diff --git a/.Rbuildignore b/.Rbuildignore
index b5a39b8..42d9471 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,4 @@
 ^pkgdown$
 ^tools$
 ^scratch\.R$
+^scratch$
diff --git a/.gitignore b/.gitignore
index d224dad..1ecff28 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,3 +50,4 @@ rsconnect/
 inst/doc
 docs
 scratch.R
+scratch/
diff --git a/DESCRIPTION b/DESCRIPTION
index 2f7f186..ce362e2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,3 +31,12 @@ Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Imports: 
+    cli,
+    dplyr,
+    fs,
+    ggplot2,
+    glue,
+    readr,
+    rlang,
+    tidyr
diff --git a/NAMESPACE b/NAMESPACE
index 6ae9268..2d4bceb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,2 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
+export(basic_burden_sanity)
+export(check_demography_alignment)
+export(check_template_alignment)
+export(const_data_colnames)
+export(impact_check)
+export(plot_age_patterns)
+export(plot_compare_demography)
+export(plot_coverage_set)
+export(plot_fvp)
+export(plot_global_burden)
+export(plot_global_burden_decades)
+export(theme_vimc)
+export(transfrom_coverage_fvps)
+export(validate_complete_incoming_files)
+export(validate_file_dict_template)
+importFrom(ggplot2,ggplot)
diff --git a/R/burden_diagnositics.R b/R/burden_diagnositics.R
new file mode 100644
index 0000000..eac40de
--- /dev/null
+++ b/R/burden_diagnositics.R
@@ -0,0 +1,512 @@
+#' Validate file dictionary template
+#'
+#' @description
+#' Function to create a `file_dictionary` template.
+#' It maps to touchstone disease scenarios and you will see expected number of
+#' scenarios i.e. the number of files that we expect from a model.
+#' Users should populate the file column to match the scenario-file.
+#' This function will run if a `file_dictionary.csv` file does not exist
+#'
+#' @param disease A disease identifier.
+#'
+#' @param path_burden A directory with burden estimate data.
+#'
+#' @return Nothing; called primarily for its side-effets.
+#' If the file `path_burden/file_dictionary.csv` does not exist, a file
+#' dictionary CSV file is written to the same location.
+#' Prints a message to screen informing the user whether any action has been
+#' taken.
+#'
+#' @keywords diagnostics
+#'
+#' @examples
+#'
+#' @export
+validate_file_dict_template <- function(
+  disease,
+  path_burden = "incoming_burden_estimates"
+) {
+  # TODO: check conditions on arg disease - what is the original source `pars`?
+
+  assert_is_directory(path_burden)
+  template <- file.path(path_burden, "file_dictionary.csv")
+
+  if (file.exists(template)) {
+    cli::cli_inform(
+      "File dictionary found at {.file {template}}, no action needed."
+    )
+  } else {
+    # TODO: resolve magic strings
+    scenario_dir <- "model_inputs"
+    checkmate::assert_directory_exists(scenario_dir)
+    scenario_data <- file.path(scenario_dir, "scenario.csv")
+    checkmate::assert_file_exists(scenario_data)
+
+    sce <- readr::read_csv(scenario_data, show_col_types = FALSE)
+
+    # NOTE: consider wrapping into check function
+    checkmate::assert_data_frame(
+      sce,
+      any.missing = FALSE,
+      min.cols = length(const_data_colnames),
+    )
+    checkmate::assert_names(
+      colnames(sce),
+      must.include = const_data_colnames
+    )
+
+    # get distinct scenario entries and add no-vax if needed
+    sce <- dplyr::select(sce, {{ const_data_colnames }})
+    sce <- dplyr::distinct(sce)
+
+    novax_scenario <- "novac"
+
+    if (!checkmate::test_subset(novax_scenario, sce$scenario_type)) {
+      sce <- dplyr::bind_rows(
+        sce,
+        make_novax_scenario(disease)
+      )
+    }
+
+    sce$file <- NA_character_ # TODO: investigate this further
+    readr::write_csv(sce, template)
+
+    cli::cli_inform(
+      "No file dictionary found at {.file {template}}; created a file \\
+      dictionary and wrote it to {.file {template}}."
+    )
+  }
+
+  # no return
+}
+
+#' Validate files in a burden estimate
+#'
+#' @description
+#' Check that incoming data files in a burden estimate are complete, and that
+#' no extra files have been included.
+#' This function expects that incoming burden files are in the
+#' directory given by `path_burden`, which holds a file dictionary which maps
+#' each data file to a specific scenario.
+#'
+#' @inheritParams validate_file_dict_template
+#'
+#' @return A `<tibble>` of the scenario file dictionary in `path_burden` if all
+#' checks pass. Otherwise, exits with informative errors on failed checks.
+#'
+#' @examples
+#'
+#' @keywords diagnostics
+#'
+#' @export
+validate_complete_incoming_files <- function(
+  path_burden = "incoming_burden_estimates"
+) {
+  assert_is_directory(path_burden)
+
+  files <- list.files(path_burden, full.names = TRUE)
+  file_dict <- file.path(path_burden, "file_dictionary.csv")
+
+  # checks on the file dictionary
+  if (file.exists(file_dict)) {
+    df_dict <- readr::read_csv(
+      file_dict,
+      show_col_types = FALSE
+    )
+
+    col_filenames <- "file" # TODO: remove/explain magic colnm
+    scenario_filenames <- df_dict[[col_filenames]]
+    df_dict <- dplyr::select(df_dict, -{{ col_filenames }})
+
+    duplicate_rows <- anyDuplicated(df_dict)
+    duplicate_filenames <- anyDuplicated(scenario_filenames)
+
+    if (duplicate_rows) {
+      cli::cli_abort(
+        "Expected file dictionary {.file {file_dict}} to have non-duplicate \\
+        entries, but found {duplicate_rows} duplicated rows!"
+      )
+    }
+    if (duplicate_filenames) {
+      cli::cli_abort(
+        "Expected file dictionary {.file {file_dict}} to have non-duplicate \\
+        scenario filenames, but found {duplicate_filenames} duplicated \\
+        filenames!"
