FDA Table 5

Duration of Treatment Exposure, Safety Population, Pooled Analyses

gtsummary Table Setup

# Load Libraries & Data
library(cardinal)

adsl <- random.cdisc.data::cadsl

# Output Table
make_table_05(df = adsl, return_ard = FALSE)

Parameter	A: Drug X N = 134¹	B: Placebo N = 134¹	C: Combination N = 132¹
Duration of Treatment, days
Mean (SD)	961.49 (208.62)	949.45 (223.73)	984.71 (200.08)
Median (Min, Max)	1,095.75 (392.79, 1,095.75)	1,095.75 (387.34, 1,095.75)	1,095.75 (368.91, 1,095.75)
Interquartile range	859.95 - 1,095.75	781.56 - 1,095.75	960.34 - 1,095.75
Total exposure (person years)	105,763.56 (289.56)	100,641.30 (275.54)	109,302.29 (299.25)
Patients Treated, by duration
Any duration (at least 1 dose)	110 (82.1%)	106 (79.1%)	111 (84.1%)
<1 month	0 (0.0%)	0 (0.0%)	0 (0.0%)
>=1 month	110 (82.1%)	106 (79.1%)	111 (84.1%)
>=3 months	110 (82.1%)	106 (79.1%)	111 (84.1%)
>=6 months	110 (82.1%)	106 (79.1%)	111 (84.1%)
>=12 months	110 (82.1%)	106 (79.1%)	111 (84.1%)
¹ n (%)

Function Details

`make_table_05()`

Required variables:

df: The variables specified by vars, arm_var, and saffl_var.
denominator (if specified): USUBJID and the variables specified by arm_var and saffl_var.

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`
`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"`
`id_var`	(`character`) Identifier variable used to count the participants within each flag.	`"USUBJID"`
`trtsdtm_var`	(`character`) Treatment start datetime variable in df.	`"TRTSDTM"`
`trtedtm_var`	(`character`) Treatment end datetime variable in df.	`"TRTEDTM"`
`u_trtdur`	(`character`) Unit for duration of treatment. Options are `"days"`, `"weeks"`, `"months"` and `"years"`.	`"days"`

Source code for this function is available here.

