WIP impact diagnostics fns

.github/workflows/R-CMD-check.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, develop]
 
 name: R-CMD-check
 

.github/workflows/lint-changed-files.yaml

@@ -3,7 +3,6 @@
 on:
   workflow_dispatch:
   pull_request:
-    branches: [main, master]
     paths:
       - '**.R'
       - '**.Rmd'

.lintr

@@ -6,6 +6,9 @@ linters: all_linters(
     object_length_linter = NULL # due to length of method names
     )
 exclusions: list(
+    "R/fn_plotting_impact.R" = list(
+      object_overwrite_linter = Inf
+    ),
     "tests/testthat.R" = list(
       unused_import_linter = Inf,
       undesirable_function_linter = Inf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: vimcheck
 Title: Diagnostics for Vaccine Impact Modelling Consortium Burden and
     Impact Estimates
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: c(
     person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),

NAMESPACE

@@ -14,6 +14,7 @@ export(MIN_TS_MONTH)
 export(MIN_TS_YEAR)
 export(N_TS_MIN_CHARS)
 export(N_TS_YEAR_CHARS)
+export(PINE)
 export(basic_burden_sanity)
 export(burden_outcome_names)
 export(check_demography_alignment)
@@ -31,12 +32,14 @@ export(gen_national_iqr)
 export(generate_diffs)
 export(plot_age_patterns)
 export(plot_compare_demography)
+export(plot_coverage_fvps)
 export(plot_coverage_set)
 export(plot_cumul)
 export(plot_diff)
 export(plot_fvp)
 export(plot_global_burden)
 export(plot_global_burden_decades)
+export(plot_impact)
 export(plot_modelling_group_variation)
 export(plot_sig_diff)
 export(plot_vaccine_gavi)

NEWS.md

@@ -1,3 +1,7 @@
+# vimcheck 0.0.5
+
+- Added functions to plot impact and FVPs and coverage.
+
 # vimcheck 0.0.4
 
 - Added impact diagnostics functions in `R/fn_impact_diagnostics.R`.

R/constants.R

@@ -215,3 +215,11 @@ DEF_TOUCHSTONE_OLD_OLD <- "202110"
 #'
 #' @export
 COLOUR_VIMC <- "#008080"
+
+#' @name constants
+#'
+#' @examples
+#' PINE
+#'
+#' @export
+PINE <- c("PAK", "IND", "NGA", "ETH")

R/example_data.R

@@ -115,6 +115,28 @@
 #' @source Prepared by the VIMC secretariat.
 "eg_fvps"
 
+#' A second FVP data example
+#'
+#' Exampled data for fully-vaccinated persons, created manually from arbitrary
+#' data.
+#'
+#' @format ## `eg_fvps_2`
+#' A data frame with 4 rows and 7 columns:
+#' \describe{
+#'   \item{country}{Country name as ISO 3 character code.}
+#'   \item{year}{Year.}
+#'   \item{activity_type}{Vaccination activity identifier.}
+#'   \item{scenario_type}{Scenario type name.}
+#'   \item{vaccine}{Vaccine identifier.}
+#'   \item{coverage_adjusted}{Ratio of adjusted FVPs to adjusted target.}
+#'   \item{fvps}{Count of fully vaccinated persons.}
+#' }
+#'
+#' @keywords data
+#'
+#' @source Example data prepared by the VIMC secretariat.
+"eg_fvps_2"
+
 #' Example of impact data
 #'
 #' Example of vaccine impact data taken from data used to test \pkg{vimpact}.
@@ -139,3 +161,21 @@
 #'
 #' @source Prepared by the VIMC secretariat.
 "eg_impact"
+
+#' Second example of impact data
+#'
+#' @format ## `eg_impact_2`
+#' A data frame with 4 rows and 6 columns:
+#' \describe{
+#'   \item{country}{Example country identifier.}
+#'   \item{year}{Year.}
+#'   \item{birth_cohort}{Numeric for the birth year.}
+#'   \item{burden_outcome}{Outcome identifier.}
+#'   \item{impact}{Numeric for impact.}
+#'   \item{short_name}{Example identifier.}
+#' }
+#'
+#' @keywords data
+#'
+#' @source Prepared manually by the VIMC secretariat.
+"eg_impact_2"