Merge branch 'release-0.1.5' into github-main

.Rprofile

@@ -1,5 +1 @@
 source("renv/activate.R")
-
-if (Sys.getenv("LOAD_MONITOS_PACKAGE") == "true") {
-  devtools::load_all(".")
-}

.gitignore

@@ -19,6 +19,7 @@
 /*.Rcheck/
 
 # RStudio files
+.Rproj.user/
 .Rproj.user
 paths
 public/
@@ -52,3 +53,4 @@ inst/doc
 
 # 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

@@ -1,3 +1,3 @@
-Version: 0.1.4
-Date: 2024-03-05 15:50:18 UTC
-SHA: 1c522f9d25643b3a09c626ef648e0b56dc08c27a
+Version: 0.1.5
+Date: 2024-03-21 19:08:12 UTC
+SHA: 0e0bf2cda5fea0dfd200beed7efd144d2f096ca8

DESCRIPTION

@@ -1,6 +1,7 @@
 Package: monitOS
 Title: Monitoring Overall Survival in Pivotal Trials in Indolent Cancers
-Version: 0.1.4
+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"),

NEWS.md

@@ -1,10 +1,18 @@
+# monitOS 0.1.5
+
+-   Improved `DESCRIPTION`, added website URL, screenshot Shiny app
+-   Improved `README`
+-   Improved code style using `styler`
+-   Fixed bug deploying `Shiny` app (relative import error)
+-   Fixed package coverage by focusing only on statistical tool (no shiny app)
+
 # monitOS 0.1.4
 
 -   Added a `NEWS.md` file to track changes to the package.
 -   Added `Shiny` section in `README.md` file.
 -   Improved `monitOS::run_app()`: new layout, new descriptions, new use case.
 -   Created `pkgdown` public website.
 
-# monitOS 0.1.3 | `2023-10-31`
+# monitOS 0.1.3
 
 -   Initial CRAN submission.

R/bounds.R

@@ -34,22 +34,26 @@
 #' @examples
 #' # Example 01: OS monitoring guideline retrospectively applied to Motivating Example 1
 #' # with delta null = 1.3, delta alt = 0.80, gamma_FA = 0.025 and  beta_PA = 0.10.
-#' bounds(events=c(60, 89, 110, 131, 178),
-#'         power_int=0.9,  # beta_PA
-#'         falsepos=0.025, # gamma_FA
-#'         hr_null = 1.3,  # delta_null
-#'         hr_alt = 0.8,   # delta_alt
-#'         rand_ratio = 1, # rand_ratio
-#'         hr_marg_benefit = NULL)
+#' bounds(
+#'   events = c(60, 89, 110, 131, 178),
+#'   power_int = 0.9, # beta_PA
+#'   falsepos = 0.025, # gamma_FA
+#'   hr_null = 1.3, # delta_null
+#'   hr_alt = 0.8, # delta_alt
+#'   rand_ratio = 1, # rand_ratio
+#'   hr_marg_benefit = NULL
+#' )
 #' # Example 02: OS monitoring guideline applied to Motivating Example 2
 #' # with delta null = 4/3, delta alt = 0.7, gamma_FA = 0.20 and beta_PA = 0.1.
-#' bounds(events=c(60, 89, 110, 131, 178),
-#'        power_int=0.9,  # beta_PA
-#'        falsepos=0.025, # gamma_FA
-#'        hr_null = 1.3,  # delta_null
-#'        hr_alt = 0.8,   # delta_alt
-#'        rand_ratio = 1, # rand_ratio
-#'        hr_marg_benefit = 0.95)
+#' bounds(
+#'   events = c(60, 89, 110, 131, 178),
+#'   power_int = 0.9, # beta_PA
+#'   falsepos = 0.025, # gamma_FA
+#'   hr_null = 1.3, # delta_null
+#'   hr_alt = 0.8, # delta_alt
+#'   rand_ratio = 1, # rand_ratio
+#'   hr_marg_benefit = 0.95
+#' )
 bounds <- function(events,
                    # OS events at each analysis
                    power_int = 0.9,
@@ -64,16 +68,15 @@ bounds <- function(events,
                    # for every patient randomized to control, rand_ratio patients are allocated to experimental intervention
                    hr_marg_benefit = NULL
                    # evaluate probability of meeting positivity thresholds under a second plausible beneficial effect of treatment on OS (HR = hr_marg_benefit)
-                   ) {
-
+) {
   # Log scale
   lhr_null <- log(hr_null)
   lhr_alt <- log(hr_alt)
 
   # Init variables
   nstage <- length(events) # total number of analyses planned
   info <-
-    rand_ratio*events / ((rand_ratio + 1)^2) # Fisher's information for log-HR at each analysis
+    rand_ratio * events / ((rand_ratio + 1)^2) # Fisher's information for log-HR at each analysis
   se <-
     sqrt(1 / info) # asymptotic standard error for log-HR at each analysis
 
@@ -100,34 +103,36 @@ bounds <- function(events,
   post_pos <- calc_posterior(lhr_pos, lhr_null, events)
   pred_pos <- calc_predictive(lhr_pos, events)
 
-  summary <- data.frame('Deaths' = events)
+  summary <- data.frame("Deaths" = events)
 
   # OS HR thresholds for positivity
-  summary$'OS HR threshold for positivity' <- round(exp(lhr_pos), 3)
+  summary$"OS HR threshold for positivity" <- round(exp(lhr_pos), 3)
 