+      )
+    }
+
+    # expect scenario files in path_burden are the same as scenario_filenames
+    sce_files <- files[files != file_dict]
+    scenario_filenames <- file.path(path_burden, scenario_filenames)
+    are_good_scefiles <- checkmate::test_permutation(
+      scenario_filenames,
+      sce_files
+    )
+
+    if (!are_good_scefiles) {
+      extra_files <- setdiff(sce_files, scenario_filenames)
+      n_extra_files <- length(extra_files)
+      missing_files <- setdiff(scenario_filenames, sce_files)
+      n_missing_files <- length(missing_files)
+
+      cli::cli_abort(
+        c(
+          "Expected as many scenario data files as scenarios \\
+          ({length(scenario_filenames)}), but found \\
+          {.emph {length(sce_files)}} instead.",
+          i = "Found {cli::no(n_extra_files)} extra files{? /}\\
+          {.file {basename(extra_files)}}, {cli::qty(n_missing_files)}
+          {?but could not find/and} \\
+          {cli::no(n_missing_files)} missing files{? /} \\
+          {.file {basename(missing_files)}}",
+          i = "Directory searched: {.file {path_burden}}"
+        ),
+      )
+    }
+  } else {
+    cli::cli_abort(
+      "Expected a file dictionary {.file {file_dict}}, but it was not found!"
+    )
+  }
+
+  df_dict
+}
+
+#' Check incoming burden set against template
+#'
+#' @description
+#'
+#' @param burden_set
+#'
+#' @param template
+#'
+#' @return
+#'
+#' @examples
+#'
+#' @keywords diagnostics
+#'
+#' @export
+check_template_alignment <- function(burden_set, template) {
+  # TODO: figure out what the args are expected to be: dfs? lists, vecs?
+  expected <- names(template)
+  provided <- names(burden_set)
+
+  missing_cols_in_burden <- setdiff(expected, provided)
+  extra_cols_in_burden <- setdiff(provided, expected)
+
+  # explicitly check each length
+  burden_cols_matches_template <- length(missing_cols_in_burden) +
+    length(extra_cols_in_burden) ==
+    0L
+
+  # TODO: make magic strings constants
+  key_cols <- c("disease", "country", "year", "age")
+  template_grid <- dplyr::distinct(
+    template,
+    dplyr::across({
+      key_cols
+    })
+  )
+  burden_grid <- dplyr::distinct(
+    burden_set,
+    dplyr::across({
+      key_cols
+    })
+  )
+
+  # TODO: if these are data.frames, this might not be the best way to check
+  # for differences
+  missing_grid_in_burden <- setdiff(template_grid, burden_grid)
+  extra_grid_in_burden <- setdiff(burden_grid, template_grid)
+  burden_grid_matches_template <- all(
+    c(
+      nrow(missing_grid_in_burden),
+      nrow(extra_grid_in_burden)
+    ) ==
+      0L
+  )
+
+  list(
+    missing_cols_in_burden = missing_cols_in_burden,
+    extra_cols_in_burden = extra_cols_in_burden,
+    burden_cols_matches_template = burden_cols_matches_template,
+    missing_grid_in_burden = missing_grid_in_burden,
+    extra_grid_in_burden = extra_grid_in_burden,
+    burden_grid_matches_template = burden_grid_matches_template
+  )
+}
+
+#' Check incoming burden cohort size against interpolated population
+#'
+#' @description
+#'
+#' @param burden_set
+#'
+#' @param wpp
+#'
+#' @param gender
+#'
+#' @return
+#'
+#' @keywords diagnostics
+#'
+#' @export
+check_demography_alignment <- function(burden_set, wpp, gender = "both") {
+  # TODO: input checks
+
+  # TODO: check if these can be made constants
+  cols_to_select <- c("country", "year", "age", "cohort_size")
+  provided <- dplyr::select(
+    burden_set,
+    {{ cols_to_select }}
+  )
+  provided <- dplyr::mutate(
+    provided = cohort_size # check if this can be made a string const
+  )
+
+  # TODO: explain what expected is
+  # TODO: replace with a right-join?
+  expected <- dplyr::filter(
+    wpp,
+    country %in%
+      provided$country &
+      year %in% provided$year &
+      age %in% provided$age,
+    gender == {{ gender }}
+  )
+
+  cols_to_select <- c("country", "year", "age", "value")
+  expected <- dplyr::select(
+    expected,
+    {{ cols_to_select }}
+  )
+  expected <- dplyr::rename(
+    expected,
+    expected = value
+  ) # TODO: prefer not to use NSE
+
+  # return left join
+  alignment <- dplyr::left_join(
+    provided,
+    expected,
+    by = c("country", "year", "age")
+  )
+  alignment <- dplyr::mutate(
+    alignment,
+    difference = provided - expected,
+    abs_diff = abs(difference),
+    prop_diff = difference / expected
+  )
+
+  alignment
+}
+
+#' Sanity checks on burden estimates
+#'
+#' @description Helper function for sanity checks on burden estimate values.
+#' Checks whether any burden estimates are non-numeric, missing, or negative.
+#'
+#' @param burden A `<data.frame>` of disease burden estimates. Must have
+#' at least a single column named `"value"` of numeric burden estimates.
+#'
+#' @return A character vector of messages generated by checks on burden
+#' estimates, with the length of the vector depending on how many checks fail.
+#'
+#' @keywords diagnostics
+#'
+#' @export
+basic_burden_sanity <- function(burden) {
+  # TODO: expectations on burden
+  mes <- "Basic sanity check for burden estimates:"
+
+  value_col <- "value"
+  value <- burden[[value_col]]
+
+  if (is.numeric(burden$value)) {
+    if (anyNA(burden$value)) {
+      mes_any_missing <- glue::glue(
+        "Warning: Burden estimates should not have missing values, but some \\
+        values are missing. Fix missing values by converting to zeros!"
