebo` `var1_C: Combination`
  <chr>                 <chr>            <chr>             <chr>                
1 "System Organ Class … "A: Drug X\n(N=… "B: Placebo\n(N=… "C: Combination\n(N=…
2 "Any SAE"             "104 ( 77.6%)"   "101 ( 75.4%)"    " 99 ( 75.0%)"       
3 "cl A"                " 48 ( 35.8%)"   " 48 ( 35.8%)"    " 50 ( 37.9%)"       
4 "   dcd A.1.1.1.2"    " 48 ( 35.8%)"   " 48 ( 35.8%)"    " 50 ( 37.9%)"       
5 "cl B"                " 79 ( 59.0%)"   " 78 ( 58.2%)"    " 76 ( 57.6%)"       
6 "   dcd B.1.1.1.1"    " 47 ( 35.1%)"   " 49 ( 36.6%)"    " 43 ( 32.6%)"       
7 "   dcd B.2.2.3.1"    " 48 ( 35.8%)"   " 54 ( 40.3%)"    " 51 ( 38.6%)"       
8 "cl D"                " 50 ( 37.3%)"   " 42 ( 31.3%)"    " 51 ( 38.6%)"       
9 "   dcd D.1.1.1.1"    " 50 ( 37.3%)"   " 42 ( 31.3%)"    " 51 ( 38.6%)"

# Load Libraries & Data
library(cardinal)

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

# Output Table
make_table_09_tplyr(adae = adae, alt_counts_df = adsl, tplyr_raw = TRUE)

`make_table_09_tplyr()`

Required variables:

adae: must contain the variables specified by id_var, arm_var, saffl_var, ser_var, soc_var, and pref_var.
alt_counts_df (if specified): must contain the variables specified by id_var, saffl_var, and arm_var.

