cicdguy
commented
3 years ago 
Provenance:
Creator: bahatskyOpen cicdguy opened 3 years ago
cicdguy
commented
3 years ago
Provenance:
Creator: bahatskyWe can't reproduce this issue.
Provenance:
Creator: qinp1I set RELSERFL = "N" in the sample code from the user guide and if I only select it I get this error message.
Provenance:
Creator: bahatskyThe shiny app looks different, there is no RELSERFL, here is what I got. Any ideas?
cicdguy
commented
3 years ago # Next two lines are for using NEST packages on BEE (r.roche.com)
<REDACTED>NEST/nest_on_bee/master/bee_nest_utils.R")
bee_use_nest(release = "2021_07_07")
library(random.cdisc.data)
library(dplyr)
library(teal.modules.clinical)
library(teal.modules.general)
library(teal.osprey)
options(teal_logging = FALSE)
ADSL <- radsl(cached = TRUE)
# derive ADSL treatment duration
adsl_labels <- rtables::var_labels(ADSL)
ADSL <- ADSL %>%
mutate(
TRTDURD = as.numeric(as.Date(TRTEDTM) - as.Date(TRTSDTM)) + 1,
DTHFL = ifelse(!is.na(DTHDT), "Y", NA),
EOSSTT = factor(EOSSTT, levels = c("COMPLETED", "ONGOING", "DISCONTINUED"))
) %>%
rtables::var_relabel(
TRTDURD = "Treatment Duration in Days",
DTHFL = "Death Flag",
DCSREAS = "Reason for Study Discontinuation",
EOSSTT = "End of Study Status"
) %>%
droplevels()
rtables::var_labels(ADSL)[c(names(adsl_labels))] <- adsl_labels
ADAE <- radae(ADSL, cached = TRUE)
# derive common flags for AEs
adae_labels <- rtables::var_labels(ADAE)
ADAE <- ADAE %>%
mutate_at(c("AESOC", "AEBODSYS", "AEHLT", "AEDECOD", "AETERM", "AELLT"), as.character) %>%
mutate(
RELFL = ifelse(AEREL == "Y", "Y", "N"),
CTC35FL = ifelse(AETOXGR %in% c("3", "4", "5"), "Y", "N"),
SERFL = ifelse(AESER == "Y", "Y", "N"),
RELSERFL = "N",
AEREL1 = (AEREL == "Y" & ACTARM == "A: Drug X"),
AEREL2 = (AEREL == "Y" & ACTARM == "B: Placebo"),
ASTDT = as.Date(ASTDTM),
AENDT = as.Date(AENDTM)
) %>%
rtables::var_relabel(
RELFL = "Related AE",
CTC35FL = "Grade >=3 AE",
SERFL = "Serious AE",
RELSERFL = "Related Serious AE",
AEREL1 = "AE related to A: Drug X",
AEREL2 = "AE related to B: Placebo",
ASTDT = "Analysis Start Date",
AENDT = "Analysis End Date",
AESOC = "Primary System Organ Class",
AEBODSYS = "Body System or Organ Class",
AEHLT = "High Level Term",
AEDECOD = "Dictionary-Derived Term",
AETERM = "Reported Term for the Adverse Event",
AELLT = "Lowest Level Term"
)
ADCM <- radcm(ADSL, cached = TRUE)
# process ADCM
ADCM <- ADCM %>%
mutate(ASTDT = as.Date(ASTDTM),
AENDT = as.Date(AENDTM)) %>%
rtables::var_relabel(
ASTDT = "Analysis Start Date",
AENDT = "Analysis End Date"
)
ADEX <- radex(ADSL, cached = TRUE)
# process ADEX
ADEX <- ADEX %>%
mutate(
ASTDT = as.Date(ASTDTM),
AENDT = as.Date(AENDTM)
) %>%
rtables::var_relabel(
ASTDT = "Analysis Start Date",
AENDT = "Analysis End Date"
)
ADTR <- radtr(ADSL, cached = TRUE)
# process ADTR
adtr_labels <- rtables::var_labels(ADTR)
ADTR <- ADTR %>%
mutate(PCHG = ifelse(AVISIT == "BASELINE", 0, PCHG),
CHG = ifelse(AVISIT == "BASELINE", 0, CHG),
AVAL = ifelse(AVISIT == "BASELINE", BASE, AVAL),
AVALC = ifelse(AVISIT == "BASELINE", as.character(BASE), AVALC)) %>%
filter(AVISIT != "SCREENING")
rtables::var_labels(ADTR) <- adtr_labels
ADTRWF <- ADTR %>%
filter(AVISIT != "BASELINE")
rtables::var_labels(ADTRWF) <- rtables::var_labels(ADTR)
# process ADRS
ADRSSWIM <- radrs(ADSL, cached = TRUE) %>%
filter(PARAMCD == "OVRINV") %>%
arrange(USUBJID)
ADRS <- radrs(ADSL, cached = TRUE)
adrs_labels <- rtables::var_labels(ADRS)
ADRS <- ADRS %>%
filter(PARAMCD %in% c("BESRSPI", "INVET")) %>%
mutate(ADT = as.Date(ADTM)) %>%
droplevels()
