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06c937d
update stan and plot
lel4011 Jan 28, 2026
f4875d6
fix unit test
lel4011 Mar 3, 2026
9575320
limit prec_sd to one parameter for both modes
stemangiola Mar 31, 2026
5ed13fe
simplify stan code
stemangiola Mar 31, 2026
23f2df3
prec_sd with sd of 1
stemangiola Mar 31, 2026
b46f1ae
normalise all alphas including intercept
stemangiola Mar 31, 2026
e193df8
update model fitting to 1 prec_sd
stemangiola Mar 31, 2026
59b9720
update plot to accept intercept only model
stemangiola Mar 31, 2026
e5b2d52
add unit test for plotting intercept-only fit
stemangiola Mar 31, 2026
5d98051
update docs
stemangiola Mar 31, 2026
bbdc33d
drop prec_sd_2 from stan generation
stemangiola Mar 31, 2026
2f0813a
update NAMESPACE
stemangiola Mar 31, 2026
594cb34
Refactor model fitting and plotting to use new parameter structure fo…
stemangiola Mar 31, 2026
ad6a2e8
Enhance model fitting by introducing conditional initialization for i…
stemangiola Mar 31, 2026
a505a2d
Update documentation for plotting functions and residuals calculation…
stemangiola Mar 31, 2026
50a422e
Remove hyper priors from the Stan model for multi beta-binomial regre…
stemangiola Mar 31, 2026
b4fe044
Refactor Stan model parameters for mean-variability regression by con…
stemangiola Mar 31, 2026
ad7d177
Enhance plotting functionality by introducing a new `plot_scatterplot…
stemangiola Mar 31, 2026
47b12ed
Enhance test coverage for plotting functions by updating significance…
stemangiola Mar 31, 2026
b18f205
Refactor plot_2D_intervals function to replace "unadjusted" terminolo…
stemangiola Mar 31, 2026
f4e4e2e
Add variability to composition mapping functionality
stemangiola Mar 31, 2026
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2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ Rplot.pdf
sccomp_draws_files
.DS_Store
docs

/.quarto/
**/*.quarto_ipynb
.Renviron
*.exe
21 changes: 20 additions & 1 deletion NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ importFrom(dplyr,all_of)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,c_across)
importFrom(dplyr,count)
importFrom(dplyr,cummean)
Expand All @@ -62,19 +63,35 @@ importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,where)
importFrom(dplyr,with_groups)
importFrom(forcats,fct_relevel)
importFrom(forcats,fct_reorder)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_alpha_manual)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_void)
importFrom(ggrepel,geom_text_repel)
importFrom(glue,glue)
importFrom(instantiate,stan_cmdstan_exists)
Expand All @@ -90,6 +107,8 @@ importFrom(magrittr,multiply_by)
importFrom(magrittr,not)
importFrom(magrittr,subtract)
importFrom(parallel,detectCores)
importFrom(patchwork,plot_annotation)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(purrr,as_mapper)
importFrom(purrr,map)
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