+      )
+
+      mes <- c(mes, mes_any_missing)
+    }
+
+    if (any(burden$value < 0, na.rm = TRUE)) {
+      mes_any_negative <- glue::glue(
+        "Warning: Burden estimates should all be positive or zero, but found \\
+        some negative estimates!"
+      )
+
+      mes <- c(mes, mes_any_negative)
+    }
+  } else {
+    mes_not_numeric <- glue::glue(
+      "Warning: Burden estimates should be of type `numeric`, but are not. \\
+      Convert burden estimates to `numeric`."
+    )
+
+    mes <- c(mes, mes_not_numeric)
+  }
+
+  if (length(mes) == 1L) {
+    mes <- c(mes, "PASS.")
+  }
+
+  mes
+}
+
+#' @title
+#'
+#' @description
+#' A short description...
+#'
+#' @param coverage
+#'
+#' @param wpp
+#'
+#' @return
+#'
+#' @examples
+#' # example code
+#'
+#' @keywords diagnostics
+#'
+#' @export
+transfrom_coverage_fvps <- function(coverage, wpp) {
+  # TODO: checks on coverage
+  # TODO: checks on wpp
+
+  cols_to_select <- c("age_from", "age_to", "gender")
+  todo_list <- dplyr::select(
+    coverage,
+    cols_to_select
+  )
+  todo_list <- dplyr::distinct(todo_list)
+  todo_list <- dplyr::mutate(
+    todo_list,
+    job = seq_along(.data$gender)
+  )
+
+  # TODO: THIS NEEDS TO BE CLEANED UP
+  # TODO: clarify structure of `coverage` and mapping of gender to age
+  pop_all <- list()
+  for (i in seq_along(todo_list$age_from)) {
+    pop_all[[i]] <- wpp %>%
+      x <- dplyr::filter(
+      wpp,
+      .data$age >= todo_list$age_from[i],
+      .data$age <= todo_list$age_to[i],
+      .data$gender == todo_list$gender[i]
+    )
+    x <- dplyr::group_by(x, .data$country, .data$year)
+    x <- dplyr::summarise(
+      x,
+      target_wpp = sum(.data$value),
+      .groups = "drop"
+    )
+    x <- dplyr::mutate(
+      x,
+      job = todo_list$job[i]
+    )
+  }
+  pop_all <- dplyr::bind_rows(pop_all)
+
+  # TODO: add comments or explain in fn docs
+  d <- dplyr::left_join(
+    coverage,
+    pop_all,
+    by = c("country", "year")
+  )
+  d <- dplyr::mutate(
+    d,
+    target = dplyr::coalesce(
+      .data$target,
+      .data$target_wpp # replace NAs in target with target_wpp
+    ),
+    fvps = .data$target * .data$coverage,
+    fvps_adjusted = dplyr::if_else(
+      .data$fvps > .data$target_wpp,
+      .data$target_wpp,
+      .data$fvps
+    ),
+    target_adjusted = dplyr::if_else(
+      .data$target > .data$target_wpp,
+      .data$target_wpp,
+      .data$target
+    ),
+    coverage_adjusted = .data$fvps_adjusted / .data$target_adjusted
+  )
+  d[["target_wpp"]] <- NULL
+
+  d
+}
+
+# TODO: fill out fn docs
+#' @title
+#'
+#' @description
+#'
+#' @param burden
+#'
+#' @param scenario_order
+#'
+#' @return
+#'
+#' @examples
+#'
+#' @keywords diagnostics
+#'
+#' @export
+impact_check <- function(burden, scenario_order) {
+  # TODO: input checks
+  scenario_cols <- c("scenario", "scenario_order")
+  scenario_order <- dplyr::select(scenario_order, {{ scenario_cols }})
+
+  d <- dplyr::summarise(
+    millions = sum(.data$value) / 1e6,
+    .by = c("scenario", "burden_outcome"),
+    .groups = "drop" # probably unnecessary as grouping is temporary
+  )
+
+  d <- dplyr::left_join(
+    d,
+    scenario_order,
+    by = "scenario"
+  )
+
+  d <- dplyr::mutate(
+    d,
+    scenario_order = glue::glue("{.data$scenario_order}:{.data$scenario}")
+  )
+
+  d$scenario <- NULL
+
+  d <- tidyr::pivot_wider(
+    d,
+    names_from = "scenario_order",
+    values_from = "million"
+  )
+
+  # TODO: CLEAN THIS UP
+  for (i in 2:nrow(scenario_order)) {
+    for (j in 1:(i - 1)) {
+      if (any(d[i + 1] > d[j + 1])) {
+        cat(sprintf(
+          "&nbsp;&nbsp;&nbsp;&nbsp;**Warning**: provided less disease burden in lower coverage scenario (%s) compared to higher coverage scenario (%s).</span>",
+          names(d)[j + 1],
+          names(d)[i + 1]
+        ))
+        cat("<br>")
+      } else {
+        cat(sprintf(
+          "&nbsp;&nbsp;&nbsp;&nbsp;**PASS**: Provided higher disease burden in scenarios with fewer FVPs.</span>"
+        ))
+        cat("<br>")
+      }
+    }
+  }
+
+  d
+}
diff --git a/R/constants.R b/R/constants.R
new file mode 100644
index 0000000..a375556
--- /dev/null
+++ b/R/constants.R
@@ -0,0 +1,14 @@
+#' Package constants
+#'
+#' @name constants
+#' @rdname constants
+#'
+#' @keywords constants
+#'
+#' @export
+const_data_colnames <- c(
+  "scenario_type",
+  "scenario_type_description",
+  "scenario",
+  "scenario_description"
+)
diff --git a/R/helpers.R b/R/helpers.R
new file mode 100644
index 0000000..eb06f52
--- /dev/null
+++ b/R/helpers.R
@@ -0,0 +1,36 @@
+#' Make data for a no-vaccination scenario
+#'
+#' @name helpers
+#' @rdname helpers
+#'
+#' @description
+#' Helper functions for burden diagnostics.