rtables::var_labels(ADRS) <- c(adrs_labels, "Analysis Date")
ADLB <- radlb(ADSL, cached = TRUE)
# process ADLB
ADLB <- ADLB %>%
mutate(ADT = as.Date(ADTM),
LBSTRESN = as.numeric(LBSTRESC)) %>%
rtables::var_relabel(
ADT = "Analysis Date",
LBSTRESN = "Numeric Result/Finding in Standard Units"
)
## Reusable Configuration For Modules
arm_vars <- c("ARMCD", "ARM", "ACTARMCD", "ACTARM", "EOSSTT")
aeflag_vars <- c("RELFL", "CTC35FL", "SERFL", "RELSERFL")
facet_vars <- c("SEX", "BMRKR2", "RACE", "STRATA1", "STRATA2")
ds_vars <- c("EOSSTT", "DCSREAS")
cs_arm_var <- choices_selected(
choices = variable_choices(ADSL, subset = arm_vars),
selected = "ARM"
)
cs_aeflag_var <- choices_selected(
choices = variable_choices(ADAE, subset = aeflag_vars),
selected = NULL
)
cs_aeterm_var <- choices_selected(
choices = variable_choices(ADAE, subset = c("AEDECOD", "AETERM", "AELLT", "AESOC", "AEBODSYS", "AEHLT")),
selected = "AEDECOD"
)
cs_facet_var <- choices_selected(
choices = variable_choices(ADSL, subset = facet_vars),
selected = NULL
)
cs_ds_var <- choices_selected(
choices = variable_choices(ADSL, ds_vars),
selected = ds_vars
)
cs_bar_var <- choices_selected(
choices = variable_choices(ADSL, c("TRTDURD", "EOSDY")),
selected = "TRTDURD"
)
cs_paramcd_rsp <- choices_selected(
choices = value_choices(ADRS, "PARAMCD", "PARAM", subset = c("BESRSPI", "INVET")),
selected = "BESRSPI"
)
cs_paramcd_tr <- choices_selected(
choices = value_choices(ADTR, "PARAMCD", "PARAM", subset = "SLDINV"),
selected = "SLDINV"
)
adsl_labels <- rtables::var_labels(ADSL)
fact_vars_asl <- names(Filter(isTRUE, sapply(ADSL, is.factor)))
date_vars_asl <- names(ADSL)[vapply(ADSL, function(x) inherits(x, c("Date", "POSIXct", "POSIXlt")), logical(1))]
demog_vars_asl <- names(ADSL)[!(names(ADSL) %in% c("USUBJID", "STUDYID", date_vars_asl))]
## Create front page for app ----
srv_front_page <- function(input, output, session, datasets, dataname) {
observeEvent(input$show_teal_setup_code, {
showModal(modalDialog(
title = "R Code Used to Setup the Current Teal Shiny App",
tags$div(
actionButton("copyRCode", "Copy to Clipboard", `data-clipboard-target` = "#r_code"),
style = 'padding-bottom: 15px;'
),
tags$div(tags$pre(id = "r_code", paste(readLines("app.R"), collapse = "\n"))),
footer = tagList(
actionButton("copyRCode", "Copy to Clipboard", `data-clipboard-target` = "#r_code"),
modalButton("Dismiss")
),
size = "l",
easyClose = TRUE
))
})
}
ui_front_page <- function(id, ...) {
ns <- NS(id)
tagList(
tags$p("The", tags$code("ADSL"), ",", tags$code("ADAE"), ",", tags$code("ADRS"), ", and ",
tags$code("ADTR"), "data in this example app has been created using random number generators."),
tags$p("", style = "height: 20px;"),
tags$p("This sample app mainly covers ", tags$code("teal.osprey"), " modules.",
"If additional safety and efficacy modules are needed,",
"please refer to the safety and efficacy sample app templates",
"to add additional modules."),
tags$p("", style = "height: 15px;"),
tags$p(paste("These apps are relatively easily setup for a study.",
"That is, the teal framework is optimized to setup one",
"Shiny App per analysis purpose. For example, the code to setup",
"the current teal app can be requested with the following button:")),
tags$p("", style = "height: 15px;"),
actionButton(ns("show_teal_setup_code"), "Show Teal Shiny App Setup R-Code", icon = icon("glyphicon-align-justify")),
tags$p("", style = "height: 20px;"),
tags$div(
tags$p(
"This is shiny app was brought to you by ED SPA. For more information please contact NEST SME team."