ARD Setup

# Load Libraries & Data
library(cardinal)

adsl <- random.cdisc.data::cadsl

# Create Table & ARD
result <- make_table_05(df = adsl)

# Output ARD
result$ard

{cards} data frame: 63 x 12

   group1 group1_level variable variable_level   context    stat_name stat_label     stat stat_fmt fmt_fn warning error
1     ARM    A: Drug X   TRTDUR                continuo…         mean       Mean  961.487   961.49   <fn>              
2     ARM    A: Drug X   TRTDUR                continuo…           sd         SD  208.615   208.62   <fn>              
3     ARM    A: Drug X   TRTDUR                continuo…       median     Median  1095.75  1095.75   <fn>              
4     ARM    A: Drug X   TRTDUR                continuo…          min        Min  392.788   392.79   <fn>              
5     ARM    A: Drug X   TRTDUR                continuo…          max        Max  1095.75  1095.75   <fn>              
6     ARM    A: Drug X   TRTDUR                continuo…          p25         Q1  859.171   859.17   <fn>              
7     ARM    A: Drug X   TRTDUR                continuo…          p75         Q3  1095.75  1095.75   <fn>              
8     ARM    A: Drug X   TRTDUR                continuo… tot_exposure  tot_expo… 105763.6 105763.6   <fn>              
9     ARM    A: Drug X   TRTDUR                continuo…   person_yrs  person_y…  289.565   289.56   <fn>              
10    ARM    B: Place…   TRTDUR                continuo…         mean       Mean  949.446   949.45   <fn>              
11    ARM    B: Place…   TRTDUR                continuo…           sd         SD  223.727   223.73   <fn>              
12    ARM    B: Place…   TRTDUR                continuo…       median     Median  1095.75  1095.75   <fn>              
13    ARM    B: Place…   TRTDUR                continuo…          min        Min  387.344   387.34   <fn>              
14    ARM    B: Place…   TRTDUR                continuo…          max        Max  1095.75  1095.75   <fn>              
15    ARM    B: Place…   TRTDUR                continuo…          p25         Q1  779.541   779.54   <fn>              
16    ARM    B: Place…   TRTDUR                continuo…          p75         Q3  1095.75  1095.75   <fn>              
17    ARM    B: Place…   TRTDUR                continuo… tot_exposure  tot_expo… 100641.3 100641.3   <fn>              
18    ARM    B: Place…   TRTDUR                continuo…   person_yrs  person_y…  275.541   275.54   <fn>              
19    ARM    C: Combi…   TRTDUR                continuo…         mean       Mean  984.705   984.71   <fn>              
20    ARM    C: Combi…   TRTDUR                continuo…           sd         SD  200.076   200.08   <fn>              
21    ARM    C: Combi…   TRTDUR                continuo…       median     Median  1095.75  1095.75   <fn>              
22    ARM    C: Combi…   TRTDUR                continuo…          min        Min  368.909   368.91   <fn>              
23    ARM    C: Combi…   TRTDUR                continuo…          max        Max  1095.75  1095.75   <fn>              
24    ARM    C: Combi…   TRTDUR                continuo…          p25         Q1   940.39   940.39   <fn>              
25    ARM    C: Combi…   TRTDUR                continuo…          p75         Q3  1095.75  1095.75   <fn>              
26    ARM    C: Combi…   TRTDUR                continuo… tot_exposure  tot_expo… 109302.3 109302.3   <fn>              
27    ARM    C: Combi…   TRTDUR                continuo…   person_yrs  person_y…  299.253   299.25   <fn>              
28    ARM    A: Drug X    D_ANY           TRUE dichotom…            n          n      110     NULL      0              
29    ARM    A: Drug X    D_ANY           TRUE dichotom…            p          %    0.821     NULL   <fn>              
30    ARM    B: Place…    D_ANY           TRUE dichotom…            n          n      106     NULL      0              
31    ARM    B: Place…    D_ANY           TRUE dichotom…            p          %    0.791     NULL   <fn>              
32    ARM    C: Combi…    D_ANY           TRUE dichotom…            n          n      111     NULL      0              
33    ARM    C: Combi…    D_ANY           TRUE dichotom…            p          %    0.841     NULL   <fn>              
34    ARM    A: Drug X    D_LT1           TRUE dichotom…            n          n        0     NULL      0              
35    ARM    A: Drug X    D_LT1           TRUE dichotom…            p          %        0     NULL   <fn>              
36    ARM    B: Place…    D_LT1           TRUE dichotom…            n          n        0     NULL      0              
37    ARM    B: Place…    D_LT1           TRUE dichotom…            p          %        0     NULL   <fn>              
38    ARM    C: Combi…    D_LT1           TRUE dichotom…            n          n        0     NULL      0              
39    ARM    C: Combi…    D_LT1           TRUE dichotom…            p          %        0     NULL   <fn>              
40    ARM    A: Drug X    D_GT1           TRUE dichotom…            n          n      110     NULL      0              
41    ARM    A: Drug X    D_GT1           TRUE dichotom…            p          %    0.821     NULL   <fn>              
42    ARM    B: Place…    D_GT1           TRUE dichotom…            n          n      106     NULL      0              
43    ARM    B: Place…    D_GT1           TRUE dichotom…            p          %    0.791     NULL   <fn>              
44    ARM    C: Combi…    D_GT1           TRUE dichotom…            n          n      111     NULL      0              
45    ARM    C: Combi…    D_GT1           TRUE dichotom…            p          %    0.841     NULL   <fn>              
46    ARM    A: Drug X    D_GT3           TRUE dichotom…            n          n      110     NULL      0              
47    ARM    A: Drug X    D_GT3           TRUE dichotom…            p          %    0.821     NULL   <fn>              
48    ARM    B: Place…    D_GT3           TRUE dichotom…            n          n      106     NULL      0              
49    ARM    B: Place…    D_GT3           TRUE dichotom…            p          %    0.791     NULL   <fn>              
50    ARM    C: Combi…    D_GT3           TRUE dichotom…            n          n      111     NULL      0              
51    ARM    C: Combi…    D_GT3           TRUE dichotom…            p          %    0.841     NULL   <fn>              
52    ARM    A: Drug X    D_GT6           TRUE dichotom…            n          n      110     NULL      0              
53    ARM    A: Drug X    D_GT6           TRUE dichotom…            p          %    0.821     NULL   <fn>              
54    ARM    B: Place…    D_GT6           TRUE dichotom…            n          n      106     NULL      0              
55    ARM    B: Place…    D_GT6           TRUE dichotom…            p          %    0.791     NULL   <fn>              
56    ARM    C: Combi…    D_GT6           TRUE dichotom…            n          n      111     NULL      0              
57    ARM    C: Combi…    D_GT6           TRUE dichotom…            p          %    0.841     NULL   <fn>              
58    ARM    A: Drug X   D_GT12           TRUE dichotom…            n          n      110     NULL      0              
59    ARM    A: Drug X   D_GT12           TRUE dichotom…            p          %    0.821     NULL   <fn>              
60    ARM    B: Place…   D_GT12           TRUE dichotom…            n          n      106     NULL      0              
61    ARM    B: Place…   D_GT12           TRUE dichotom…            p          %    0.791     NULL   <fn>              
62    ARM    C: Combi…   D_GT12           TRUE dichotom…            n          n      111     NULL      0              
63    ARM    C: Combi…   D_GT12           TRUE dichotom…            p          %    0.841     NULL   <fn>