+#'
+#' @inheritParams validate_file_dict_template
+#'
+#' @keywords internal
+#'
+#' @return
+#'
+#' - `make_novax_scenario()` returns a tibble with the minimum required column
+#' names, and entries corresponding to a 'no-vaccination' scenario for
+#' `disease`.
+make_novax_scenario <- function(disease) {
+  v <- c(
+    "novac",
+    "No Vaccination",
+    glue::glue("{disease}-no-vaccination"),
+    "No vaccination"
+  )
+
+  # internal function without input checking
+  df <- dplyr::tibble(
+    variable = need_colnames,
+    value = v
+  )
+
+  tidyr::pivot_wider(
+    df,
+    names_from = "variable"
+  )
+}
diff --git a/R/import-standalone-utils-assert-path.R b/R/import-standalone-utils-assert-path.R
new file mode 100644
index 0000000..673fb8e
--- /dev/null
+++ b/R/import-standalone-utils-assert-path.R
@@ -0,0 +1,157 @@
+# Standalone file: do not edit by hand
+# Source: https://github.com/reside-ic/reside.utils/blob/HEAD/R/standalone-utils-assert-path.R
+# Generated by: usethis::use_standalone("reside-ic/reside.utils", "utils-assert-path")
+# ----------------------------------------------------------------------
+#
+# ---
+# repo: reside/reside.utils
+# file: standalone-utils-assert-path.R
+# dependencies: standalone-utils-assert.R
+# imports: [cli, fs]
+# ---
+assert_file_exists <- function(files, name = "File", call = parent.frame(),
+                               arg = NULL) {
+  err <- !file.exists(files)
+  ## TODO: throughout this file it would be nice to use cli's '.file'
+  ## class and ector contraction, *but* it renders poorly on default
+  ## black backgfrounds (dark blue) and makes testing a bit harder
+  ## because the rendering depends on cli options.
+  ##
+  ## TODO: add a canonical case check, as for the relative path bit.
+  if (any(err)) {
+    ## Because we interpolate both 'name' and the file list, we need
+    ## to disambiguate the quantity.
+    n <- cli::qty(sum(err))
+    cli::cli_abort(
+      "{name}{n}{?s} {?does/do} not exist: {format_file_list(files[err])}",
+      call = call, arg = arg)
+  }
+}
+
+
+assert_file_exists_relative <- function(files, workdir, name,
+                                        call = parent.frame(),
+                                        arg = NULL) {
+  assert_relative_path(files, name, workdir, call)
+
+  assert_character(files, name, call = call)
+  err <- !file_exists(files, workdir = workdir)
+  if (any(err)) {
+    n <- cli::qty(sum(err))
+    cli::cli_abort(
+      c("{name}{n}{?s} {?does/do} not exist: {format_file_list(files[err])}",
+        i = "Looked within directory '{workdir}'"),
+      call = call)
+  }
+
+  files_canonical <- file_canonical_case(files, workdir)
+  err <- is.na(files_canonical) | fs::path(files) != files_canonical
+  if (any(err)) {
+    i <- err & !is.na(files_canonical)
+    hint_case <- sprintf("For '%s', did you mean '%s'?",
+                         files[i], files_canonical[i])
+    names(hint_case) <- rep("i", length(hint_case))
+    n <- cli::qty(sum(err))
+    cli::cli_abort(
+      c("{name}{n}{?s} {?does/do} not exist: {format_file_list(files[err])}",
+        hint_case,
+        i = paste("If you don't use the canonical case for a file, your code",
+                  "is not portable across different platforms"),
+        i = "Looked within directory '{workdir}'"),
+      call = call)
+  }
+}
+
+
+assert_is_directory <- function(path, name = "Directory", call = parent.frame(),
+                                arg = NULL) {
+  assert_scalar_character(path, arg = arg, call = call)
+  assert_file_exists(path, name = name, arg = arg, call = call)
+  if (!fs::is_dir(path)) {
+    cli::cli_abort("Path exists but is not a directory: {path}",
+                   call = call, arg = arg)
+  }
+}
+
+
+assert_relative_path <- function(files, name, workdir, call = parent.frame(),
+                                 arg = NULL) {
+  err <- fs::is_absolute_path(files)
+  if (any(err)) {
+    n <- cli::qty(sum(err))
+    files_err <- files[err]
+    names(files_err) <- rep("x", length(files_err))
+    cli::cli_abort(
+      c("{name}{n}{?s} must be {?a/} relative path{?s}",
+        files_err,
+        i = "Path was relative to directory '{workdir}'"),
+      call = call, arg = arg)
+  }
+
+  err <- vapply(fs::path_split(files), function(x) any(x == ".."), TRUE)
+  if (any(err)) {
+    n <- cli::qty(sum(err))
+    files_err <- files[err]
+    names(files_err) <- rep("x", length(files_err))
+    cli::cli_abort(
+      c("{name}{n}{?s} must not contain '..' (parent directory) components",
+        files_err,
+        i = "Path was relative to directory '{workdir}'"),
+      call = call, arg = arg)
+  }
+}
+
+
+assert_directory_does_not_exist <- function(x, name = "Directory", arg = NULL,
+                                            call = parent.frame()) {
+  ok <- !fs::dir_exists(x)
+  if (!all(ok)) {
+    cli::cli_abort("{name}{?s} already exists: {format_file_list(x[!ok])}",
+                   call = call, arg = arg)
+  }
+  invisible(x)
+}
+
+
+file_canonical_case <- function(path, workdir) {
+  if (length(path) != 1) {
+    return(vapply(path, file_canonical_case, "", workdir, USE.NAMES = FALSE))
+  }
+  stopifnot(!fs::is_absolute_path(path))
+  path_split <- fs::path_split(path)[[1]]
+  base <- workdir
+  ret <- character(length(path_split))
+  for (i in seq_along(path_split)) {
+    pos <- dir(base, all.files = TRUE, no.. = TRUE)
+    el <- path_split[[i]]
+    j <- which(tolower(el) == tolower(pos))
+    if (length(j) == 1) {
+      el <- pos[[j]]
+    } else if (el %in% pos) {
+      # We might want to warn here?
