Odin-default-model by bahadzie · Pull Request #263 · epiverse-trace/epidemics

bahadzie · 2025-04-02T13:42:58Z

This PR fixes #254 by replacing the C++ code for the

default/seirv
diptheria
vacamole

models with odin compatible versions to simplify

new model creation
package maintenance

github-actions · 2025-04-02T13:46:42Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

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github-actions · 2025-04-02T14:54:18Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-04-02T14:56:09Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-04-03T19:13:22Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-04-03T19:30:02Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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Degoot-AM · 2025-04-07T09:28:32Z

vignettes/design-principles.Rmd

 - Function naming: Function names aim to contain verbs that indicate the function behaviour. Internal input checking functions follow the _checkmate_ naming style (e.g. `assert_*()`).

- Function naming: Internal functions aim to begin with a `.` (e.g. `.model_default_cpp()`) to more clearly indicate that they are not for direct use.
+- Function naming: Internal functions aim to begin with a `.` (e.g. .model_default_cpp()) to more clearly indicate that they are not for direct use.


Suggested change

- Function naming: Internal functions aim to begin with a `.` (e.g. .model_default_cpp()) to more clearly indicate that they are not for direct use.

- Function naming: Internal functions aim to begin with a `.` (e.g., .model_default_cpp()) to more clearly indicate that they are not for direct use.

Also, this statment should be removed "....pidemics attempts to balance performance and maintainability through minimum sufficient use of C++, and not attempting to write a domain-specific language (such as odin)." after including odin stuff.

Add odin to the list of dependent pkgs

Degoot-AM · 2025-04-07T09:39:23Z

DESCRIPTION

    https://epiverse-trace.github.io/epidemics/
 BugReports: https://github.com/epiverse-trace/epidemics/issues
 Imports:
+    odin,


Good, odin has been added as a dependency pkg

NAMESPACE

R/epidemics-package.R

Degoot-AM · 2025-04-07T11:19:11Z

tests/testthat/test-model_default.R

  )
  # expect epidemic size is lower for combined intervention
+  # Epidemic size differs depending on model_default() or model_default().
+  # Not sure how large of a discrepancy is expected.


This test file has failed

testthat::test_file("tests/testthat/test-model_default.R") is now passing 88 tests. Please review and confirm

Degoot-AM

@bahadzie good work.

test-model_vacamole.R has failed, be check.

github-actions · 2025-04-08T22:18:35Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-04-08T23:35:31Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-04-25T12:01:27Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-04-25T12:15:40Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-05-05T15:44:05Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-05-05T20:39:27Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2025-05-05T21:44:13Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2025-05-05T22:12:23Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-05-05T22:24:04Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2025-05-05T22:30:05Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2025-05-08T09:23:56Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

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github-actions · 2025-05-08T09:42:37Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

Rmd with multi-intervention odin model (interventions currently disabled to match README example)

Note issue with L165 currently – log transformation is overestimating reduction. Reason currently unclear.

With outputs consistent with epidemics

github-actions · 2025-06-13T14:13:43Z

This pull request:

Adds 4 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

bahadzie requested a review from Degoot-AM April 3, 2025 19:29

Degoot-AM reviewed Apr 7, 2025

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NAMESPACE Show resolved Hide resolved

Degoot-AM reviewed Apr 7, 2025

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R/epidemics-package.R Show resolved Hide resolved

Degoot-AM reviewed Apr 7, 2025

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Degoot-AM requested changes Apr 7, 2025

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Degoot-AM approved these changes Jun 11, 2025

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adamkucharski added 5 commits June 13, 2025 14:09

Initial version of model

d8a9a02

Rmd with multi-intervention odin model (interventions currently disabled to match README example)

Add scenario interventions

924ef07

Note issue with L165 currently – log transformation is overestimating reduction. Reason currently unclear.

Tidy code

cb8a701

Update modelling_scenarios_odin.Rmd

2e561e3

Convert to function

0bf2eb9

With outputs consistent with epidemics

bahadzie and others added 26 commits June 13, 2025 14:09

ci: added ability to manually trigger R-CMD-check github action

f0cb909

Add check to avoid negative values in Vaccinated

5dfd294

Fix remove references to C in model_diphtheria

fe8a514

change for consistency between models

3b05634

chore: remove C++ related code from package

7d0df39

chore: remove reference too C++ code in function documentation

5c3c1d0

chore: update package documentation via devtools::check()

15c1ebd

chore: remove Rcpp and RcppEigen package dependencies

4e81a18

chore: remove Rcpp and RcppEigin package dependencies

86ccda8

chore: remove C++ ci linting

679c759

chore: fix lintr errors in odin model files

efbce62

ci: remove failing touchstone GH actions

2f067ff

chore: fix lintr warnings

04aa9ae

chore: additional lintr fixes

5caf12b

chore: update function documentation

3333e4d

chore: fix lintr error

fc24bf4

ci: update snapshot to fix failing PR tests

3247773

ci: snapshot formatting to fix PR test failing

7a72b5d

fix: population snapshot test formatting

7350b7b

fix: format failing population test

67ee357

fix: failing expect_snapshot() tests using transform param

e6ac5f9

fix: expect_snapshot() formatting changes

ab1c59d

fix: expect_snapshot() formatting changes

959a74c

fix: expect_snapshot() formatting changes

9493df9

Addition to contributors

da2d184

Update author list in documentation

9a5a6d8

bahadzie force-pushed the odin-default-model branch from 810f270 to 9a5a6d8 Compare June 13, 2025 14:11

bahadzie merged commit f064fc4 into main Jun 13, 2025
11 checks passed

bahadzie deleted the odin-default-model branch June 13, 2025 14:33

	- Function naming: Internal functions aim to begin with a `.` (e.g. .model_default_cpp()) to more clearly indicate that they are not for direct use.
	- Function naming: Internal functions aim to begin with a `.` (e.g., .model_default_cpp()) to more clearly indicate that they are not for direct use.

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