Comments (2)
Can you provide code example to reproduce error message?
Provenance:
Creator: junlue
from tern.
Error message due to missing values in required variables, e.g. AEBODSYS, AEDECOD, etc.:
Tried to evaluate following code:
{ tbl <- t_events_per_term_grade_id(terms = ANL[, c("AEBODSYS", "AEDECOD"), drop = FALSE], id = ANL[["USUBJID"]], grade = ANL[["AETOXGR"]], col_by = as.factor(ANL[["ARM"]]), col_N = table(ADSL_P[["ARM"]]), total = "All Patients") tbl}
Got following error message:
subscript out of bounds
The error is not super informative that the issue is missing values. Another solution might be for NEST to impute missing values with "Unknown" or "Missing" on its own so no error is produced. Here's the code:
<REDACTED>NEST/nest_on_bee/master/bee_nest_utils.R")
bee_use_nest(release = "2020_08_20")
library(teal)
library(teal.modules.general)
library(teal.modules.clinical)
library(SAICE)
initialize_connection()
ADSL <- read_entimice("<path>/adsl.sas7bdat")
ADAE <- read_entimice("<path>/adae.sas7bdat")
close_connection()
ADAE = ADAE %>%
mutate(AETOXGR = as.factor(AETOXGR))
library(random.cdisc.data)
library(dplyr)
app <- teal::init(
data = cdisc_data(
cdisc_dataset("ADSL", ADSL),
cdisc_dataset("ADAE", ADAE),
code = 'ADSL <- radsl(cached = TRUE)
ADAE <- radae(cached = TRUE)',
check = FALSE
),
modules = root_modules(
tm_t_events_by_grade(
label = "AE Table by Grade",
dataname = 'ADAE',
arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
llt = choices_selected(
choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
selected = c("AEDECOD")
),
hlt = choices_selected(
choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
selected = "AEBODSYS"
),
grade = choices_selected(
choices = variable_choices(ADAE, c("AETOXGR")),
selected = "AETOXGR"
),
add_total = TRUE
)
)
)
shinyApp(app$ui, app$server)
Provenance:
Creator: harric17
from tern.
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