+      # message("Multiple casings present; this is not portable")
+    } else {
+      return(NA_character_)
+    }
+    ret[[i]] <- el
+    base <- file.path(base, el)
+  }
+  paste(ret, collapse = "/")
+}
+
+
+file_exists <- function(..., workdir = NULL) {
+  files <- c(...)
+  if (!is.null(workdir)) {
+    assert_scalar_character(workdir)
+    owd <- setwd(workdir) # nolint
+    on.exit(setwd(owd)) # nolint
+  }
+  fs::file_exists(files)
+}
+
+
+format_file_list <- function(x) {
+  cli::cli_vec(sprintf("'%s'", x),
+               style = list("vec-sep2" = ", ", "vec-last" = ", "))
+}
diff --git a/R/import-standalone-utils-assert.R b/R/import-standalone-utils-assert.R
new file mode 100644
index 0000000..441503d
--- /dev/null
+++ b/R/import-standalone-utils-assert.R
@@ -0,0 +1,251 @@
+# Standalone file: do not edit by hand
+# Source: https://github.com/reside-ic/reside.utils/blob/HEAD/R/standalone-utils-assert.R
+# Generated by: usethis::use_standalone("reside-ic/reside.utils", "utils-assert")
+# ----------------------------------------------------------------------
+#
+# ---
+# repo: reside/reside.utils
+# file: standalone-utils-assert.R
+# imports: cli
+# ---
+assert_scalar <- function(x, name = deparse(substitute(x)), arg = name,
+                          call = parent.frame())  {
+  if (length(x) != 1) {
+    cli::cli_abort(
+      c("'{name}' must be a scalar",
+        i = "{name} has length {length(x)}"),
+      call = call, arg = arg)
+  }
+  invisible(x)
+}
+
+
+assert_character <- function(x, name = deparse(substitute(x)),
+                             arg = name, call = parent.frame()) {
+  if (!is.character(x)) {
+    cli::cli_abort("Expected '{name}' to be character", call = call, arg = arg)
+  }
+  invisible(x)
+}
+
+
+assert_numeric <- function(x, name = deparse(substitute(x)),
+                           arg = name, call = parent.frame()) {
+  if (!is.numeric(x)) {
+    cli::cli_abort("Expected '{name}' to be numeric", call = call, arg = arg)
+  }
+  invisible(x)
+}
+
+
+assert_integer <- function(x, name = deparse(substitute(x)),
+                           tolerance = NULL, arg = name,
+                           call = parent.frame()) {
+  if (is.numeric(x)) {
+    rx <- round(x)
+    if (is.null(tolerance)) {
+      tolerance <- sqrt(.Machine$double.eps)
+    }
+    if (!isTRUE(all.equal(x, rx, tolerance = tolerance))) {
+      cli::cli_abort(
+        c("Expected '{name}' to be integer",
+          i = paste("{cli::qty(length(x))}The provided",
+                    "{?value was/values were} numeric, but not very close",
+                    "to integer values")),
+        arg = arg, call = call)
+    }
+    x <- as.integer(rx)
+  } else {
+    cli::cli_abort("Expected '{name}' to be integer", call = call, arg = arg)
+  }
+  invisible(x)
+}
+
+
+assert_logical <- function(x, name = deparse(substitute(x)),
+                          arg = name, call = parent.frame()) {
+  if (!is.logical(x)) {
+    cli::cli_abort("Expected '{name}' to be logical", arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_nonmissing <- function(x, name = deparse(substitute(x)),
+                              arg = name, call = parent.frame()) {
+  if (anyNA(x)) {
+    cli::cli_abort("Expected '{name}' to be non-NA", arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_scalar_character <- function(x, name = deparse(substitute(x)),
+                                    allow_null = FALSE,
+                                    arg = name, call = parent.frame()) {
+  if (allow_null && is.null(x)) {
+    return(invisible(x))
+  }
+  assert_scalar(x, name, arg = arg, call = call)
+  assert_character(x, name, arg = arg, call = call)
+  assert_nonmissing(x, name, arg = arg, call = call)
+}
+
+
+assert_scalar_numeric <- function(x, name = deparse(substitute(x)),
+                                  allow_null = FALSE,
+                                  arg = name, call = parent.frame()) {
+  if (allow_null && is.null(x)) {
+    return(invisible(x))
+  }
+  assert_scalar(x, name, arg = arg, call = call)
+  assert_numeric(x, name, arg = arg, call = call)
+  assert_nonmissing(x, name, arg = arg, call = call)
+}
+
+
+assert_scalar_integer <- function(x, name = deparse(substitute(x)),
+                                  tolerance = NULL, allow_null = FALSE,
+                                  arg = name, call = parent.frame()) {
+  if (allow_null && is.null(x)) {
+    return(invisible(x))
+  }
+  assert_scalar(x, name, arg = arg, call = call)
+  assert_integer(x, name, tolerance = tolerance, arg = arg, call = call)
+  assert_nonmissing(x, name, arg = arg, call = call)
+}
+
+
+assert_scalar_logical <- function(x, name = deparse(substitute(x)),
+                                  allow_null = FALSE,
+                                  arg = name, call = parent.frame()) {
+  if (allow_null && is.null(x)) {
+    return(invisible(x))
+  }
+  assert_scalar(x, name, arg = arg, call = call)
+  assert_logical(x, name, arg = arg, call = call)
+  assert_nonmissing(x, name, arg = arg, call = call)
+}
+
+
+assert_scalar_size <- function(x, allow_zero = TRUE, allow_null = FALSE,
+                               name = deparse(substitute(x)),
+                               arg = name, call = parent.frame()) {
+  if (allow_null && is.null(x)) {
+    return(invisible(x))
+  }
+  assert_scalar_integer(x, name = name, arg = arg, call = call)
