---
title: AEL02_ED
subtitle: Listing of Adverse Events (for Early Development Studies)
---
------------------------------------------------------------------------
{{< include ../../_utils/envir_hook.qmd >}}
```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
library(dplyr)
library(rlistings)
library(lubridate)
adae <- random.cdisc.data::cadae
adae_anl <- adae %>%
filter(SAFFL == "Y") %>%
mutate(
DHM = as.period(LDOSEDTM %--% ASTDTM),
TMOM = minute(DHM) + ifelse(second(DHM) >= 30, 1, 0),
TMOH = hour(DHM) + ifelse(TMOM == 60, 1, 0),
TMOD = day(DHM) + ifelse(TMOH == 24, 1, 0)
) %>%
mutate(
TMOM = TMOM %% 60,
TMOH = TMOH %% 24
)
out <- adae_anl %>%
mutate(
ADURN = AENDY - ASTDY + 1,
cent_subj = paste(SITEID, SUBJID, sep = "/"),
ASR = paste(AGE, SEX, RACE, sep = "/"),
AESER_F = if_else(AESER == "Y", "Yes", "No", ""),
AEREL_F = if_else(AEREL == "Y", "Yes", "No", ""),
AECONTRT_F = if_else(AECONTRT == "Y", "Yes", "No", ""),
AEOUT_F = case_when(
AEOUT == "FATAL" ~ 1,
AEOUT == "NOT RECOVERED/NOT RESOLVED" ~ 2,
AEOUT == "RECOVERED/RESOLVED" ~ 3,
AEOUT == "RECOVERED/RESOLVED WITH SEQUELAE" ~ 4,
AEOUT == "RECOVERING/RESOLVING" ~ 5,
AEOUT == "UNKNOWN" ~ 6
),
AEACN_F = case_when(
AEACN == "DOSE INCREASED" ~ 1,
AEACN == "DOSE NOT CHANGED" ~ 2,
AEACN == "DOSE REDUCED" | AEACN == "DOSE RATE REDUCED" ~ 3,
AEACN == "DRUG INTERRUPTED" ~ 4,
AEACN == "DRUG WITHDRAWN" ~ 5,
AEACN == "NOT APPLICABLE" | AEACN == "NOT EVALUABLE" ~ 6,
AEACN == "UNKNOWN" ~ 7
)
) %>%
select(
cent_subj, ASR, TRT01A, AEDECOD, ASTDY, TMOD, TMOH, TMOM,
ADURN, AESER_F, AESEV, AEREL_F, AEOUT_F, AECONTRT_F, AEACN_F
)
out <- out %>% var_relabel(
cent_subj = "Center/Patient ID",
ASR = "Age/Sex/Race",
TRT01A = "Treatment",
AEDECOD = "Adverse\nEvent MedDRA\nPreferred Term",
ASTDY = "Study\nDay of\nOnset",
TMOD = "Time from\nLast Dose\nto Onset\ndays",
TMOH = "Time from\nLast Dose\nto Onset\nhrs",
TMOM = "Time from\nLast Dose\nto Onset\nmins",
ADURN = "AE\nDuration\nin Days",
AESER_F = "Serious",
AESEV = "Most\nExtreme\nIntensity",
AEREL_F = "Caused by\nStudy\nDrug",
AEOUT_F = "Outcome\n(1)",
AECONTRT_F = "Treatment\nfor AE",
AEACN_F = "Action\nTaken\n(2)"
)
```
```{r include = FALSE}
webr_code_labels <- c("setup")
```
{{< include ../../_utils/webr_no_include.qmd >}}
## Output
:::: panel-tabset
## Standard Listing
::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview
```{r lsting, test = list(lsting = "lsting")}
lsting <- as_listing(
out,
key_cols = c("TRT01A", "cent_subj", "ASR"),
disp_cols = names(out),
main_title = "Listing of Adverse Events (for early development studies)",
main_footer = "
(1) Outcome: 1 = fatal; 2 = not recovered/not resolved; 3 = recovered/resolved;
4 = recovered/resolved with sequelae; 5 = recovering/resolving; 6 = unknown.
(2) Action taken with study drug: 1 = dose increased; 2 = dose not changed;
3 = dose reduced; 4 = drug interrupted; 5 = drug withdrawn; 6 = not applicable;
7 = unknown.
* Study day derived from imputed onset date.
** Duration derived from imputed onset date and/or end date."
)
head(lsting, 20)
```
```{r include = FALSE}
webr_code_labels <- c("lsting")
```
{{< include ../../_utils/webr.qmd >}}
:::
## Data Setup
```{r setup}
#| code-fold: show
```
::::
{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}