   # One sided false positive error_rate at each analysis
-  summary$'One-sided false positive error rate' <- round(falsepos_all, 3)
+  summary$"One-sided false positive error rate" <- round(falsepos_all, 3)
 
   # Level of 2-sided CI needed to rule out δnull at given analysis (%)
-  summary$'Level of 2-sided CI needed to rule out delta null' <- round(pmax(0, CI_level_monit_null), 0)
+  summary$"Level of 2-sided CI needed to rule out delta null" <- round(pmax(0, CI_level_monit_null), 0)
 
   # Probability of meeting positivity threshold under plausible OS benefit
-  summary$'Probability of meeting positivity threshold under delta alt' <- round(power_all, 3)
+  summary$"Probability of meeting positivity threshold under delta alt" <- round(power_all, 3)
 
   # Pr(true OS HR >= detrimental OS HR | current data)
-  summary$'Posterior probability the true OS HR exceeds delta null given the data' <- round(post_pos, 3)
-  summary$'Predictive probability the OS HR estimate at Final Analysis does not exceed the positivity threshold' <- c(round(pred_pos * 100, 3), NA)
+  summary$"Posterior probability the true OS HR exceeds delta null given the data" <- round(post_pos, 3)
+  summary$"Predictive probability the OS HR estimate at Final Analysis does not exceed the positivity threshold" <- c(round(pred_pos * 100, 3), NA)
 
   if (!is.null(hr_marg_benefit)) {
     # calculate the probability of meeting positivity thresholds under lhr_marg_benefit
-    summary$'Probability of meeting positivity threshold under incremental benefit' <-
-      round(meeting_probs(
-        summary = summary,
-        lhr_pos = lhr_pos,
-        lhr_target = log(hr_marg_benefit),
-        rand_ratio = rand_ratio
-      ),
-      3)
+    summary$"Probability of meeting positivity threshold under incremental benefit" <-
+      round(
+        meeting_probs(
+          summary = summary,
+          lhr_pos = lhr_pos,
+          lhr_target = log(hr_marg_benefit),
+          rand_ratio = rand_ratio
+        ),
+        3
+      )
   }
 
   return(list(
@@ -136,5 +141,4 @@ bounds <- function(events,
     lhr_pos = lhr_pos,
     summary = summary
   ))
-
 }

R/posteriors.R

@@ -42,7 +42,7 @@ calc_predictive <- function(lhr_con, events) {
     pred_pos[i] <- pnorm(
       lhr_con[nstage] * sqrt(info[nstage]),
       mean = lhr_con[i] * sqrt(info[i]) * sqrt(info[nstage] /
-                                                 info[i]),
+        info[i]),
       sd = sqrt((info[nstage] - info[i]) / info[i])
     )
   }

R/probs.R

@@ -14,16 +14,17 @@ meeting_probs <-
            rand_ratio = 1) {
     events <- summary$Deaths
     info <-
-      rand_ratio * events / ((rand_ratio + 1) ^ 2) # Fisher's information for log-HR at each analysis
+      rand_ratio * events / ((rand_ratio + 1)^2) # Fisher's information for log-HR at each analysis
     se <-
       sqrt(1 / info) # asymptotic standard error for log-HR at each analysis
     prob <- list()
     for (i in 1:length(events)) {
       prob[i] <-
         pnorm(lhr_pos[i],
-              mean = lhr_target,
-              sd = se[i],
-              lower.tail = TRUE)
+          mean = lhr_target,
+          sd = se[i],
+          lower.tail = TRUE
+        )
     }
     return(as.numeric(prob))
   }

R/runApp.R

@@ -5,6 +5,7 @@
 #' @import shiny
 #' @export
 #' @return No return value, runs shiny app
+# nocov start
 run_app <- function() {
   shinyApp(
     ui = app_ui,
@@ -15,4 +16,4 @@ run_app <- function() {
     # uiPattern = uiPattern
   )
 }
-
+# nocov end

R/server.R

@@ -3,15 +3,18 @@
 #' @param input generic shiny var
 #' @param output generic shiny var
 #' @param session generic shiny var
+# nocov start
 app_server <- function(input, output, session) {
   wrap <-
-    function(X, decimal = 3)
+    function(X, decimal = 3) {
       return(paste(round(X, decimal), collapse = ","))
+    }
   unwrap <-
-    function(X)
+    function(X) {
       return(as.numeric(unlist(strsplit(
         gsub(" ", "", X), ","
       ))))
+    }
 
   # Core reactive function - OCs plots & results
   react <- reactive({
@@ -21,7 +24,7 @@ app_server <- function(input, output, session) {
     updateTextInput(session, "events", value = wrap(events))
 
     # boundaries
-    boundaries = bounds(
+    boundaries <- bounds(
       events = events,
       power_int = input$power_int,
       falsepos = input$falsepos,
@@ -32,7 +35,7 @@ app_server <- function(input, output, session) {
     )
 
 
-    hr_pos = exp(boundaries$lhr_pos)
+    hr_pos <- exp(boundaries$lhr_pos)
     updateTextInput(session, "hr_pos", value = wrap(hr_pos))
 
 
@@ -49,11 +52,10 @@ app_server <- function(input, output, session) {
     # ) # Optional
     # names(boundaries$summary) <- columns
 
-  return(boundaries)
-
+    return(boundaries)
   })
 
   # Rendering
-  output$bounds <- renderTable(react()$summary[,-c(6, 7)])
-
+  output$bounds <- renderTable(react()$summary[, -c(6, 7)])
 }
+# nocov end