+  assert_nonmissing(x, name, arg = arg, call = call)
+  min <- if (allow_zero) 0 else 1
+  if (x < min) {
+    cli::cli_abort("'{name}' must be at least {min}", arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_length <- function(x, len, name = deparse(substitute(x)), arg = name,
+                          call = parent.frame()) {
+  if (length(x) != len) {
+    cli::cli_abort(
+      "Expected '{name}' to have length {len}, but was length {length(x)}",
+      arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_is <- function(x, what, name = deparse(substitute(x)), arg = name,
+                      call = parent.frame()) {
+  if (!inherits(x, what)) {
+    cli::cli_abort("Expected '{name}' to be a '{what}' object",
+                   arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_list <- function(x, name = deparse(substitute(x)), arg = name,
+                        call = parent.frame()) {
+  if (!is.list(x)) {
+    cli::cli_abort("Expected '{name}' to be a list",
+                   arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_scalar_positive_numeric <- function(x, allow_zero = TRUE,
+                                           name = deparse(substitute(x)),
+                                           arg = name, call = parent.frame()) {
+  assert_scalar_numeric(x, name = name, call = call)
+  if (allow_zero) {
+    if (x < 0) {
+      cli::cli_abort("'{name}' must be at least 0", arg = arg, call = call)
+    }
+  } else {
+    if (x <= 0) {
+      cli::cli_abort("'{name}' must be greater than 0", arg = arg, call = call)
+    }
+  }
+  invisible(x)
+}
+
+
+assert_scalar_positive_integer <- function(x, allow_zero = TRUE,
+                                           name = deparse(substitute(x)),
+                                           tolerance = NULL, arg = name,
+                                           call = parent.frame()) {
+  assert_scalar_integer(x, name, tolerance = tolerance, arg = arg, call = call)
+  min <- if (allow_zero) 0 else 1
+  if (x < min) {
+    cli::cli_abort("'{name}' must be at least {min}", arg = arg, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_raw <- function(x, len = NULL, name = deparse(substitute(x)),
+                       arg = name, call = parent.frame()) {
+  if (!is.raw(x)) {
+    cli::cli_abort("'{name}' must be a raw vector", arg = arg, call = call)
+  }
+  if (!is.null(len)) {
+    assert_length(x, len, name = name, call = call)
+  }
+  invisible(x)
+}
+
+
+assert_named <- function(x, unique = FALSE, name = deparse(substitute(x)),
+                         arg = name, call = parent.frame()) {
+  nms <- names(x)
+  if (is.null(nms)) {
+    cli::cli_abort("'{name}' must be named", call = call, arg = arg)
+  }
+  if (anyNA(nms) || any(nms == "")) {
+    cli::cli_abort("All elements of '{name}' must be named",
+                   call = call, arg = arg)
+  }
+  if (unique && anyDuplicated(names(x))) {
+    dups <- sprintf("'%s'", unique(names(x)[duplicated(names(x))]))
+    cli::cli_abort(
+      c("'{name}' must have unique names",
+        i = "Found {length(dups)} duplicate{?s}: {dups}"),
+      call = call, arg = arg)
+  }
+  invisible(x)
+}
+
+
+match_value <- function(x, choices, name = deparse(substitute(x)), arg = name,
+                        call = parent.frame()) {
+  assert_scalar_character(x, call = call, name = name, arg = arg)
+  if (!(x %in% choices)) {
+    choices_str <- paste(sprintf("'%s'", choices), collapse = ", ")
+    cli::cli_abort(c("'{name}' must be one of {choices_str}",
+                     i = "Instead we were given '{x}'"), call = call,
+                   arg = arg)
+  }
+  x
+}
diff --git a/R/plotting.R b/R/plotting.R
new file mode 100644
index 0000000..80c9b43
--- /dev/null
+++ b/R/plotting.R
@@ -0,0 +1,315 @@
+#' Plotting theme for vimcheck
+#'
+#' @description
+#' A simple plotting theme building on [ggplot2::theme_bw()].
+#'
+#'
+#' @name plotting_theme
+#' @rdname plotting_theme
+#'
+#' @param x_text_angle
+#'
+#' @param y_text_angle
+#'
+#' @param ... <[`dynamic-dots`][rlang::dyn-dots]> Other arguments passed to
+#' [ggplot2::theme()].
+#'
+#' @return A `ggplot2` theme that can be added to `ggplot2` plots or objects.
+#'
+#' @export
+theme_vimc <- function(x_text_angle = 45, y_text_angle = 0, ...) {
+  ggplot2::theme_bw() +
+    ggplot2::theme(
+      axis.text.x = ggplot2::element_text(
+        size = 10,
+        angle = x_text_angle
+      ),
+      strip.text.y = ggplot2::element_text(
+        angle = y_text_angle
+      ),
+      plot.margin = ggplot2::margin(1, 0, 1, 0, "cm"),
+      ...
+    )
+}
+
+#' Plot burden and impact diagostics
+#'
+#' @name plotting
+#' @rdname plotting
+#'
+#' @importFrom ggplot2 ggplot
+#'
+#' @description
+#' Plotting functions for burden and impact diagnostics. This documentation
+#' holds all plotting functions for now.
+#'
+#' @param d
+#'
+#' @param fig_number
+#'
+#' @return A `<ggplot>` object that can be printed to screen in the plot frame
+#' or saved to an output device (i.e., saved as an image file).
+#'
+#' @examples
+#'
+#' @export
+plot_compare_demography <- function(d, fig_number) {
+  num_countries <- length(unique(d$country))
+  names_melting_data <- c(
+    "scenario",
+    "age",
+    "year",
+    "expected",
+    "provided",
+    "difference"
+  )
+  names_melting_by <- c("scenario", "age", "year")
+
+  # TODO: use tidyr; BIG PICTURE: NO DATA PREP IN PLOTTING FUNCTIONS!
