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export abn output to other format(s)#227

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matteodelucchi merged 54 commits intomainfrom
226-export-abn-to-json-abn-for-bnviz-compatibility
Nov 18, 2025
Merged

export abn output to other format(s)#227
matteodelucchi merged 54 commits intomainfrom
226-export-abn-to-json-abn-for-bnviz-compatibility

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@matteodelucchi matteodelucchi commented Sep 10, 2025 •
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Closing #226
Addressing #63

Implementation roadmap for export function of abnFit objects

  • method = "mle" without group.var
  • method = "mle" with group.var
  • method = "bayes"

@matteodelucchi matteodelucchi self-assigned this Sep 10, 2025
@matteodelucchi matteodelucchi added the enhancement New feature or request label Sep 10, 2025
@matteodelucchi matteodelucchi linked an issue Sep 10, 2025 that may be closed by this pull request
export abn to "JSON abn" for BNviz compatibility #226
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matteodelucchi commented Sep 10, 2025
View reviewed changes
tests/testthat/test-export.R
abn_fit <- create_test_abnfit_mle()
test_that("export_abnFit works for MLE method without group.var", {
suppressMessages({
suppressWarnings({
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@matteodelucchi matteodelucchi Sep 10, 2025

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The current implementation of export_abnFit() generates a warning because some arc arguments (frequency, significance, constraints) are not yet implemented. This is expected behavior; therefore, the tests currently suppress warnings.

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codecov bot commented Sep 10, 2025 •
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Codecov Report

❌ Patch coverage is 86.62420% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 67.03%. Comparing base (d7b018c) to head (b3deb48).
⚠️ Report is 52 commits behind head on main.

Files with missing lines Patch % Lines
R/export.R 86.98% 19 Missing ⚠️
R/abn-methods.R 81.81% 2 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #227      +/-   ##
==========================================
+ Coverage   66.30%   67.03%   +0.72%     
==========================================
  Files          53       50       -3     
  Lines       10399    10535     +136     
==========================================
+ Hits         6895     7062     +167     
+ Misses       3504     3473      -31
Files with missing lines Coverage Δ
R/abn-methods.R 69.28% <81.81%> (+0.97%) ⬆️
R/export.R 86.98% <86.98%> (ø)

... and 3 files with indirect coverage changes

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@matteodelucchi
changed export_to_json to new structure and simplified.
8541a48
@matteodelucchi
updated test for export_abnFit() with new structure
26e2397
@matteodelucchi
added optional scenario_id and label
4a821eb
@matteodelucchi
updated export_abnFit_mle to new structure.
6cd7e92
@matteodelucchi
updated export_abnFit_mle_nodes to new format.
e388f73
@matteodelucchi
updated extract_parameters_by_distribution to new format.
d36c547
@matteodelucchi
first implementation of export_abnFit_mle_grouped_nodes
5c1b9e7
@matteodelucchi
updated export_abnFit_mle_graph to new structure
67bfcc5
@matteodelucchi
prepared code skeleton for exporting abnFit with method = "bayes".
9d3f6b7
@matteodelucchi
replaced extract_parameters_mixed_effects with `extract_parameters_…
f71cc25 
…mixed_effects` to adhere to new structure.
@matteodelucchi
minor bug fix in extracting the dag as a matrix from the abnFit object.
e53a1fb
@matteodelucchi
Fixed bug since childs are in rows and parents in columns.
5a47630
@matteodelucchi
update tests for optional top-level scenario_id and label
e991356
@matteodelucchi
removed deprecated test of graph metadata since it's not applicable a…
5bc9880 
…nymore
@matteodelucchi
check JSON for correct variable structure.
5932693
@matteodelucchi
updated test to check the parameter array
51cf55c
@matteodelucchi
updated tests to check the arc structure correctly.
b113dd0
@matteodelucchi
test grouped mle model exports parameters correctly.
621a718
@matteodelucchi
test link function mapping.
b61c766
@matteodelucchi
suppress warnings related to non-convergence in poisson CPP
7c67bce
@matteodelucchi
fixed error in roxygen2 writing the function documentations. Doesn't …
acc0b0d 
…like "|" in a function name.
@matteodelucchi
generated function documentation for updated export functions.
f1a58eb
@matteodelucchi
updated INLA version in renv.lock file
2002396
@matteodelucchi matteodelucchi marked this pull request as ready for review November 18, 2025 10:55
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matteodelucchi commented Nov 18, 2025

Let me bypass the CRAN checks. The containers are still not working as they fail to install the devtools library...

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matteodelucchi commented Nov 18, 2025

This implements only the export of abnFit object generated with method = "mle"! The Bayesian case (method = "bayes") is not implemented yet and will return a placeholder skeleton.

@matteodelucchi matteodelucchi mentioned this pull request Nov 18, 2025
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@matteodelucchi matteodelucchi merged commit 286bea8 into main Nov 18, 2025
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@j-i-l j-i-l mentioned this pull request Jan 7, 2026
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export abn to "JSON abn" for BNviz compatibility

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