Response to reviewers

.Rbuildignore

@@ -7,6 +7,7 @@
 ^pkgdown$
 ^README\.Rmd$
 ^LICENSE\.md$
+^LICENSE\.note$
 ^vignettes/web_only
 ^vignettes/denim_benchmark.Rmd
 ^vignettes/denim_vs_deSolve.Rmd
@@ -20,4 +21,5 @@
 ^extra_benchmark$
 ^manuscript_plots$
 ^\.vscode$
-^logo\.svg$
+^logo\.svg$
+^CODE_OF_CONDUCT\.md$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at anhptq@oucru.org. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

.github/CONTRIBUTING.md

@@ -0,0 +1,60 @@
+---
+editor_options: 
+  markdown: 
+    wrap: sentence
+---
+
+# Contributing to denim
+
+This outlines how to propose a change to the package denim.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the *source* file, meaning:
+
+-   YES: you edit a [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in a `.R` file below `R/`.
+
+-   NO: you edit an `.Rd` file below `man/`.
+
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it's needed.
+
+If you've found a bug, please file an issue that illustrates the bug with a reproducible example, preferrably using [reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+-   Fork the package and clone onto your computer.
+    If you haven't done this before, we recommend using `usethis::create_from_github("thinhong/denim", fork = TRUE)`.
+
+-   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`.
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing.
+
+-   Create a Git branch for your pull request (PR).
+    We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+-   Make your changes, keep in mind that
+
+    -   We use [roxygen2](#0), for documentation.
+
+    -   We use [testthat](#0) for unit testings.
+        Contributions with test cases included are easier to accept.
+
+    -   New code should follow the tidyverse [style guide](https://style.tidyverse.org).
+        You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
+
+-   Commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+-   For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header).
+    Follow the style described in <https://style.tidyverse.org/news.html>.
+
+## Code of Conduct
+
+Please note that the `denim` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md).
+By contributing to this project you agree to abide by its terms.

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 1.2.2
-Date: 2025-08-18 05:41:32 UTC
-SHA: 0d64dc2b4afd1b166100d94463729a191a8ce96c
+Date: 2025-08-21 04:31:08 UTC
+SHA: efec9ea304554e3cb0dfd99a39401ae47a5115dd

DESCRIPTION

@@ -10,10 +10,14 @@ Authors@R: c(
            comment = c(ORCID = "0009-0000-2129-435X")),
     person("Marc", "Choisy", , "mchoisy@oucru.org", role = "aut",
            comment = c(ORCID = "0000-0002-5187-6390")),
-    person("Niels", "Lohman", ,role = "ctb"),
-    person("Bjoern", "Hoehrmann", ,email = "bjoern@hoehrmann.de", role = "ctb"),
-    person("Florian", "Loitsch", ,role = "ctb"),
-    person("Ingo", "Berg", ,role = "ctb")
+    person("Niels", "Lohman", ,role = c("ctb", "cph"), 
+          comment="Author for the bundled JSON C++ library"),
+    person("Bjoern", "Hoehrmann", ,email = "bjoern@hoehrmann.de", role = c("ctb", "cph"),
+          comment="Contributor for the bundled JSON C++ library"),
+    person("Florian", "Loitsch", ,role = c("ctb", "cph"),
+          comment="Contributor for the bundled JSON C++ library"),
+    person("Ingo", "Berg", ,role = c("ctb", "cph"),
+          comment="Author for the bundled MuParser C++ library")
   )
 Description: R package to build and simulate deterministic compartmental models that can be non-Markovian. Length of stay in each compartment can be defined to follow a parametric distribution (d_exponential(), d_gamma(), d_weibull(), d_lognormal()) or a non-parametric distribution (nonparametric()). Other supported types of transition from one compartment to another includes fixed transition (constant()), multinomial (multinomial()), fixed transition probability (transprob()).
 License: MIT + file LICENSE

LICENSE.note

@@ -0,0 +1,5 @@
+The denim package as a whole is distributed under MIT. The denim package includes other open source software components. The following is a list of these components:
+
+* muParser: BSD
+* JSON: MIT
+* diffviewer: written by package authors

src/Compartment.cpp

@@ -23,10 +23,9 @@ void Compartment::setOutValues() {
     outTotals.resize(outTransitions.size(), 0);
 }
 
-// TODO: set length for nested subCompartment
 void Compartment::setLengthSubCompartment() {
     size_t maxLength {0};
-    // TODO: if competitive risk -> same subCompartment chain
+    // if competitive risk -> same subCompartment chain
     // ignore option to distribute initial values 
 
