Fix filter scoping, quosure misuse, noisy stdout, and missing forcats import - #267

Merged

stemangiola merged 74 commits into

improvements-stefano

Jul 15, 2026

Commits on Apr 7, 2026

update stan and plot

lel4011
authored and
stemangiola
committed
a3ece63
fix unit test

lel4011
authored and
stemangiola
committed
d54417a
limit prec_sd to one parameter for both modes
stemangiola
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20fed92
simplify stan code
stemangiola
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1c450b3
prec_sd with sd of 1
stemangiola
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fc2aa1a
normalise all alphas including intercept
stemangiola
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40dfc23
update model fitting to 1 prec_sd
stemangiola
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1e13573
update plot to accept intercept only model
stemangiola
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9e1ec96
add unit test for plotting intercept-only fit
stemangiola
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2f95cdd
update docs
stemangiola
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a5498b7
drop prec_sd_2 from stan generation
stemangiola
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814dcf8
update NAMESPACE
stemangiola
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3570e02
Refactor model fitting and plotting to use new parameter structure for mean-variability regression. Replace 'prec_coeff' with 'prec_intercept' and 'prec_slope' parameters across relevant functions …
stemangiola
committed
e51de8a
Enhance model fitting by introducing conditional initialization for intercept parameters based on design specifications. Update Stan model to reflect intercept-centered priors for the first column …
stemangiola
committed
6a9fd3c
Update documentation for plotting functions and residuals calculation. Added missing commas in `plot_1D_intervals` and `plot_2D_intervals` documentation. Clarified description of `residuals_unconst…
stemangiola
committed
2c0e749
Remove hyper priors from the Stan model for multi beta-binomial regression, streamlining the parameterization and reducing complexity in the model specification.
stemangiola
committed
57a3d8a
Refactor Stan model parameters for mean-variability regression by consolidating intercepts into a single array structure. Update initialization logic in model fitting to accommodate bimodal associa…
stemangiola
committed
78313bc
Enhance plotting functionality by introducing a new `plot_scatterplot` function for visualizing cell-group proportions. Update `plot.sccomp_tbl` to utilize quosures for improved data handling and s…
stemangiola
committed
57a0b1e
Enhance test coverage for plotting functions by updating significance checks in `test-plot.R`. Introduce a new helper function to correctly extract captions from patchwork plots, ensuring accurate …
stemangiola
committed
2e66340
Refactor plot_2D_intervals function to replace "unadjusted" terminology with "raw" for clarity. Update data handling and parameter filtering to reflect this change, ensuring consistency across plot…
stemangiola
committed
1240b63
Add variability to composition mapping functionality
stemangiola
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80c69e0
Add factor argument to plotting functions and implement subsetting by factor
stemangiola
committed
53d543d
Refactor plotting functions to use new naming conventions and enhance functionality
stemangiola
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2c83149
Enhance variability to composition mapping functionality
stemangiola
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47981a8
Enhance Stan model integration and update plotting functions
stemangiola
committed
13ae3f1
Refactor tests for parameter incorporation in Stan models
stemangiola
committed
01adf1e
Refactor sccomp_estimate and sccomp_remove_outliers for improved parameter handling
stemangiola
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a178f39
Refactor file deletion logic in sccomp_estimate for improved error handling
stemangiola
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52a459b
Update version to 2.1.31 and refine alpha normalization handling
stemangiola
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4d6d429
Enhance statistical summarization in draws_to_statistics function
stemangiola
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215c681
update docs
stemangiola
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8ab8957
Refactor parameter incorporation functions for improved flexibility
stemangiola
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5cf93ae
Refactor parameter naming for consistency in incorporation functions
stemangiola
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8a48453
Refactor parameter loading in incorporation functions for simplification
stemangiola
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8983354

Commits on Apr 8, 2026

Commits on Apr 9, 2026

Address review comments: imports, filter .env$, cat->message, !!.cell_group

Copilot
and
stemangiola
authored
49e590b
Use !!factor instead of .env$factor in subset_results_by_factor filter

Copilot
and
stemangiola
authored
66226bd

Commits on Apr 10, 2026

Merge branch 'improvements-stefano' of https://github.com/MangiolaLaboratory/sccomp into improvements-stefano
stemangiola
committed
d995f4c

Commits on Apr 13, 2026

Commits on May 11, 2026

Commits on May 15, 2026

Merge pull request #276 from MangiolaLaboratory/refactor_stan_association_function
stemangiola
authored
8557700

Commits on May 16, 2026

Commits on May 17, 2026

Commits on May 19, 2026

This commit updates the package version to 2.1.33 and introduces functionality for handling smooth terms (`s()` and `t2()`) in sccomp formulas. Key changes include the addition of new utility funct…
stemangiola
committed
3201197

Commits on Jul 15, 2026

Fix CI: splines vignette basis access and missing docs

stemangiola
and
cursoragent
committed
37dcad6