init

.Rbuildignore

@@ -0,0 +1,16 @@
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^\.gitlab-ci\.yml$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^app\.R$
+^R/rsconnect$
+^rsconnect$
+^\.covrignore$
+^public$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.covrignore

@@ -0,0 +1,3 @@
+R/runApp.R
+R/server.R
+R/ui.R

.gitignore

@@ -0,0 +1,56 @@
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+.Rproj.user
+paths
+public/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+.Rproj.user
+
+# images
+*.jpeg
+inst/doc
+
+
+# Shiny
+**/rsconnect/
+
+# vim
+*.swp
+docs

.gitlab-ci.yml

@@ -0,0 +1,97 @@
+stages:          # List of stages for jobs, and their order of execution
+  - setup
+  - check
+  - coverage
+  - rhub
+  - shiny
+  - deploy_pages
+
+before_script: ## Check this part
+
+  - export http_proxy=http://proxy.eu.novartis.net:2010/
+  - export https_proxy=http://proxy.eu.novartis.net:2010/
+  - export NOT_CRAN=true
+  - export CCACHE_DIR=/tmp
+  - export PATH=/usr/lib/ccache:$PATH
+
+
+# <DON'T REMOVE!>
+variables:
+  RENV_PATHS_CACHE: "~/.renv/cache"
+  RENV_PATHS_LIBRARY_ROOT: "~/.renv/library"
+
+# <DON'T REMOVE!>
+cache:
+  key: ${CI_JOB_NAME}
+  paths:
+    - ${RENV_PATHS_CACHE}
+    - ${RENV_PATHS_LIBRARY}
+
+Setup:
+  stage: setup
+  script:
+    - >
+      if [ ! -d "$RENV_PATHS_CACHE" ]; then
+        mkdir -p $RENV_PATHS_CACHE;
+        echo "Installing RENV_PATHS_CACHE in ${RENV_PATHS_CACHE}...";
+      fi
+    - Rscript -e "if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv');"
+    - Rscript -e "renv::restore();"
+
+Check:
+  stage: check
+  allow_failure: true
+  script:
+    - Rscript -e "if (!requireNamespace('devtools', quietly = TRUE)) install.packages('devtools');"
+    - Rscript -e 'devtools::check()'
+
+Coverage:
+  stage: coverage
+  only:
+    - main
+    - dev
+  allow_failure: true
+  script:
+    - Rscript -e "if (!requireNamespace('covr', quietly = TRUE)) install.packages('covr');"
+    - Rscript -e "if (!requireNamespace('DT', quietly = TRUE)) install.packages('DT');"
+    - Rscript -e 'covr::gitlab(quiet = FALSE)'
+
+RHUB:
+  stage: rhub
+  only:
+    - main
+    - dev
+  script:
+    - Rscript -e "if (!requireNamespace('devtools', quietly = TRUE)) install.packages('devtools');"
+    - Rscript -e "if (!requireNamespace('rhub', quietly = TRUE)) install.packages('rhub');"
+    - Rscript -e "rhub::validate_email(email = $RHUB_EMAIL, token = $RHUB_TOKEN);"
+    - Rscript -e "devtools::check_rhub()"
+
+Shiny:
+  stage: shiny
+  only:
+    - shiny
+  allow_failure: true
+  script:
+    - Rscript -e 'source("inst/shiny/deploy.R"); deploy_app_rsc()'
+
+pages:
+  stage: deploy_pages
+  script:
+    - echo "We are on branch $CI_COMMIT_REF_NAME"
+    - mkdir -p public/$CI_COMMIT_REF_NAME
+    - Rscript -e "if (!requireNamespace('pkgdown', quietly = TRUE)) install.packages('pkgdown');"
+    - Rscript -e "if (!requireNamespace('devtools', quietly = TRUE)) install.packages('devtools');"
+    - Rscript -e "devtools::build('.')"
+    - export LOAD_MONITOS_PKG=TRUE
+    - Rscript -e "pkgdown::build_site(override = list(destination = 'public/$CI_COMMIT_REF_NAME'))"
+  artifacts:
+    name: "$CI_COMMIT_REF_NAME"
+    paths:
+      - public
+    expire_in: never
+  only:
+    - dev
+    - main
+  except:
+    - schedules

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.1.3
+Date: 2023-10-26 21:43:27 UTC
+SHA: 13f862586279e5ca7bef0aa244b9ffa74178ecc0

DESCRIPTION

@@ -0,0 +1,35 @@
+Package: monitOS
+Title: Monitoring Overall Survival in Pivotal Trials in Indolent Cancers
+URL: https://opensource.nibr.com/monitOS/
+Version: 0.1.5
+Authors@R: c(
+    person("Thomas", "Fleming", email = "[email protected]", role ="ctb"),
+    person("Lisa", "Hampson", email = "[email protected]", role ="aut"),
+    person("Bharani", "Bharani-Dharan", email = "[email protected]", role ="ctb"),
+    person("Frank", "Bretz", email = "[email protected]", role = "ctb"),
+    person("Arunava", "Chakravartty", email = "[email protected]", role = "ctb"),
+    person("Thibaud", "Coroller", email = "[email protected]", role = c("aut", "cre")),
+    person("Evanthia", "Koukouli", email = "[email protected]", role = "aut"),
+    person("Janet", "Wittes", email = "[email protected]", role = "ctb"),
+    person("Nigel", "Yateman", email = "[email protected]", role = "ctb"),
+    person("Emmanuel", "Zuber", email = "[email protected]", role = "ctb"),
+    person("Novartis", "Pharma AG", role = "cph")
+          )
+Description: These guidelines are meant to provide a pragmatic, yet rigorous, help to drug developers and decision makers, since they are shaped by three fundamental ingredients: the clinically determined margin of detriment on OS that is unacceptably high (delta null); the benefit on OS that is plausible given the mechanism of action of the novel intervention (delta alt); and the quantity of information (i.e. survival events) it is feasible to accrue given the clinical and drug development setting. The proposed guidelines facilitate transparent discussions between stakeholders focusing on the risks of erroneous decisions and what might be an acceptable trade-off between power and the false positive error rate. 
+License: GPL (>= 3)
+Maintainer: Thibaud Coroller <[email protected]>
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports:
+    stats,
+    glue,
+    shiny,
+    shinydashboard,
+Suggests:
+    testthat (>= 3.0.0),
+    covr,
+    knitr,
+    rmarkdown,
+    pkgdown
+VignetteBuilder: knitr