)
)
)
}
# create cdisc_dataset objects to pass into app
adsl <- cdisc_dataset(
dataname = "ADSL",
x = ADSL,
code = 'ADSL <- radsl(cached = TRUE)
adsl_labels <- rtables::var_labels(ADSL)
ADSL <- ADSL %>%
mutate(
TRTDURD = as.numeric(as.Date(TRTEDTM) - as.Date(TRTSDTM)) + 1,
DTHFL = ifelse(!is.na(DTHDT), "Y", NA),
EOSSTT = factor(EOSSTT, levels = c("COMPLETED", "ONGOING", "DISCONTINUED"))
) %>%
rtables::var_relabel(
TRTDURD = "Treatment Duration in Days",
DTHFL = "Death Flag",
DCSREAS = "Reason for Study Discontinuation",
EOSSTT = "End of Study Status"
) %>%
droplevels()
rtables::var_labels(ADSL)[c(names(adsl_labels))] <- adsl_labels'
)
adae <- cdisc_dataset(
dataname = "ADAE",
x = ADAE,
keys = c("STUDYID", "USUBJID", "AETERM", "AESEQ"),
code = 'ADAE <- radae(ADSL, cached = TRUE)
# derive common flags for AEs
ADAE <- ADAE %>%
mutate_at(
c("AESOC", "AEBODSYS", "AEHLT", "AEDECOD", "AETERM", "AELLT"),
as.character
) %>%
mutate(
RELFL = ifelse(AEREL == "Y", "Y", "N"),
CTC35FL = ifelse(AETOXGR %in% c("3", "4", "5"), "Y", "N"),
SERFL = ifelse(AESER == "Y", "Y", "N"),
RELSERFL = "N",
AEREL1 = (AEREL == "Y" & ACTARM == "A: Drug X"),
AEREL2 = (AEREL == "Y" & ACTARM == "B: Placebo"),
ASTDT = as.Date(ASTDTM),
AENDT = as.Date(AENDTM)
) %>%
rtables::var_relabel(
RELFL = "Related AE",
CTC35FL = "Grade >=3 AE",
SERFL = "Serious AE",
RELSERFL = "Related Serious AE",
AEREL1 = "AE related to A: Drug X",
AEREL2 = "AE related to B: Placebo",
ASTDT = "Analysis Start Date",
AENDT = "Analysis End Date",
AESOC = "Primary System Organ Class",
AEBODSYS = "Body System or Organ Class",
AEHLT = "High Level Term",
AEDECOD = "Dictionary-Derived Term",
AETERM = "Reported Term for the Adverse Event",
AELLT = "Lowest Level Term"
)',
vars = list(ADSL = adsl)
)
adcm <- cdisc_dataset(
dataname = "ADCM",
x = ADCM,
code = 'ADCM <- radcm(ADSL, cached = TRUE)
ADCM <- ADCM %>%
mutate(
ASTDT = as.Date(ASTDTM),
AENDT = as.Date(AENDTM)
) %>%
rtables::var_relabel(
ASTDT = "Analysis Start Date",
AENDT = "Analysis End Date"
)',
vars = list(ADSL = adsl)
)
adex <- cdisc_dataset(
dataname = "ADEX",
x = ADEX,
code = 'ADEX <- radex(ADSL, cached = TRUE)
ADEX <- ADEX %>%
mutate(
ASTDT = as.Date(ASTDTM),
AENDT = as.Date(AENDTM)
) %>%
rtables::var_relabel(
ASTDT = "Analysis Start Date",
AENDT = "Analysis End Date"
)',
vars = list(ADSL = adsl)
)
adtr <- cdisc_dataset(
dataname = "ADTR",
x = ADTR,
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
code = 'ADTR <- radtr(ADSL, cached = TRUE)
adtr_labels <- rtables::var_labels(ADTR)
ADTR <- ADTR %>%
mutate(
PCHG = ifelse(AVISIT == "BASELINE", 0, PCHG),
CHG = ifelse(AVISIT == "BASELINE", 0, CHG),
AVAL = ifelse(AVISIT == "BASELINE", BASE, AVAL),
AVALC = ifelse(AVISIT == "BASELINE", as.character(BASE), AVALC)
) %>%
dplyr::filter(AVISIT != "SCREENING")
rtables::var_labels(ADTR) <- adtr_labels',
var = list(ADSL = adsl)
)
adtrwf <- cdisc_dataset(
dataname = "ADTRWF",
x = ADTRWF,
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
code = 'ADTRWF <- ADTR %>%
dplyr::filter(AVISIT != "BASELINE")
rtables::var_labels(ADTRWF) <- rtables::var_labels(ADTR)',
vars = list(ADTR = adtr))
adrs <- cdisc_dataset(
dataname = "ADRS",
x = ADRS,
code = 'ADRS <- radrs(ADSL, cached = TRUE)
