Initial commit.

.Rbuildignore

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+R/write_mod_signature.R
+.*Rproj
+^\.Rproj\.user$
+^LICENSE$
+^LICENSE\.md$
+^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+.lintr
+_tests_
+^.*\.Rproj$

.github/CODEOWNERS

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+*   @boehringer-ingelheim/davinci

.github/workflows/ci.yml

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+---
+name: Checks 🧩
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  run-shared-ci:
+    name: Shared
+    uses: boehringer-ingelheim/dv.templates/.github/workflows/shared_ci.yml@main

.gitignore

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+.vscode
+.Rproj.user
+.Rhistory
+*.Rproj
+*.swp
+*.sh
+.vimlocal
+docs
+shiny_bookmarks
+inst/validation/validation_report.html
+tests/test-out.xml

.lintr.R

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+linters <- lintr::default_linters             # -[ diff with dv.templates 3ca8d7a10cfc7ad2307644dcac603e1f1f0feb72]-
+linters <- lintr::modify_defaults(
+  linters
+  , line_length_linter = NULL                 # we see how long lines are when we write them
+  , indentation_linter = NULL
+  , trailing_whitespace_linter = NULL
+  , cyclocomp_linter = NULL                   # prevents trivial amount of nesting and long but straightforward functions
+  , object_name_linter = NULL                 # we have reasons to capitalize. nobody in our team CamelCase. shiny does
+  , object_length_linter = NULL               # we don't type long var names just because
+  , pipe_continuation_linter = NULL           # wickham being overly prescriptive
+  , trailing_blank_lines_linter = NULL        # natural extension of trailing_whitespace_linter, present on the template
+)
+
+if(identical(Sys.getenv('CI'), "true")){
+  linters <- lintr::modify_defaults(
+    linters
+    , object_usage_linter = NULL              # R lacks var declarations; it's easy to assign to the wrong variable by mistake
+  )                                           # We only disable this lint rule on github because it fails there because
+}                                             # of a long-standing lintr bug 
+
+linters

DESCRIPTION

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+Package: dv.papo
+Title: Patient Profile
+Version: 2.0.0
+Date: 2024-07-02
+Authors@R: 
+    c(person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
+      person(given = "Korbinian",
+             family = "Matthias",
+             role = c("cre"),
+             email =  "[email protected]"),
+      person(given = "Miguel",
+             family = "Lechón", 
+             role = c("aut"), 
+             email = "[email protected]"),
+      person(given = "Yuzheng",
+             family = "Ou",
+             role = "aut")
+	)
+Description: Patient Profile Module.
+License: Apache License (>= 2)
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.0
+Depends: 
+    R (>= 4.1.0)
+Imports:
+    checkmate,
+    DT,
+    ggplot2,
+    plotly,
+    rlang,
+    shiny,
+    shinyWidgets,
+    fontawesome
+Suggests:
+    dv.manager (>= 2.1.0),
+    knitr,
+    safetyData,
+    shinytest2,
+    testthat,
+    jsonlite,
+    withr,
+    dplyr
+Remotes: boehringer-ingelheim/dv.manager@main
+VignetteBuilder: knitr
+Config/testthat/edition: 3

LICENSE

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+Copyright 2024 Boehringer-Ingelheim Pharma GmbH & Co.KG
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method("$",pack_of_constants)
+S3method("[",pack_of_constants)
+S3method("[[",pack_of_constants)
+export(explorer_app)
+export(mock_patient_profile_UI)
+export(mock_patient_profile_app)
+export(mock_patient_profile_server)
+export(mock_with_mm_app)
+export(mod_patient_profile)
+export(mod_patient_profile_UI)
+export(mod_patient_profile_server)
+importFrom(rlang,.data)