+  tot <- reshape2::melt(d[, names_melting_data], id.vars = names_melting_by)
+  dat <- tot %>%
+    dplyr::group_by(variable, scenario, year, age) %>%
+    dplyr::summarise(value = sum(value)) %>%
+    dplyr::mutate(millions = value / 1e6) %>%
+    dplyr::arrange(age)
+
+  # TODO: use .data and .vars, import or namespace functions
+  g <- ggplot(data = dat, aes(x = year, y = millions, fill = age)) +
+    geom_bar(stat = "identity") +
+    facet_wrap(~ scenario + variable, ncol = 3) +
+    scale_fill_distiller(palette = "PuOr") +
+    geom_hline(yintercept = 0, color = 'red') +
+    labs(
+      x = "calendar year",
+      y = glue::glue("people (in millions"),
+      title = glue::glue(
+        "Fig. {fig_number}. Comparison between interpolated population and \\
+        cohort size ({num_countries} countries)."
+      )
+    ) +
+    theme_vimc()
+
+  g
+}
+
+#' @name plotting
+#'
+#' @param burden
+#'
+#' @export
+plot_age_patterns <- function(burden, fig_number) {
+  # TODO: REMOVE DATA PREP FROM PLOTTING FNS
+  d <- burden %>%
+    group_by(scenario, burden_outcome, age) %>%
+    summarise(millions = sum(value) / 1e6)
+
+  g <- ggplot(d, aes(x = age, y = millions)) +
+    geom_bar(stat = "identity") +
+    facet_grid(
+      burden_outcome ~ scenario,
+      scales = "free_y",
+      labeller = labeller(scenario = label_wrap_gen(10))
+    ) +
+    coord_cartesian(xlim = c(0, max(d$age) + 1)) +
+    labs(
+      y = "people (in millions)",
+      title = glue::glue(
+        "Fig. {fig_number}. Burden age patterns across all countries and years"
+      )
+    ) +
+    theme_vimc()
+
+  g
+}
+
+#' @name plotting
+#'
+#' @param year_max
+#'
+#' @export
+plot_global_burden_decades <- function(burden, year_max, fig_number) {
+  # TODO: prefer moving these conditional checks elsewhere
+  # TODO: prefer moving data prep outside plotting fn
+  stopifnot(year_max %% 10 == 0)
+  d <- burden %>%
+    filter(year <= year_max) %>%
+    mutate(year2 = ifelse(year == year_max, year_max - 1, year)) %>%
+    mutate(decade = floor(year2 / 10) * 10) %>%
+    mutate(
+      decade_label = ifelse(
+        decade == year_max - 10,
+        paste0(decade, "-", decade + 10),
+        paste0(decade, "-", decade + 9)
+      )
+    ) %>%
+    group_by(scenario, burden_outcome, decade_label) %>%
+    summarise(millions = sum(value) / 1e6)
+
+  g <- ggplot(d, aes(x = scenario, y = millions, fill = scenario)) +
+    geom_bar(stat = "identity") +
+    facet_grid(burden_outcome ~ decade_label, scales = "free_y") +
+    labs(
+      y = "people (in millions)",
+      title = glue::glue(
+        "Fig. {fig_number}. Global disease burden trends"
+      )
+    ) +
+
+    # TODO: reconcile with theme_vimc() or make new theme
+    theme_bw() %+replace%
+      theme(
+        axis.title.x = element_blank(),
+        axis.text.x = element_blank(),
+        axis.ticks.x = element_blank()
+      )
+
+  g
+}
+
+#' @name plotting
+#'
+#' @param d
+#'
+#' @param outcome
+#'
+#' @export
+plot_global_burden <- function(d, outcome, fig_number) {
+  data_ <- dplyr::filter(
+    d,
+    .data$burden_outcome == outcome
+  )
+
+  g <- ggplot(
+    data,
+    aes(x = year, y = millions, fill = age)
+  ) +
+    geom_bar(stat = "identity", aes(fill = age)) +
+    facet_grid(
+      ~scenario,
+      scales = "free_y",
+      labeller = labeller(scenario = label_wrap_gen(10)) # TODO: avoid magic numbers
+    ) +
+    scale_fill_distiller(palette = "Spectral") +
+    labs(
+      x = "calendar year",
+      y = paste(outcomes_list[i], "(in millions)"), # TODO: where is outcomes_list!?
+      title = glue::glue(
+        "Fig. {fig_number}: Global trends of disease burden ({outcome})."
+      )
+    ) +
+    theme_vimc(x_text_angle = 90)
+
+  g
+}
+
+#' @name plotting
+#'
+#' @param cov
+#'
+#' @export
+plot_coverage_set <- function(cov, figure_number) {
+  # TODO: remove data prep
+  no_vacc <- expand_grid(
+    year = unique(cov$year),
+    country = unique(cov$country)
+  ) %>%
+    mutate(
+      coverage = 0,
+      delivery = "none",
+      scenario_description = "No vaccination"
+    )
+
+  cov1 <- cov %>%
+    mutate(delivery = paste(vaccine, activity_type, sep = "-")) %>%
+    select(scenario_description, delivery, country, year, coverage) %>%
+    bind_rows(no_vacc)
+
+  g <- ggplot(cov1, aes(x = year, y = coverage, fill = delivery)) +
+    geom_bar(
+      stat = "identity",
+      position = position_dodge(width = 0.9),
+      alpha = 0.7
+    ) +
+    facet_grid(
+      "country ~ scenario_description",
+      scales = "free_y",
+      labeller = labeller(scenario_description = label_wrap_gen(10))
+    ) +
+    scale_x_continuous(breaks = pretty(unique(cov1$year))) +
+    labs(
+      x = "calendar year",
+      y = "Proportion of target population",
+      title = glue::glue(
+        "Fig. {figure_number}: Coverage sets for {cov$disease[1]}"
+      )
+    ) +
+    theme_vimc(90)
+
+  g
+}
+
+#' @name plotting
+#'
+#' @param fvp
+#'
+#' @param year_min
+#'
+#' @param year_max
+#'
+#' @export
+plot_fvp <- function(fvp, year_min, year_max, figure_number) {
+  # TODO: PREFER TO REMOVE DATA PREP CODE
+  no_vacc <- expand_grid(
+    year = unique(fvp$year),
+    country = unique(fvp$country)
+  ) %>%
+    mutate(fvps_adjusted = 0, scenario_description = "No vaccination")
+
+  fvp_final <- bind_rows(fvp, no_vacc) %>%