adrs_labels <- rtables::var_labels(ADRS)
ADRS <- ADRS %>%
filter(PARAMCD %in% c("BESRSPI", "INVET")) %>%
mutate(ADT = as.Date(ADTM)) %>%
droplevels()
rtables::var_labels(ADRS) <- c(adrs_labels, "Analysis Date")',
vars = list(ADSL = adsl))
adrsswim <- cdisc_dataset(
dataname = "ADRSSWIM",
x = ADRSSWIM,
keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"),
code = 'ADRSSWIM <- radrs(ADSL, cached = TRUE) %>%
dplyr::filter(PARAMCD == "OVRINV") %>%
arrange(USUBJID)',
vars = list(ADSL = adsl)
)
adlb <- cdisc_dataset(
dataname = "ADLB",
x = ADLB,
code = 'ADLB <- radlb(ADSL, cached = TRUE)
ADLB <- ADLB %>%
mutate(
ADT = as.Date(ADTM),
LBSTRESN = as.numeric(LBSTRESC)
) %>%
rtables::var_relabel(
ADT = "Analysis Date",
LBSTRESN = "Numeric Result/Finding in Standard Units"
)',
vars = list(ADSL = adsl))
## Setup App
app <- teal::init(
data = cdisc_data(
adsl,
adae,
adex,
adcm,
adtr,
adtrwf,
adrs,
adrsswim,
adlb,
check = TRUE),
modules = root_modules(
module(
label = "App Information",
server = srv_front_page,
ui = ui_front_page,
filters = "all"
),
tm_data_table("Data Table"),
tm_variable_browser("Variable Browser"),
modules(
"Adverse Events",
tm_g_events_term_id(
label = "Common AE Plot",
dataname = "ADAE",
term_var = cs_aeterm_var,
arm_var = cs_arm_var,
plot_height = c(800, 200, 2000)
),
tm_g_ae_oview(
label = "AE Overview Plot",
dataname = "ADAE",
arm_var = cs_arm_var,
add_flag = choices_selected(choices = variable_choices(ADAE, c("AEREL1", "AEREL2")),
selected = NULL),
plot_height = c(800, 200, 2000)
),
tm_g_butterfly(
label = "Butterfly Plot",
dataname = "ADAE",
filter_var = cs_aeflag_var,
right_var = cs_arm_var,
left_var = cs_arm_var,
category_var = choices_selected(
choices = variable_choices(ADAE, subset = c("AEDECOD", "AETERM", "AESOC", "AEBODSYS")),
selected = "AEBODSYS"
),
color_by_var = choices_selected(
choices = c(variable_choices(ADAE, "AETOXGR"), "None"),
selected = "AETOXGR"),
count_by_var = choices_selected(choices = c("# of patients", "# of AEs"),
selected = "# of patients"),
facet_var = cs_facet_var,
sort_by_var = choices_selected(choices = c("count", "alphabetical"), selected = "count"),
legend_on = TRUE,
plot_height = c(600, 200, 2000)
),
tm_g_ae_sub(
label = "AE by Subgroup",
dataname = "ADAE",
arm_var = choices_selected(
selected = "ACTARMCD",
choices = c("ACTARM", "ACTARMCD")
),
group_var = choices_selected(
selected = c("SEX", "REGION1", "RACE"),
choices = c("SEX", "REGION1", "RACE")
),
plot_height = c(600, 200, 2000)
)
),
tm_t_summary(
label = "Disposition Table",
dataname = "ADSL",
arm_var = cs_arm_var,
summarize_vars = cs_ds_var,
useNA = "no"
),
tm_g_spiderplot(
label = "Spider plot",
dataname = "ADTR",
paramcd = cs_paramcd_tr,
x_var = choices_selected(choices = variable_choices(ADTR, "ADY"), selected = "ADY"),
y_var = choices_selected(choices = variable_choices(ADTR, c("PCHG", "CHG", "AVAL")),
selected = "PCHG"),
marker_var = choices_selected(choices = variable_choices(ADSL, c("SEX", "RACE")),
selected = "SEX"),
line_colorby_var = cs_arm_var,
xfacet_var = cs_facet_var,
yfacet_var = cs_facet_var,
vref_line = "42",
href_line = "-20, 0, 30",
anno_txt_var = TRUE,
legend_on = FALSE,
plot_height = c(600, 200, 2000)
),
tm_g_swimlane(
label = "Swimlane Plot",