NEWS.md

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+# dv.papo 2.0.0
+
+- Major API redesign with the following breaking changes `mod_patient_profile()`:
+  - The name of the subject-level dataset is now explicitly provided through the `subject_level_dataset_name` parameter.
+  - `key` has been renamed to `subjid_var`.
+  - `pt_info` is now called `summary` and has been simplified. It only allows to specify a _single_ dataframe 
+    from which to select columns. Its `row_item` submember has been renamed to `column_count`.
+  - `tables` is now called `listings` and is a named list of pairs of `dataset` and `default_vars`. This allows 
+    control over which columns are shown by default for each dataset.
+  - The legacy `basic_info`, `vlines` and `plots` are all now collected under a single `plots` parameter. They have been
+    restructured for clarity and are also accompanied by a `palette` field that makes it possible for the caller to
+    specify individual colors. See the main vignette for more information.
+  - All parameters referring to Study Days have been reframed to point to absolute days. This ensures consistency of the
+    time axis of plots.
+  - The module now accepts datetimes as well as dates for easier joint configuration with `dv.clinlines`. The "time"
+    part of datetimes is simply discarded.
+  - Configuration helper functions have been removed in favor of documentation templates.
+  - `jumping_vars` is now called `sender_ids` for consistency across davinci modules.
+
+- The module is now easier to configure because it:
+  - Makes all of its main three sections (`summary`, `listings` and `plots`) optional, which facilitates having a base
+    working configuration.
+  - Provides clear start-up warnings and messages when the module is misconfigured with respect to input datasets. 
+    The app creator can safely assume that if no such message appears, the module will not misbehave when interacted 
+    with due to misconfiguration. Any remaining error rests solely on the module developer's shoulders or on those of 
+    the platform provider.
+
+- Bug fixes:
+  - Day labels now follow the standard CDISC behavior of skipping day 0 on plots (day 1 refers to the Treatment Start
+    Date; day -1 is the day before).
+  - Vertical lines now cross all plots.
+
+
+# dv.papo 1.0.2
+
+- bugfix: With the new version of dv.filter 2.1.0 the patient selector did not work. This is now fixed.
+
+# dv.papo 1.0.1
+
+- bugfix: Updating patient selector after jumping from another module didn't work. This is now fixed.
+
+# dv.papo 1.0.0
+
+- Primary interface: `mod_patient_profile()`
+
+- Launch mock app for demo and testing via `mock_with_mm_app()`
+
+- Enables bookmarking state of Shiny app via URL
+
+# dv.papo 0.1
+
+*  Plot section added.
+
+# dv.papo 0.0.2
+
+*  Shinydashboard element removed.
+
+# dv.papo 0.0.1
+
+* Added a `NEWS.md` file to track changes to the package.
+
+

R/aaa_preface.R

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+# THIS FILE IS NAMED aaa_preface.R SO IT IS LOADED BEFORE ALL OTHER FILES
+# DO NOT CHANGE ITS NAME. IT MUST BE THE FIRST ONE ALPHABETICALLY.
+
+#' Build a collection of named constants
+#'
+#' @param ... Named parameters to be collected as constants
+#'
+#' @keywords internal
+#'
+#' @details
+#' Shiny uses strings as IDs to link UI and server elements. E.g:
+#'   foo_UI(id = ns("foo")) ...
+#'   foo_server(id = "foo")
+#'
+#' This pattern makes it easy for programmers to fall on the trap of modifying one instance of the string literal "foo"
+#' without modifying the rest and be unaware of the problem until a bug is hit. It's also easy to mistakes uses of "foo"
+#' as an identifier from other uses (text labels, ...) when, as it's often the case, the parameter is not explicitly
+#' named.
+#' One easy fix consists in using global variables instead of plain string literals. In the case of the previous
+#' example, that would mean:
+#'   ID_FOO <- "foo"
+#'   foo_UI(ns(ID_FOO)) ...
+#'   foo_server(ID_FOO)
+#'
+#' That simple addition makes the purpose of ID_FOO clear and also fails gracefully when not all ID_FOO instances are
+#' updated synchronously along a codebase. It has the drawback of polluting the global namespace with identifier
+#' variables. That's easily solved by creating a container of constants, which is the purpose of this pack_of_constants
+#' alias.
+#'  ID <- pack_of_constants(FOO = "foo", BAR = "bar")
+#'  ID$FOO
+#'  "foo"
+#'  ID$BA
+#'  Error in `$.pack_of_constants`(ID, BA) :
+#'  Pack of constants "ID" does not contain "BA"
+#'
+#' The pack of constants is a plain named list that enforces that all elements have unique, non-null names.
+#' It is tagged as an S3 object to override its extraction operators.
+#'
+#' The use of checkmate is unnecessary, but it's a Good Library(TM) and your module should rely on it anyways
+pack_of_constants <- function(...) {
+  result <- list(...)
+  checkmate::assert_list(result, any.missing = FALSE, names = "unique")
+  class(result) <- c("pack_of_constants", class(result))
+  result
+}
+
+#' Extract constant from pack
+#'
+#' @param pack pack_of_constants
+#' @param name target constant
+#'
+#' This function differs from the base list extraction method in that it avoids partial matching of keys and throws
+#' an error if the looked-for constant is not contained within the pack.
+#'
+#' @keywords internal
+#'
+#' @export
+`$.pack_of_constants` <- function(pack, name) {
+  checkmate::assert_true(name %in% names(pack), .var.name = paste0(deparse(substitute(pack)), "$", name))
+  NextMethod()
+}
+
+# This exports are recent requirement for devtools check https://github.com/r-lib/roxygen2/issues/1592#issue-2121199122
+#'
+#' @keywords internal
+#'
+#' @export
+`[[.pack_of_constants` <- `$.pack_of_constants`
+
+#' @keywords internal
+#' @export
+`[.pack_of_constants` <- function(pack, name) {
+  stop("Invalid pack_of_constants method")
+}
+
+poc <- pack_of_constants