Separate plotting code from data prep #13

pratikunterwegs · 2026-01-20T12:23:21Z

This PR separates the data preparation for plotting into intermediate functions prefixed prep_plot_*().

Known issues:
~~- Two functions in burden_diagnostics.R are yet to be worked on~~; now removed.

Some plotting preparation and plotting functions need better tests.

github-actions · 2026-01-22T15:04:21Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 0 existing dependencies (direct and indirect)
Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2026-01-26T14:38:10Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2026-01-26T15:03:33Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2026-01-26T15:04:52Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

xiangli313 · 2026-01-30T06:58:42Z

R/constants.R

 )
+
+#' @name constants
+burden_outcome_names <- c(


we also have deaths_cwyx, cases_cwyx, dalys_cwyx, yll_cwyx, rubella_deaths_congenital and rubella_cases_congenital.

github-actions · 2026-01-30T10:34:07Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2026-01-30T10:48:33Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

xiangli313

I think this is looking good. I am approving it; and will be using it once merged (will feedback).

pratikunterwegs · 2026-01-30T11:35:39Z

R/plotting_prep.R

+#' @param year_min Minimum year.
+#'
+#' @export
+prep_plot_fvp <- function(fvp, year_min, year_max) {


@xiangli313 - I had a question regarding this function that prepares the FVP data for plotting. This function is used to generate the data for the FVPs-over-time plot (usually Fig. 2 in burden diagnostics reports). Where can I find an example of the FVPs dataset that is used to make the FVPs plot? The related plotting function is plot_fvp().

FVP data is derived from both coverage and wpp data. It is calculated given specific version of coverage and wpp. If you just need example dataset, please find fvps.rds from here https://montagu.vaccineimpact.org/packit/rapid-model-run-burden/20251218-112844-86af9b70/downloads

kgaythorpe

fantastic, thanks Pratik, happy to approve from my side

pratikunterwegs · 2026-01-30T11:38:53Z

R/plotting_prep.R

+#' @param coverage WIP. Coverage data.
+#'
+#' @export
+prep_plot_coverage_set <- function(coverage) {


@xiangli313 - similar question/request for some example coverage set data so that this function can be tested. This function prepares data that is used to generate the coverage set data (usually Fig. 1 in diagnostics reports). The related plotting function is plot_coverage_set().

You may use coverage_scenario.csv from here https://montagu.vaccineimpact.org/packit/rapid-model-run-coverage/20251121-174950-8ce647c0/downloads

github-actions · 2026-01-30T12:29:05Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

zegibney

Looks really good Pratik and very easy to follow, grateful for it all being in one place! A few minor comments.

zegibney · 2026-02-02T10:43:53Z

R/burden_diagnostics.R

Minor typo in the file name, only figured it out when I was questioning my ability to spell diagnostics!

zegibney · 2026-02-02T10:49:03Z

R/burden_diagnostics.R

  checkmate::assert_data_frame(burden_set)
  checkmate::assert_data_frame(wpp)

  gender <- rlang::arg_match(gender)

-  cols_to_select <- c("country", "year", "age", "cohort_size")
+  cols_to_select <- c("country", "year", "age", "cohort_size", "scenario")


Could wait until the end to standardise across files but can we make this scenario_type to match existing conventions? @xiangli313 what do you think? I see in constants.R there is the file dict.

Totally agree. We used to have scenario/scenario_type as enum tables in montagu. For the future, we can create a similar constant table for vimcheck.

Just to check - should I change scenario to scenario_type throughout?

Actually, rethink about, let's keep scenario. Usually, for per scenario_type, there could be a few incremental scenarios. And scenario naming convention usually have scenario_type as an suffix.

Sure - I'll keep it as it is.

zegibney · 2026-02-02T11:17:48Z

R/constants.R

@@ -21,3 +21,28 @@ scenario_data_colnames <- c(
  "scenario",


See comment about scenario/scenario_type.

github-actions · 2026-02-02T15:13:52Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

github-actions · 2026-02-02T15:25:37Z

This pull request:

Adds 1 new dependencies (direct and indirect)
Adds 1 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

pratikunterwegs · 2026-02-02T16:17:20Z

I'm going to try and get the failing MacOS check to pass - seems like a question of waiting until the runner recovers - and then merge.

pratikunterwegs added 9 commits January 20, 2026 12:19

Separate plotting code from data prep

7176d82

MInor fixes to burden diagnostics

23a1703

Edits to plotting prep fns

e9b6838

Edits to plotting fns

a90723b

Add constants

cc69283

Add scenario colm to burden example

0e2ccaf

Update docs and data desc

caf2bf8

Initial tests for plotting prep and plots

fd17892

Update pkg infra

1c10efb

pratikunterwegs added 2 commits January 26, 2026 14:35

Update fn ops and docs

e13e0fa

Update tests for fns

0b70dfe

pratikunterwegs added 2 commits January 26, 2026 15:02

Add vignette showing plotting

c9d1ab0

Update wordlist

ff4017a

xiangli313 reviewed Jan 30, 2026

View reviewed changes

pratikunterwegs added 2 commits January 30, 2026 10:14

Add snapshot for global burden plot

5be3808

Add extra burden outcomes

71aadc1

Remove global state checker

f506502

pratikunterwegs self-assigned this Jan 30, 2026

xiangli313 approved these changes Jan 30, 2026

View reviewed changes

pratikunterwegs commented Jan 30, 2026

View reviewed changes

kgaythorpe approved these changes Jan 30, 2026

View reviewed changes

pratikunterwegs commented Jan 30, 2026

View reviewed changes

pratikunterwegs added 2 commits January 30, 2026 12:10

Remove provisional fns

dd70521

Minor fixes

e911b86

pratikunterwegs marked this pull request as ready for review January 30, 2026 12:29

zegibney reviewed Feb 2, 2026

View reviewed changes

pratikunterwegs added 3 commits February 2, 2026 15:11

Add more exampled data

e7e767c

Add plotting fns to vignette

9573595

Increase test coverage

4cb5f9d

Correct filename

a7066f8

Separate plotting code from data prep #13

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