 
@@ -257,8 +256,6 @@ void Compartment::updateSubCompByDist(size_t iter, size_t outIndex) {
         for (size_t i = 0; i <= endIndex; ++i) { 
             // if competing risks, compute out population using tmpSubComp instead
             double out = tmpSubComp[i] * (i >= transProbRef.size() ? 0 : transProbRef[i]);
-            // TODO: check formulation with 1 - exp(-rate) instead 
-            // double out = tmpSubComp[i] * (i >= transProbRef.size() ? 0 : transProbRef[i]);
             outTotals[outIndex] += out;
             subCompartments[0][i] -= out;
         }   
@@ -268,8 +265,6 @@ void Compartment::updateSubCompByDist(size_t iter, size_t outIndex) {
 
         for (size_t i = 0; i <= endIndex; ++i) { 
             double out = subCompartments[outIndex][i] * (i >= transProbRef.size() ? 0 : transProbRef[i]);
-            // TODO: check formulation with 1 - exp(-rate) instead 
-            // double out = subCompartments[outIndex][i] * (1 - exp(-(i >= transProbRef.size() ? 0 : transProbRef[i])));
             outTotals[outIndex] += out;
             subCompartments[outIndex][i] -= out;
         }

src/test-denim.cpp

@@ -44,7 +44,11 @@ context("Lognormal distribution") {
   test_polymorphism = std::make_shared<TransitionLogNormal>(1, 0.25);
 
   test_that("getTransitionProb") {
+    // Check the resulting transition prob
+    expect_true(distr.getTransitionProb(0) == Approx(3.167e-05).margin(1e-06));
+    expect_true(distr.getTransitionProb(1) == Approx(0.1098).margin(0.01));
     expect_true(distr.getTransitionProb(2) == Approx(0.6106).margin(0.01));
+    expect_true(distr.getTransitionProb(3) == Approx(0.8236).margin(0.01));
   }
 
   test_that("maxDay") {
@@ -60,7 +64,11 @@ context("Gamma distribution") {
   TransitionDiscreteGamma distr(1, 3);
 
   test_that("getTransitionProb") {
-    expect_true(distr.getTransitionProb(4) == Approx(0.4764).margin(0.01));
+    expect_true(distr.getTransitionProb(0) == Approx(0.0803).margin(0.001));
+    expect_true(distr.getTransitionProb(1) == Approx(0.2642).margin(0.001));
+    expect_true(distr.getTransitionProb(2) == Approx(0.3746).margin(0.001));
+    expect_true(distr.getTransitionProb(3) == Approx(0.4373).margin(0.001));
+    expect_true(distr.getTransitionProb(4) == Approx(0.4764).margin(0.001));
   }
 
   test_that("getRate") {
@@ -76,7 +84,11 @@ context("Exponential distribution") {
   TransitionDiscreteExponential distr(0.5);
 
   test_that("getTransitionProb") {
+    // expect the same transprob for exponential distribution (i.e. constant hazard rate)
+    expect_true(distr.getTransitionProb(0) == Approx(0.3934).margin(0.01));
+    expect_true(distr.getTransitionProb(1) == Approx(0.3934).margin(0.01));
     expect_true(distr.getTransitionProb(2) == Approx(0.3934).margin(0.01));
+    expect_true(distr.getTransitionProb(3) == Approx(0.3934).margin(0.01));
   }
 
   test_that("getRate") {
@@ -96,7 +108,10 @@ context("Weibull distribution") {
   TransitionDiscreteWeibull distr(3, 5);
 
   test_that("getTransitionProb") {
-    expect_true(distr.getTransitionProb(2) == Approx(0.5803).margin(0.01));
+    expect_true(distr.getTransitionProb(0) == Approx(0.0041).margin(0.001));
+    expect_true(distr.getTransitionProb(1) == Approx(0.1197).margin(0.001));
+    expect_true(distr.getTransitionProb(2) == Approx(0.5803).margin(0.001));
+    expect_true(distr.getTransitionProb(3) == Approx(0.9598).margin(0.001));
   }
 
   test_that("getScale") {
@@ -210,11 +225,11 @@ context("Testing distributions in model"){
         expect_true(comp->getCompTotal()[1] == Approx(2).margin(0.001e-03));
         break;
       case 4:
-        // check value for compartment V
+        // check value for compartment D
         expect_true(comp->getCompTotal()[1] == Approx(3.167e-06).margin(0.001e-06));
         break;
       case 5:
-        // check value for compartment V
+        // check value for compartment R
         expect_true(comp->getCompTotal()[1] == Approx(0.04016).margin(0.001e-03));
         break;
       }