Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(admiraldev)
## ---- warning=FALSE, message=FALSE--------------------------------------------
library(admiral)
library(dplyr, warn.conflicts = FALSE)
## ---- eval = TRUE-------------------------------------------------------------
data(admiral_adlb)
adlb <- admiral_adlb %>%
filter(PARAMCD %in% c("AST", "ALT", "BILI") & is.na(DTYPE))
## ---- echo = FALSE------------------------------------------------------------
head(adlb) %>%
dataset_vignette()
## -----------------------------------------------------------------------------
adlb_annotated <- adlb %>%
mutate(
CRIT1 = case_when(
PARAMCD == "AST" ~ "AST >=3xULN",
PARAMCD == "ALT" ~ "ALT >=3xULN",
PARAMCD == "BILI" ~ "BILI >=2xULN"
),
CRIT1FL = if_else(
(AVAL / ANRHI >= 3 & PARAMCD %in% c("AST", "ALT")) |
(AVAL / ANRHI >= 2 & PARAMCD == "BILI"),
"Y",
NA_character_
)
) %>%
select(STUDYID, USUBJID, TRT01A, PARAMCD, LBSEQ, ADT, AVISIT, ADY, AVAL, ANRHI, CRIT1, CRIT1FL)
## ---- echo = FALSE------------------------------------------------------------
dataset_vignette(adlb_annotated)
## ---- warning = FALSE---------------------------------------------------------
altast_records <- adlb_annotated %>%
filter(PARAMCD %in% c("AST", "ALT"))
bili_records <- adlb_annotated %>%
filter(PARAMCD %in% c("BILI"))
hylaw_records <- derive_vars_joined(
dataset = altast_records,
dataset_add = bili_records,
by_vars = exprs(STUDYID, USUBJID),
order = exprs(ADY),
filter_join = 0 <= ADT.join - ADT & ADT.join - ADT <= 14 & CRIT1FL == "Y" & CRIT1FL.join == "Y",
new_vars = exprs(BILI_DT = ADT, BILI_CRITFL = CRIT1FL),
mode = "first"
)
## ---- echo = FALSE------------------------------------------------------------
hylaw_records %>%
arrange(desc(BILI_CRITFL), desc(CRIT1FL)) %>%
dataset_vignette()
## -----------------------------------------------------------------------------
hylaw_records_pts_visits <- hylaw_records %>%
select(STUDYID, USUBJID, TRT01A) %>% # add AVISIT, ADT for by visit
distinct()
hylaw_records_fls <- hylaw_records %>%
select(STUDYID, USUBJID, TRT01A, CRIT1FL, BILI_CRITFL) %>% # add AVISIT, ADT for by visit
distinct()
hylaw_params <- derive_param_exist_flag(
dataset_ref = hylaw_records_pts_visits,
dataset_add = hylaw_records_fls,
condition = CRIT1FL == "Y" & BILI_CRITFL == "Y",
false_value = "N",
missing_value = "N",
by_vars = exprs(STUDYID, USUBJID, TRT01A), # add AVISIT, ADT for by visit
set_values_to = exprs(
PARAMCD = "HYSLAW",
PARAM = "ALT/AST >= 3xULN and BILI >= 2xULN",
AVAL = yn_to_numeric(AVALC)
)
)
## ---- echo = FALSE------------------------------------------------------------
hylaw_params %>%
arrange(desc(AVAL)) %>%
dataset_vignette()
## -----------------------------------------------------------------------------
adlbhy <- adlb_annotated %>%
bind_rows(hylaw_params)
## ---- echo = FALSE------------------------------------------------------------
dataset_vignette(adlbhy)
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