show all points in funnel chart

[tomjemmett]

shows all providers in the funnel chart. non-peers are shown as a transparent dot, leaving the peers/provider as highlighted points

[Copilot]

Pull request overview

This PR refactors the rates funnel plotting to use U‑Prime calculations, updates the funnel and box plots to display all providers while visually emphasising peers and the selected provider, and introduces more flexible y‑axis label formatting for trend plots. It also aligns several exported function interfaces and their documentation with current usage.

Changes:

• Replace the old generate_rates_funnel_data() data-preparation path with a new uprime_calculations() helper and updated funnel plotting logic that draws U‑Prime control lines.
• Update the Shiny modules and trend/funnel plotting functions to use configuration-driven y‑axis label formatters and to show all providers with peers/provider highlighted via colour/alpha.
• Simplify Azure input handling by moving container acquisition inside get_all_geo_data() and partially updating documentation for get_container().

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
R/utils_plot.R	Adds uprime_calculations() for computing U‑Prime control limits and adjusts baseline data preparation to keep all providers for plotting.
R/fct_plots.R	Updates plot_rates_trend() to accept a y_labels formatter and reworks plot_rates_funnel()/plot_rates_box() to use U‑Prime calculations and alpha/colour to highlight peers vs non‑peers.
R/mod_plot_rates.R	Wires in uprime_calculations() as a reactive, derives y‑axis limits from filtered baseline data and trend rates, and passes y‑label formatters and new funnel inputs into the child modules.
R/mod_plot_rates_funnel.R	Updates the server module to accept funnel calculations in addition to rates and pass them through to plot_rates_funnel().
NAMESPACE	Removes the export for the deleted generate_rates_funnel_data() and exports the new uprime_calculations() function.
man/uprime_calculations.Rd	Documents the new uprime_calculations() helper for U‑Prime funnel charts.
man/plot_rates_trend.Rd	Documents the new y_labels argument used to format y‑axis labels in trend plots.
man/plot_rates_funnel.Rd	Updates the funnel plot documentation to reflect the new funnel_calculations argument and simpler rates_funnel_data input.
man/get_container.Rd	Updates usage for get_container() to match the current function signature, though arguments still list obsolete parameters.
man/get_all_geo_data.Rd	Aligns get_all_geo_data() documentation with its simplified interface that constructs the Azure container internally.

Comments suppressed due to low confidence (1)

R/mod_plot_rates.R:83

• generate_rates_funnel_data() is still being called here, but the function has been removed from R/utils_plot.R and is no longer exported in NAMESPACE, so this reactive will throw an error as soon as it is evaluated. Either reintroduce generate_rates_funnel_data() or update this reactive (and any callers) to use the new uprime_calculations() output directly, removing this now-unused rates_funnel_data reactive if it is no longer needed.

    rates_funnel_data <- shiny::reactive({
      shiny::req(rates_baseline_data())
      rates_baseline_data() |> generate_rates_funnel_data()
    })

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[Copilot]

The get_container() Rd lists tenant and app_id as arguments here, but the function signature now only takes ep_uri and container_name, so these parameters are no longer valid for callers and the docs are misleading. Consider removing these items (and the corresponding roxygen @param tags) so that the documented interface matches the actual function definition.

Suggested change

	\item{tenant}{Character. Tenant ID.}
	\item{app_id}{Character. App ID.}

[matt-dray]

Great, thanks for doing the legwork on this. You screenshared this and I can reproduce it locally as expected.

I've added minor suggestions: black dashed lines for plot, some inline comments.

I'll let you react to Copilot's thoughts as you see fit.

[tomjemmett]

should remove this unused code

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

man/uprime_calculations.Rd:12

• The argument name documented here (rates_baseline_data) no longer matches the function signature in \usage{}, which now uses df; this mismatch can confuse users and should be updated so the \arguments{} entry uses the same name as the actual parameter.

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[matt-dray]

Cracking, thanks for incorporating these changes. Looks good to me locally.