SRC does not capture title and footnotes for modules which use ui_g_decorate

[nikolas-burkoff]

https://rsconnect.roche.com/content/6127/

For example:

Give SRC without title and footnote:

# 
# Automatically generated R code
# 
#   Running: /opt/rstudio-connect/mnt/app
#        on: rkaub00459.kau.roche.com
# R version: R version 4.0.3 (2020-10-10)
#      Date: Mon Oct  4 16:12:01 2021
# 
# Current libraries loaded (derived by .libPaths()):
#   - /opt/bee/share/nest-packages/UAT_2021_10_01_fin/4.0.3/libs
#   - /opt/bee_tools/R/4.0.3/lib64/R/library
# 
# Packages versions: teal.osprey (0.1.11), osprey (0.1.11), teal.modules.general
#                    (0.2.11), ggmosaic (0.3.3), teal.modules.clinical (0.8.10),
#                    tern (0.7.5), optimx (2020-4.2), rtables (0.3.8.9101),
#                    magrittr (1.5), teal (0.10.0), ggplot2 (3.3.2), dplyr
#                    (1.0.2), scda (0.1.1), reticulate (1.18), shiny (1.5.0)
# 
# You can run this code interactively on http://r.roche.com
# 

# Next two lines are for using NEST packages on BEE (r.roche.com)
source("https://raw.github.roche.com/NEST/nest_on_bee/master/bee_nest_utils.R")
bee_use_nest(release = "UAT_2021_10_01_fin")

library(shiny)
library(reticulate)
library(scda)
library(dplyr)
library(ggplot2)
library(teal)
library(magrittr)
library(rtables)
library(optimx)
library(tern)
library(teal.modules.clinical)
library(ggmosaic)
library(teal.modules.general)
library(osprey)
library(teal.osprey)

ADSL <- synthetic_cdisc_data("latest")$adsl
adsl_labels <- rtables::var_labels(ADSL)
ADSL <- ADSL %>%
  mutate(TRTDURD = as.numeric(as.Date(TRTEDTM) - as.Date(TRTSDTM)) + 1, DTHFL = ifelse(!is.na(DTHDT), "Y", NA), EOSSTT = factor(EOSSTT, levels = c("COMPLETED", "ONGOING", "DISCONTINUED"))) %>%
  rtables::var_relabel(TRTDURD = "Treatment Duration in Days", DTHFL = "Death Flag", DCSREAS = "Reason for Study Discontinuation", EOSSTT = "End of Study Status") %>%
  droplevels()
rtables::var_labels(ADSL)[c(names(adsl_labels))] <- adsl_labels
ADAE <- synthetic_cdisc_data("latest")$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 = ifelse(AEREL == "Y" & AESER == "Y", "Y", "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"
  )



## NOTE: Reproducibility of data import and preprocessing was not
## explicitly checked (argument "check = FALSE" is set).
## The app developer has the choice to check the reproducibility
## and might have omitted this step for some reason. Please reach
## out to the app developer for details.

# ADSL MD5 hash at the time of analysis: 5682036b72676588166a34045edb7cfe
# ADAE MD5 hash at the time of analysis: 1c289c802f0c346ed30725f1cf116ff1


ADSL_FILTERED <- ADSL
ADAE_FILTERED_ALONE <- ADAE
ADAE_FILTERED <- dplyr::inner_join(x = ADAE_FILTERED_ALONE, y = ADSL_FILTERED[, c("STUDYID", "USUBJID"), drop = FALSE], by = c("STUDYID", "USUBJID"))



ANL <- merge(x = ADSL_FILTERED[, c("USUBJID", "STUDYID", "ARM"), drop = FALSE], y = ADAE_FILTERED[, c("USUBJID", "STUDYID", "AEDECOD"), drop = FALSE], all.x = FALSE, all.y = FALSE, by = c("USUBJID", "STUDYID"))
term <- ANL[["AEDECOD"]]
id <- ANL$USUBJID
arm <- ANL[["ARM"]]
arm_N <- table(ADSL_FILTERED[["ARM"]])
ref <- "A: Drug X"
trt <- "B: Placebo"
osprey::g_events_term_id(term = term, id = id, arm = arm, arm_N = arm_N, ref = "A: Drug X", trt = "B: Placebo", sort_by = NULL, rate_range = c(0.1, 1), diff_range = c(-0.5, 0.5), reversed = FALSE, conf_level = 0.95, diff_ci_method = "wald", axis_side = "left", fontsize = 5L, draw = TRUE)

[pawelru]

this has been already reported in the past and the conclusion is that was never needed / required - closing

[pawelru]

Looks that I was wrong with my previous statement. I checked it and indeed it was reported but not closed. Moving to the main backlog then

[pawelru]

would be good to wait with that until more general approach would be in place https://github.com/insightsengineering/coredev-tasks/issues/361

[gogonzo]

It needs some solution. We have title, subtitle, footnote reproducible in tmc, and tmg where we use

• teal.widgets::ggplot2_args which can't be used here (with grid plots). Extend ggplot2_args? (rather not)

• We might consider here not using ui_g_decorate to decorate the object but maybe returning a call to be used in chunks.

• We can also add title and footnotes in the chunks directly in each module (without srv_g_decorate).