Add pressure testing functions

.Rbuildignore

@@ -16,3 +16,4 @@
 ^scratch\.R$
 ^scratch$
 ^data-raw$
+^jarl\.toml$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: vimcheck
 Title: Diagnostics for Vaccine Impact Modelling Consortium Burden and
     Impact Estimates
-Version: 0.0.3
+Version: 0.0.4
 Authors@R: c(
     person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),
@@ -24,13 +24,17 @@ Depends:
 Imports: 
     checkmate,
     cli,
+    diffdf,
     dplyr,
     forcats,
     ggplot2,
+    ggridges,
     glue,
+    here,
     readr,
     rlang,
     scales,
+    stats,
     stringr,
     tidyr
 Suggests: 
@@ -48,4 +52,4 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,20 +1,56 @@
 # Generated by roxygen2: do not edit by hand
 
+export(COLNAMES_INTEREST_PRESSURE_TEST)
+export(COLNAMES_KEY_PRESSURE_TEST)
+export(COLOUR_VIMC)
+export(DEF_TOUCHSTONE_NEW)
+export(DEF_TOUCHSTONE_OLD)
+export(DEF_TOUCHSTONE_OLD_OLD)
+export(EXCLUDED_DISEASES)
+export(IMPACT_OUTCOMES)
+export(MAX_TS_MONTH)
+export(MAX_TS_YEAR)
+export(MIN_TS_MONTH)
+export(MIN_TS_YEAR)
+export(N_TS_MIN_CHARS)
+export(N_TS_YEAR_CHARS)
 export(basic_burden_sanity)
+export(burden_outcome_names)
 export(check_demography_alignment)
+export(colnames_df_missing_cols)
+export(colnames_plot_demog_compare)
+export(compare_natl_subreg)
 export(file_dict_colnames)
+export(filter_excluded_diseases_ts)
+export(filter_invalid_trajectories)
+export(filter_recent_ts)
+export(flag_duplicates)
+export(flag_large_diffs)
+export(gen_combined_df)
+export(gen_national_iqr)
+export(generate_diffs)
 export(plot_age_patterns)
 export(plot_compare_demography)
 export(plot_coverage_set)
+export(plot_cumul)
+export(plot_diff)
 export(plot_fvp)
 export(plot_global_burden)
 export(plot_global_burden_decades)
+export(plot_modelling_group_variation)
+export(plot_sig_diff)
+export(plot_vaccine_gavi)
 export(prep_plot_age)
 export(prep_plot_burden_decades)
 export(prep_plot_coverage_set)
+export(prep_plot_cumul)
 export(prep_plot_demography)
 export(prep_plot_fvp)
 export(prep_plot_global_burden)
+export(prep_plot_mod_grp_varn)
+export(prep_plot_vax_gavi)
+export(save_outputs)
+export(scenario_data_colnames)
 export(theme_vimc)
 export(theme_vimc_noxaxis)
 export(validate_complete_incoming_files)
@@ -26,12 +62,16 @@ importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,label_wrap_gen)
 importFrom(ggplot2,labeller)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_fill_distiller)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,vars)
+importFrom(rlang,":=")
 importFrom(rlang,.data)

NEWS.md

@@ -1,3 +1,15 @@
+# vimcheck 0.0.4
+
+- Added impact diagnostics functions in `R/fn_impact_diagnostics.R`.
+
+- Added test data originally used in [vimpact](https://github.com/vimc/vimpact) for use with vimcheck.
+
+- Added plotting preparation functions and plotting functions in `R/fn_plotting_prep_impact_diagnostics.R` and `R/fn_plotting_impact_diagnostics.R`.
+
+- Added dependencies _diffdf_ and _here_.
+
+- Added vignette on design decisions and pressure testing functions.
+
 # vimcheck 0.0.3
 
 - Separated data-prep for plotting from plotting functions.

R/constants.R

@@ -1,10 +1,17 @@
 #' Package constants
 #'
+#' @description
+#' Constant values used in _vimcheck_. See the **Examples** section for the
+#' constant values.
+#'
 #' @name constants
 #' @rdname constants
 #'
 #' @keywords constants
 #'
+#' @examples
+#' file_dict_colnames
+#'
 #' @export
 file_dict_colnames <- c(
   "scenario_type",
@@ -15,6 +22,11 @@ file_dict_colnames <- c(
 )
 
 #' @name constants
+#'
+#' @examples
+#' scenario_data_colnames
+#'
+#' @export
 scenario_data_colnames <- c(
   "scenario_type",
   "scenario_type_description",
@@ -23,6 +35,11 @@ scenario_data_colnames <- c(
 )
 
 #' @name constants
+#'
+#' @examples
+#' burden_outcome_names
+#'
+#' @export
 burden_outcome_names <- c(
   "cases",
   "deaths",
@@ -37,6 +54,11 @@ burden_outcome_names <- c(
 )
 