Argument	Description	Default
`adae`	(`data.frame`) Adverse events dataset (typically ADAE) required to build table.	No default
`alt_counts_df`	(`character`) Alternative dataset used only to calculate column counts.	`NULL`
`id_var`	(`character`) Name of the unique subject identifiers variable.	`"USUBJID"`
`arm_var`	(`character`) Name of the treatment arm variable used to split table into columns.	`"ARM"`
`saffl_var`	(`character`) Name of the safety flag variable which must contain at least “Y” for “Yes”.	`"SAFFL"`
`ser_var`	(`character`) Name of the serious adverse event flag variable which must contain at least “Y” for “Yes”.	`"AESER"`
`soc_var`	(`character`) Name of the system organ class variable from `adae` to include in the table.	`"AESOC"`
`pref_var`	(`character`) Name of the preferred term variable from `adae` to include in the table.	`"AEDECOD"`
`lbl_soc_var`	(`character`) Label corresponding to system organ class variable `soc_var` to print in the table.	`"System Organ Class"`
`lbl_pref_var`	(`character`) Label corresponding to preferred term variable `pref_var` to print in the table.	`"Reported Term for Adverse Event"`
`risk_diff_pairs`	(`list` of `character` vectors) Each vector contains two treatment arm names to calculate risk difference for. The names must exist in the `arm_var` column of the `adae` dataset.	`NULL`
`show_colcounts`	(`boolean`) Whether column counts should be printed.	`TRUE`
`lbl_overall`	(`character`) If specified, an overall column will be added to the table with the given value as the column label.	`NULL`
`prune_0`	(`flag`) Whether all-zero rows should be removed from the table.	`TRUE`
`tplyr_raw`	(`flag`) Whether the raw `tibble` created using `Tplyr` functions should be returned or a presentation ready `gt_table` (default).	`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 9 subtitle: Patients With Serious Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analyses format: html --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_09.png){fig-align="center" width="78%"} ## rtables Table ```{r tbl, message=FALSE, warning=FALSE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Select Preferred Term Variable pref_var <- "AEDECOD" # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional make_table_09(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_09` ### `make_table_09()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `USUBJID`, `AESER`, `AESOC`, and the variables specified by `pref_var`, `arm_var`, and `saffl_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 (typically ADSL) 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 from `adae` to include in the table. | `"AEDECOD"` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `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]` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `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. | `TRUE` | +------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------+ | `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_09.R#L24). ## gt Table ```{r tbl_gt, message=FALSE, warning=FALSE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Output Table make_table_09_gtsum(adae = adae, alt_counts_df = adsl) ``` ## gt Table Setup ```{r tbl_gt, eval=FALSE, echo=TRUE} ``` ## Function Details: `make_table_09_gtsum` ### `make_table_09_gtsum()` ------------------------------------------------------------------------ Required variables: - **`adae`**: `SAFFL`, `USUBJID`, `AESER`, `AESOC`, and the variables specified by `pref_var` and `arm_var`. - **`alt_counts_df`** (if specified): `SAFFL`, `USUBJID`, and the variable specified by `arm_var`. | **Argument** | **Description** | **Default** | |:-----------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------| | `adae` | (`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` | | `arm_var` | (`character`) Arm variable used to split table into columns. | `"ARM"` | | `saffl_var` | (`character`) Safety population flag variable from `adae` to include in the table. | `"SAFFL"` | | `ser_var` | (`character`) Serious Event variable from `adae` to include in the table. | `"AESER"` | | `pref_var` | (`character`) Preferred term variable from `adae` to include in the table. | `"AEDECOD"` | | `soc_var` | (`character`) Preferred term variable from `adae` to include in the table. | `"AESOC"` | | `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]` | | `lbl_soc_var` | (`character`) Label corresponding to system organ class 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` | | `prune_0` | (`flag`) Whether all-zero rows should be removed from the table. | `TRUE` | | `annotations` | (named `list` of `character`) List of annotations to add to the table. Valid annotation types are `title`, `subtitles`, and a list of characters called `footnotes`. Each name-value pair should use the annotation type as name and the desired string as value. | `NULL` | | `risk_diff` | (`list` of `character` vectors) List of character vectors. Each vector must be of length 2 and contain the name of treatment arms to calculate risk difference and its 95% CI for. Those names must exist in the `arm_var` column of the dataset specified in `adae`. | `NULL` | Source code for this function is available [here](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_09.R). ## Tplyr Table ```{r tbl_tplyr, message=FALSE, warning=FALSE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Output Table make_table_09_tplyr(adae = adae, alt_counts_df = adsl, tplyr_raw = TRUE) ``` ## Tplyr Table Setup ```{r tbl_tplyr, eval=FALSE, echo=TRUE} ``` ## Function Details: `make_table_09_tplyr` ### `make_table_09_tplyr()` ------------------------------------------------------------------------ Required variables: - **`adae`**: must contain the variables specified by `id_var`, `arm_var`, `saffl_var`, `ser_var`, `soc_var`, and `pref_var`. - **`alt_counts_df`** (if specified): must contain the variables specified by `id_var`, `saffl_var`, and `arm_var`. | **Argument** | **Description** | **Default** | |:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------| | `adae` | (`data.frame`) Adverse events dataset (typically ADAE) required to build table. | *No default* | | `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` | | `id_var` | (`character`) Name of the unique subject identifiers variable. | `"USUBJID"` | | `arm_var` | (`character`) Name of the treatment arm variable used to split table into columns. | `"ARM"` | | `saffl_var` | (`character`) Name of the safety flag variable which must contain at least "Y" for "Yes". | `"SAFFL"` | | `ser_var` | (`character`) Name of the serious adverse event flag variable which must contain at least "Y" for "Yes". | `"AESER"` | | `soc_var` | (`character`) Name of the system organ class variable from `adae` to include in the table. | `"AESOC"` | | `pref_var` | (`character`) Name of the preferred term variable from `adae` to include in the table. | `"AEDECOD"` | | `lbl_soc_var` | (`character`) Label corresponding to system organ class variable `soc_var` to print in the table. | `"System Organ Class"` | | `lbl_pref_var` | (`character`) Label corresponding to preferred term variable `pref_var` to print in the table. | `"Reported Term for Adverse Event"` | | `risk_diff_pairs` | (`list` of `character` vectors) Each vector contains two treatment arm names to calculate risk difference for. The names must exist in the `arm_var` column of the `adae` dataset. | `NULL` | | `show_colcounts` | (`boolean`) Whether column counts should be printed. | `TRUE` | | `lbl_overall` | (`character`) If specified, an overall column will be added to the table with the given value as the column label. | `NULL` | | `prune_0` | (`flag`) Whether all-zero rows should be removed from the table. | `TRUE` | | `tplyr_raw` | (`flag`) Whether the raw `tibble` created using `Tplyr` functions should be returned or a presentation ready `gt_table` (default). | `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_09.R). :::