rtables Table Setup

# Load Libraries & Data
library(cardinal)

adsl <- random.cdisc.data::cadsl

# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_05_rtables(df = adsl, risk_diff = risk_diff)

                                           A: Drug X                    B: Placebo                 C: Combination         Risk Difference (%) (95% CI)
Parameter                                   (N=134)                      (N=134)                      (N=132)                       (N=268)           
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Duration of Treatment, days                                                                                                                           
  Mean (SD)                             961.49 (208.62)              949.45 (223.73)              984.71 (200.08)                      NA             
  Median (min - max)               1095.75 (392.79 - 1095.75)   1095.75 (387.34 - 1095.75)   1095.75 (368.91 - 1095.75)                NA             
  Interquartile range                   859.95 - 1095.75             781.56 - 1095.75             960.34 - 1095.75                     NA             
  Total exposure (person years)        105763.56 (289.56)           100641.30 (275.54)           109302.29 (299.25)                    NA             
Patients Treated, by duration                                                                                                                         
  Any duration (at least 1 dose)          110 (82.1%)                  106 (79.1%)                  111 (84.1%)                -3.0 (-12.4 - 6.5)     
  <1 month                                     0                            0                            0                      0.0 (0.0 - 0.0)       
  >=1 month                               110 (82.1%)                  106 (79.1%)                  111 (84.1%)                -3.0 (-12.4 - 6.5)     
  >=3 months                              110 (82.1%)                  106 (79.1%)                  111 (84.1%)                -3.0 (-12.4 - 6.5)     
  >=6 months                              110 (82.1%)                  106 (79.1%)                  111 (84.1%)                -3.0 (-12.4 - 6.5)     
  >=12 months                             110 (82.1%)                  106 (79.1%)                  111 (84.1%)                -3.0 (-12.4 - 6.5)