 #' @name constants
+#'
+#' @examples
+#' colnames_plot_demog_compare
+#'
+#' @export
 colnames_plot_demog_compare <- c(
   "variable",
   "scenario",
@@ -46,3 +68,150 @@ colnames_plot_demog_compare <- c(
   "value",
   "value_millions"
 )
+
+#' @name constants
+#'
+#' @examples
+#' colnames_df_missing_cols
+#'
+#' @export
+colnames_df_missing_cols <- c(
+  "country_name",
+  "vaccine",
+  "activity_type",
+  "year",
+  "modelling_group"
+)
+
+#' @name constants
+#'
+#' @examples
+#' COLNAMES_KEY_PRESSURE_TEST
+#'
+#' @export
+COLNAMES_KEY_PRESSURE_TEST <- c(
+  "country",
+  "country_name",
+  "vaccine",
+  "activity_type",
+  "year",
+  "disease",
+  "modelling_group"
+)
+
+#' @name constants
+#'
+#' @examples
+#' COLNAMES_INTEREST_PRESSURE_TEST
+#'
+#' @export
+COLNAMES_INTEREST_PRESSURE_TEST <- union(
+  COLNAMES_KEY_PRESSURE_TEST,
+  c(
+    "fvps",
+    "target_population",
+    "coverage",
+    "deaths_averted",
+    "dalys_averted",
+    "deaths_averted_rate",
+    "dalys_averted_rate"
+  )
+)
+
+#' @name constants
+#'
+#' @examples
+#' IMPACT_OUTCOMES
+#'
+#' @export
+IMPACT_OUTCOMES <- c("deaths_averted", "dalys_averted")
+
+IMPACT_GROUP_VARS <- c("activity_type", "vaccine")
+
+#' @name constants
+#'
+#' @examples
+#' EXCLUDED_DISEASES
+#'
+#' @export
+EXCLUDED_DISEASES <- c("Hib", "PCV", "Rota", "JE")
+
+#' @name constants
+#'
+#' @examples
+#' N_TS_MIN_CHARS
+#'
+#' @export
+N_TS_MIN_CHARS <- 6L
+
+#' @name constants
+#'
+#' @examples
+#' N_TS_YEAR_CHARS
+#'
+#' @export
+N_TS_YEAR_CHARS <- 4L
+
+#' @name constants
+#'
+#' @examples
+#' MIN_TS_YEAR
+#'
+#' @export
+MIN_TS_YEAR <- 2000
+
+#' @name constants
+#'
+#' @examples
+#' MAX_TS_YEAR
+#'
+#' @export
+MAX_TS_YEAR <- 2100
+
+#' @name constants
+#'
+#' @examples
+#' MIN_TS_MONTH
+#'
+#' @export
+MIN_TS_MONTH <- 1
+
+#' @name constants
+#'
+#' @examples
+#' MAX_TS_MONTH
+#'
+#' @export
+MAX_TS_MONTH <- 12
+
+#' @name constants
+#'
+#' @examples
+#' DEF_TOUCHSTONE_OLD
+#'
+#' @export
+DEF_TOUCHSTONE_OLD <- "201910"
+
+#' @name constants
+#'
+#' @examples
+#' DEF_TOUCHSTONE_NEW
+#'
+#' @export
+DEF_TOUCHSTONE_NEW <- "202310"
+
+#' @name constants
+#'
+#' @examples
+#' DEF_TOUCHSTONE_OLD_OLD
+#'
+#' @export
+DEF_TOUCHSTONE_OLD_OLD <- "202110"
+
+#' @name constants
+#'
+#' @examples
+#' COLOUR_VIMC
+#'
+#' @export
+COLOUR_VIMC <- "#008080"

R/data_who_subregions.R

@@ -0,0 +1,23 @@
+#' Data on countries in WHO subregions
+#'
+#' Data that groups countries into WHO subregions.
+#'
+#' @format ## `who_subregions`
+#' A data frame with 249 rows and 9 columns:
+#' \describe{
+#'   \item{choice_subregion}{Sub-region three character code with added letter
+#' identifier.}
+#'   \item{country_name}{Country name in long form.}
+#'   \item{country}{ISO 3 character country code.}
+#'   \item{Global.Name}{A constant, 'World'.}
+#'   \item{Region.Name}{Continent-scale region identifier.}
+#'   \item{Sub.region}{Sub-continental scale region identifier.}
+#'   \item{Intermediate.Region.Name}{Alternative regional scale identifier.}
+#'   \item{subregion}{Sub-regional identifier.}
+#'   \item{vimc117}{Logical identifier.}
+#' }
+#'
+#' @keywords data
+#'
+#' @source Prepared by the VIMC secretariat.
+"who_subregions"

R/example_data.R

@@ -114,3 +114,28 @@
 #'
 #' @source Prepared by the VIMC secretariat.
 "eg_fvps"
+
+#' Example of impact data
+#'
+#' Example of vaccine impact data taken from data used to test \pkg{vimpact}.
+#' This data is primarily used for testing here too.
+#'
+#' @format ## `eg_impact`
+#' A data frame with 5396 rows and 9 columns:
+#' \describe{
+#'   \item{disease}{Disease name.}
+#'   \item{vaccine}{Vaccine identifier.}
+#'   \item{modelling_group}{Modelling group name.}
+#'   \item{country}{Country ISO 3-character code.}
+#'   \item{country_name}{Country name.}
+#'   \item{year}{Year for which impacts are modelled.}
+#'   \item{activity_type}{Activity type: either "routine" or "campaign."}
+#'   \item{burden_outcome}{Name of the burden outcome; one of "deaths_averted"
+#' or "dalys_averted".}
+#'   \item{impact}{Value of the impact}.
+#' }
+#'
+#' @keywords data
+#'
+#' @source Prepared by the VIMC secretariat.
+"eg_impact"