dataname = "ADRSSWIM",
bar_var = cs_bar_var,
bar_color_var = choices_selected(
choices = variable_choices(ADSL, fact_vars_asl),
selected = "EOSSTT"
),
sort_var = choices_selected(
choices = variable_choices(ADSL, c(arm_vars, "TRTDURD")),
selected = arm_vars[1]
),
marker_pos_var = choices_selected(choices = c(variable_choices(ADRS, "ADY")),
selected = "ADY"),
marker_shape_var = choices_selected(c(variable_choices(ADRS, c("AVALC", "AVISIT"))),
selected = "AVALC"),
marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "Death" = 8),
marker_color_var = choices_selected(choices = c(variable_choices(ADRS, c("AVALC", "AVISIT"))),
selected = "AVALC"),
marker_color_opt = c("CR" = "green", "PR" = "blue", "SD" = "goldenrod",
"PD" = "red", "Death" = "black"),
vref_line = c(30, 60),
anno_txt_var = choices_selected(
choices = variable_choices(ADSL, intersect(arm_vars, fact_vars_asl)),
selected = arm_vars[1]
)
),
tm_g_waterfall(
label = "Waterfall Plot",
dataname_tr = "ADTRWF",
dataname_rs = "ADRS",
bar_paramcd = cs_paramcd_tr,
bar_var = choices_selected(variable_choices(ADTRWF, "PCHG"), "PCHG"),
bar_color_var = choices_selected(variable_choices(ADSL, fact_vars_asl), "ARMCD"),
sort_var = choices_selected(variable_choices(ADSL, fact_vars_asl), NULL),
add_label_var_sl = choices_selected(variable_choices(ADSL, fact_vars_asl), NULL),
add_label_paramcd_rs = cs_paramcd_rsp,
anno_txt_var_sl = choices_selected(variable_choices(ADSL, fact_vars_asl), NULL),
anno_txt_paramcd_rs = cs_paramcd_rsp,
facet_var = cs_facet_var,
ytick_at = 20,
href_line = "-30, 20",
gap_point_val = NULL,
plot_height = c(1200L, 400L, 5000L)
),
tm_g_patient_profile(
label = "Patient Profile Plot",
patient_id = choices_selected(
choices = unique(ADSL$USUBJID),
selected = unique(ADSL$USUBJID)[1]
),
sl_dataname = "ADSL",
ex_dataname = "ADEX",
ae_dataname = "ADAE",
rs_dataname = "ADRS",
cm_dataname = "ADCM",
lb_dataname = "ADLB",
show_ex_plot = TRUE,
show_ae_plot = TRUE,
show_rs_plot = TRUE,
show_cm_plot = FALSE,
show_lb_plot = TRUE,
sl_start_date = choices_selected(
selected = "TRTSDTM",
choices = variable_choices(ADSL, subset = c("TRTSDTM", "RANDDT"))),
ex_var = choices_selected(
selected = "PARCAT2",
choices = variable_choices(ADEX, "PARCAT2")),
ae_var = choices_selected(
selected = "AEDECOD",
choices = variable_choices(ADAE, c("AEDECOD", "AESOC"))),
ae_line_col_var = choices_selected(
selected = "AESER",
choices = variable_choices(ADAE, c("AESER", "AEREL"))),
ae_line_col_opt = c("Y" = "red", "N" = "blue"),
rs_var = choices_selected(
selected = "PARAMCD",
choices = variable_choices(ADRS, c("PARAMCD", "PARAM"))),
cm_var = choices_selected(
selected = "CMDECOD",
choices = variable_choices(ADCM, c("CMDECOD", "CMCAT"))),
lb_var = choices_selected(
selected = "PARAMCD",
choices = variable_choices(ADLB, c("PARAMCD", "PARAM"))),
x_limit = "-28, 750",
plot_height = c(1200, 400, 5000)
)
),
header = div(
class = "",
style = "margin-bottom: 2px;",
tags$h1("Demo ED Onco teal app with random ADaM data", tags$span("ED SPA", class = "pull-right"))
),
footer = tags$p(class="text-muted", "Source: agile-R:Teal:Sample Teal Apps:Osprey")
)
## Start Teal Shiny App ----
shinyApp(app$ui, app$server)
Provenance:
Creator: bahatsky
Provenance: