Prepare impact diagnostics for plotting — plot_prep_impact

A suite of helper functions that sit between impact diagnostics functions and plotting functions. These functions transform and aggregate impact estimates to prepare them for visualisation. Functions have basic checks on input data but otherwise assume users will not modify inputs.

Usage

prep_plot_mod_grp_varn(df2, df3, outcome = IMPACT_OUTCOMES)

prep_plot_vax_gavi(
  data,
  prev_data,
  outcome = IMPACT_OUTCOMES,
  touchstone_old = DEF_TOUCHSTONE_OLD,
  touchstone_new = DEF_TOUCHSTONE_NEW
)

prep_plot_cumul(
  data,
  outcome,
  disease,
  touchstone_old = DEF_TOUCHSTONE_OLD,
  touchstone_new = DEF_TOUCHSTONE_NEW
)

Arguments

df2: A <tibble> of impact estimates with at least columns modelling_group, vaccine, outcome variable, and fvps (doses delivered). Used as the primary data source for calculations in prep_plot_mod_grp_varn().
df3: A <tibble> of modelling group and vaccine combinations, typically with one row per modelling group per vaccine. Joined with df2 to ensure complete group coverage in prep_plot_mod_grp_varn().
outcome: A character string for the impact outcome. Must be one of "deaths_averted" or "dalys_averted". For prep_plot_cumul(), data must include columns named {outcome}_old and {outcome}_new.
data: A <tibble> of impact estimates with columns including at least those in COLNAMES_KEY_PRESSURE_TEST, the outcome variable, and potentially other columns for analysis.
prev_data: A <tibble> of impact estimates from a previous touchstone, used as a comparison baseline. Should have the same structure as data.
touchstone_old: A six-character touchstone identifier (YYYYMM format) for the previous dataset. Defaults to DEF_TOUCHSTONE_OLD. Used in prep_plot_vax_gavi() and prep_plot_cumul().
touchstone_new: A six-character touchstone identifier (YYYYMM format) for the current dataset. Defaults to DEF_TOUCHSTONE_NEW. Used in prep_plot_vax_gavi() and prep_plot_cumul().
disease: A character string specifying a single disease for filtering and analysis.

Value

prep_plot_mod_grp_varn() returns a grouped <tibble> (grouped by vaccine) with all columns from df2 and df3 plus derived columns: adj_outc (adjusted outcome with small offset), outcome_name (input outcome), and mean_outc (vaccine-level weighted mean outcome).
prep_plot_vax_gavi() returns a <tibble> with columns disease, year, yearly_outcome, dataset (factor with levels for old touchstone, "Difference", and new touchstone), and outcome_name. Summarizes outcomes by disease and year across two touchstones.
prep_plot_cumul() returns a <tibble> with columns year, modelling_group, touchstone, value (cumulative or average outcome), line_type ("solid" for individual models, "dashed" for model average), and outcome_name. Returns NULL if the specified disease has no non-zero data to plot.