Improve variability formula generality by stemangiola · Pull Request #271 · MangiolaLaboratory/sccomp

update stan and plot

lel4011

authored and

stemangiola

committed

06c937d

fix unit test

lel4011

authored and

stemangiola

committed

f4875d6

limit prec_sd to one parameter for both modes

stemangiola

committed

9575320

simplify stan code

stemangiola

committed

5ed13fe

prec_sd with sd of 1

stemangiola

committed

23f2df3

normalise all alphas including intercept

stemangiola

committed

b46f1ae

update model fitting to 1 prec_sd

stemangiola

committed

e193df8

update plot to accept intercept only model

stemangiola

committed

59b9720

add unit test for plotting intercept-only fit

stemangiola

committed

e5b2d52

update docs

stemangiola

committed

5d98051

drop prec_sd_2 from stan generation

stemangiola

committed

bbdc33d

update NAMESPACE

stemangiola

committed

2f0813a

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

594cb34

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

ad6a2e8

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

a505a2d

Remove hyper priors from the Stan model for multi beta-binomial regression, streamlining the parameterization and reducing complexity in the model specification.

stemangiola

committed

50a422e

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

b4fe044

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

ad7d177

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

47b12ed

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

b18f205

Add variability to composition mapping functionality

stemangiola

committed

f4e4e2e

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Improve variability formula generality - #271

Improve variability formula generality#271
stemangiola wants to merge 21 commits into
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improve-variability-formula-generality

Commits on Mar 31, 2026

update stan and plot

fix unit test

limit prec_sd to one parameter for both modes

simplify stan code

prec_sd with sd of 1

normalise all alphas including intercept

update model fitting to 1 prec_sd

update plot to accept intercept only model

add unit test for plotting intercept-only fit

update docs

drop prec_sd_2 from stan generation

update NAMESPACE

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 …

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 …

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…

Remove hyper priors from the Stan model for multi beta-binomial regression, streamlining the parameterization and reducing complexity in the model specification.

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…

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…

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 …

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…

Add variability to composition mapping functionality