Function Details

`make_table_05_rtables()`

Required variables:

df: The variables specified by vars, arm_var, and saffl_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 ADSL) required to build table.	No default
`alt_counts_df`	(`character`) Alternative dataset used only to calculate column counts.	`NULL`
`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"`
`id_var`	(`character`) Identifier variable used to count the participants within each flag.	`"USUBJID"`
`trtsdtm_var`	(`character`) Treatment start datetime variable in df.	`"TRTSDTM"`
`trtedtm_var`	(`character`) Treatment end datetime variable in df.	`"TRTEDTM"`
`u_trtdur`	(`character`) Unit for duration of treatment. Options are `"days"`, `"weeks"`, `"months"` and `"years"`.	`"days"`
`lbl_trtdur`	(`character`) Label for treatment duration variable `u_trtdur`.	`paste("Duration of Treatment,", u_trtdur)`
`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.

--- title: FDA Table 5 subtitle: Duration of Treatment Exposure, Safety Population, Pooled Analyses --- ::: panel-tabset ## Spec. Screenshot ![](../assets/images/screenshots/table_05.png){fig-align="center"} ## gtsummary Table <details> <summary>gtsummary Table Setup</summary> ```{r tbl2, eval=FALSE, echo=TRUE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl # Output Table make_table_05(df = adsl, return_ard = FALSE) ``` </details> ```{r tbl2, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `make_table_05()` ------------------------------------------------------------------------ Required variables: - **`df`**: The variables specified by `vars`, `arm_var`, and `saffl_var`. - **`denominator`** (if specified): `USUBJID` and the variables specified by `arm_var` and `saffl_var`. | | | | |-----------------|----------------------------------------------------------------------------------------------------------|--------------| | **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` | | `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"` | | `id_var` | (`character`) Identifier variable used to count the participants within each flag. | `"USUBJID"` | | `trtsdtm_var` | (`character`) Treatment start datetime variable in df. | `"TRTSDTM"` | | `trtedtm_var` | (`character`) Treatment end datetime variable in df. | `"TRTEDTM"` | | `u_trtdur` | (`character`) Unit for duration of treatment. Options are `"days"`, `"weeks"`, `"months"` and `"years"`. | `"days"` | Source code for this function is available [here](https://github.com/pharmaverse/cardinal/blob/main/R/fda-table_05.R). </details> ## ARD <details> <summary>ARD Setup</summary> ```{r tbl1, echo=TRUE, message=FALSE, warning=FALSE, results='hide'} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl # Create Table & ARD result <- make_table_05(df = adsl) # Output ARD result$ard ``` </details> ```{r tbl1-print, echo=FALSE} options(width = 9999) print(result$ard, columns = "all", n = Inf) ``` ## rtables Table <details> <summary>rtables Table Setup</summary> ```{r tbl3, eval=FALSE, echo=TRUE} # Load Libraries & Data library(cardinal) adsl <- random.cdisc.data::cadsl # Output Table risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional make_table_05_rtables(df = adsl, risk_diff = risk_diff) ``` </details> ```{r tbl3, message=FALSE, warning=FALSE, eval=TRUE} ``` <details> <summary>Function Details</summary> ### `make_table_05_rtables()` ------------------------------------------------------------------------ Required variables: - **`df`**: The variables specified by `vars`, `arm_var`, and `saffl_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 ADSL) required to build table. | *No default* | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `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"` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `id_var` | (`character`) Identifier variable used to count the participants within each flag. | `"USUBJID"` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `trtsdtm_var` | (`character`) Treatment start datetime variable in df. | `"TRTSDTM"` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `trtedtm_var` | (`character`) Treatment end datetime variable in df. | `"TRTEDTM"` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `u_trtdur` | (`character`) Unit for duration of treatment. Options are `"days"`, `"weeks"`, `"months"` and `"years"`. | `"days"` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `lbl_trtdur` | (`character`) Label for treatment duration variable `u_trtdur`. | `paste("Duration of Treatment,", u_trtdur)` | +-----------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------+ | `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_05.R). </details> :::