FDA Table 9

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

gtsummary Table Setup

# Load Libraries & Data
library(cardinal)

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

# Output Table
make_table_09(df = adae, denominator = adsl, return_ard = FALSE)

Primary System Organ Class Dictionary-Derived Term	A: Drug X N = 134¹	B: Placebo N = 134¹	C: Combination N = 132¹
Any SAE	104 (78%)	101 (75%)	99 (75%)
cl A	48 (36%)	48 (36%)	50 (38%)
dcd A.1.1.1.2	48 (36%)	48 (36%)	50 (38%)
cl B	79 (59%)	78 (58%)	76 (58%)
dcd B.1.1.1.1	47 (35%)	49 (37%)	43 (33%)
dcd B.2.2.3.1	48 (36%)	54 (40%)	51 (39%)
cl D	50 (37%)	42 (31%)	51 (39%)
dcd D.1.1.1.1	50 (37%)	42 (31%)	51 (39%)
¹ n (%)

Function Details

`make_table_09()`

Required variables:

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

Argument	Description	Default
`df`	(`data.frame`) Dataset (typically ADSL) required to build table.	No default
`denominator`	(`character`) Alternative dataset used only to calculate column counts.	`NULL`
`return_ard`	(`flag`) Whether an ARD should be returned.	`TRUE`
`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"`
`ser_var`	(`character`) FMQ scope variable to use in table.	`"AESER"`
`soc_var`	(`character`) FMQ reference name variable to use in table.	`"AESOC"`
`pref_var`	(`character`) FMQ scope, can be ‘“NARROW”’ or ‘“BROAD”’.	`"AEDECOD"`
`lbl_overall`	(`character`) (if specified): an overall column will be added to the table with the given value as the column label.	`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 & ARD
result <- make_table_09(df = adae, denominator = adsl)

# Output ARD
result$ard

$tbl_hierarchical

{cards} data frame: 81 x 15

   group1 group1_level group2 group2_level                     variable variable_level   context stat_name stat_label  stat stat_fmt fmt_fn warning error gts_column
1     ARM    A: Drug X   <NA>                                     AESOC           cl A hierarch…         n          n    48       48   <fn>                   stat_1
2     ARM    A: Drug X   <NA>                                     AESOC           cl A hierarch…         N          N   134      134   <fn>                   stat_1
3     ARM    A: Drug X   <NA>                                     AESOC           cl A hierarch…         p          % 0.358       36   <fn>                   stat_1
4     ARM    A: Drug X   <NA>                                     AESOC           cl B hierarch…         n          n    79       79   <fn>                   stat_1
5     ARM    A: Drug X   <NA>                                     AESOC           cl B hierarch…         N          N   134      134   <fn>                   stat_1
6     ARM    A: Drug X   <NA>                                     AESOC           cl B hierarch…         p          %  0.59       59   <fn>                   stat_1
7     ARM    A: Drug X   <NA>                                     AESOC           cl D hierarch…         n          n    50       50   <fn>                   stat_1
8     ARM    A: Drug X   <NA>                                     AESOC           cl D hierarch…         N          N   134      134   <fn>                   stat_1
9     ARM    A: Drug X   <NA>                                     AESOC           cl D hierarch…         p          % 0.373       37   <fn>                   stat_1
10    ARM    A: Drug X   <NA>              ..ard_hierarchical_overall..           TRUE hierarch…         n          n   104      104   <fn>                   stat_1

ℹ 71 more rows

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

rtables Table Setup

# 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_rtables(adae = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff)

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)

Function Details

`make_table_09()_rtables`

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.

gt Table Setup

# 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)

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%)

Function Details

`make_table_09_gtsum()`

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`) 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"`
`id_var`	(`character`) Name of the unique subject identifiers variable.	`"USUBJID"`
`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.

Tplyr Table Setup

# 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)

row_label1	var1_A: Drug X	var1_B: Placebo	var1_C: Combination
System Organ Class
Reported Term for Adverse Event	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%)

Function Details

`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%"} ## gtsummary Table <details> <summary>gtsummary Table Setup</summary> ```{r tbl_gtsummary, eval=FALSE, echo=TRUE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl adae <- random.cdisc.data::cadae # Output Table make_table_09(df = adae, denominator = adsl, return_ard = FALSE) ``` </details> ```{r tbl_gtsummary, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `make_table_09()` ------------------------------------------------------------------------ Required variables: - **`df`**: must contain the variables specified by `id_var`, `arm_var`, `saffl_var`, `ser_var`, `soc_var`, and `pref_var`. - **`denominator`** (if specified): must contain the variables specified by `id_var`, `saffl_var`, and `arm_var`. | | | | |-----------------|----------------------------------------------------------------------------------------------------------------------|--------------| | **Argument** | **Description** | **Default** | | `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* | | `denominator` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` | | `return_ard` | (`flag`) Whether an ARD should be returned. | `TRUE` | | `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"` | | `ser_var` | (`character`) FMQ scope variable to use in table. | `"AESER"` | | `soc_var` | (`character`) FMQ reference name variable to use in table. | `"AESOC"` | | `pref_var` | (`character`) FMQ scope, can be '"NARROW"' or '"BROAD"'. | `"AEDECOD"` | | `lbl_overall` | (`character`) (if specified): an overall column will be added to the table with the given value as the column label. | `NULL` | Source code for this function is available [here](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_09.R). </details> ## ARD <details> <summary>ARD Setup</summary> ```{r ard, 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 & ARD result <- make_table_09(df = adae, denominator = adsl) # Output ARD result$ard ``` </details> ```{r ard_print, echo=FALSE} withr::local_options(width = 9999) print(result$ard, columns = "all") ``` ## rtables Table <details> <summary>rtables Table Setup</summary> ```{r tbl_rtables, echo=TRUE, eval=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_rtables(adae = adae, alt_counts_df = adsl, pref_var = pref_var, risk_diff = risk_diff) ``` </details> ```{r tbl_rtables, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `make_table_09()_rtables` ------------------------------------------------------------------------ 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). </details> ## gt Table <details> <summary>gt Table Setup</summary> ```{r tbl_gt, echo=TRUE, eval=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) ``` </details> ```{r tbl_gt, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `make_table_09_gtsum()` ------------------------------------------------------------------------ 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`) 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"` | | `id_var` | (`character`) Name of the unique subject identifiers variable. | `"USUBJID"` | | `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). </details> ## Tplyr Table <details> <summary>Tplyr Table Setup</summary> ```{r tbl_typlr, echo=TRUE, eval=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) ``` </details> ```{r tbl_typlr, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `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). </details> :::