+    filter(year >= year_min & year <= year_max) %>%
+    mutate(scenario = as.factor(scenario_description))
+
+  fvp_final$scenario <- relevel(fvp_final$scenario, "No vaccination")
+  fvp_final$scenario <- gsub(tolower(fvp$disease[1L]), "", fvp_final$scenario)
+  fvp_final$scenario <- gsub("-", " ", fvp_final$scenario)
+
+  scenario_order <- c(names(sort(tapply(
+    fvp_final$fvps_adjusted,
+    fvp_final$scenario,
+    sum,
+    na.rm = TRUE
+  ))))
+
+  fvp_final$scenario <- forcats::fct_relevel(fvp_final$scenario, scenario_order)
+
+  fvp_agg <-
+    fvp_final %>%
+    dplyr::group_by(year, scenario, disease) %>%
+    dplyr::summarise(fvp = sum(fvps_adjusted, na.rm = TRUE))
+
+  # TODO: prefer to use a scale transform rather than touching data
+  g <- ggplot(fvp_agg, aes(x = year, y = fvp / 1e6, fill = scenario)) +
+    geom_bar(
+      stat = "identity",
+      colour = "midnightblue",
+      fill = "midnightblue"
+    ) +
+    facet_grid(
+      ~scenario,
+      scales = "free_y",
+      labeller = labeller(scenario = label_wrap_gen(10))
+    ) +
+    scale_x_continuous(breaks = pretty(unique(fvp_agg$year))) +
+    ylab(paste("FVP (in millions)")) +
+    labs(
+      x = "calendar year",
+      y = "FVP (in millions)",
+      title = glue::glue(
+        "Fig. {figure_number}: Fully Vaccinated Persons at global level by \\
+        scenario for {fvp$disease[1L]}"
+      )
+    ) +
+    theme_vimc(90, legend.position = "none")
+
+  g
+}
diff --git a/R/vimcheck.R b/R/vimcheck.R
index a65cf64..9428bd0 100644
--- a/R/vimcheck.R
+++ b/R/vimcheck.R
@@ -1,6 +1,8 @@
-#' @keywords internal
+#' @keywords package_doc
 "_PACKAGE"
 
 ## usethis namespace: start
 ## usethis namespace: end
 NULL
+
+#' @import rlang
diff --git a/_pkgdown.yml b/_pkgdown.yml
index ca4c87b..79b8dfd 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -3,3 +3,25 @@
 url: ~
 template:
   bootstrap: 5
+
+reference:
+  - title: Package-level documentation
+    contents:
+    - has_keyword("package_doc")
+  - title: Diagnostic functions
+    desc: Package diagnostic functions.
+    contents:
+    - has_keyword("diagnostics")
+  - title: Plotting functions
+    desc: Package plotting functions.
+    contents:
+    - plotting
+    - plotting_theme
+  - title: Internal functions
+    desc: Internal helper functions.
+    contents:
+    - has_keyword("internal")
+  - title: Constants
+    desc: Package constants.
+    contents:
+    - has_keyword("constants")
diff --git a/man/basic_burden_sanity.Rd b/man/basic_burden_sanity.Rd
new file mode 100644
index 0000000..1abd7fe
--- /dev/null
+++ b/man/basic_burden_sanity.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/burden_diagnositics.R
+\name{basic_burden_sanity}
+\alias{basic_burden_sanity}
+\title{Sanity checks on burden estimates}
+\usage{
+basic_burden_sanity(burden)
+}
+\arguments{
+\item{burden}{A \verb{<data.frame>} of disease burden estimates. Must have
+at least a single column named \code{"value"} of numeric burden estimates.}
+}
+\value{
+A character vector of messages generated by checks on burden
+estimates, with the length of the vector depending on how many checks fail.
+}
+\description{
+Helper function for sanity checks on burden estimate values.
+Checks whether any burden estimates are non-numeric, missing, or negative.
+}
+\keyword{diagnostics}
diff --git a/man/check_demography_alignment.Rd b/man/check_demography_alignment.Rd
new file mode 100644
index 0000000..31e7338
--- /dev/null
+++ b/man/check_demography_alignment.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/burden_diagnositics.R
+\name{check_demography_alignment}
+\alias{check_demography_alignment}
+\title{Check incoming burden cohort size against interpolated population}
+\usage{
+check_demography_alignment(burden_set, wpp, gender = "both")
+}
+\arguments{
+\item{burden_set}{}
+
+\item{wpp}{}
+
+\item{gender}{}
+}
+\description{
+Check incoming burden cohort size against interpolated population
+}
+\keyword{diagnostics}
diff --git a/man/check_template_alignment.Rd b/man/check_template_alignment.Rd
new file mode 100644
index 0000000..b22480e
--- /dev/null
+++ b/man/check_template_alignment.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/burden_diagnositics.R
+\name{check_template_alignment}
+\alias{check_template_alignment}
+\title{Check incoming burden set against template}
+\usage{
+check_template_alignment(burden_set, template)
+}
+\arguments{
+\item{burden_set}{}
+
+\item{template}{}
+}
+\description{
+Check incoming burden set against template
+}
+\keyword{diagnostics}
diff --git a/man/constants.Rd b/man/constants.Rd
new file mode 100644
index 0000000..e883e95
--- /dev/null
+++ b/man/constants.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/constants.R
+\docType{data}
+\name{constants}
+\alias{constants}
+\alias{const_data_colnames}
+\title{Package constants}
+\format{
+An object of class \code{character} of length 4.
+}
+\usage{
+const_data_colnames
+}
+\description{
+Package constants
+}
+\keyword{constants}
diff --git a/man/helpers.Rd b/man/helpers.Rd
new file mode 100644
index 0000000..fb9c4df
--- /dev/null
+++ b/man/helpers.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{helpers}
+\alias{helpers}
+\alias{make_novax_scenario}
+\title{Make data for a no-vaccination scenario}
+\usage{
+make_novax_scenario(disease)
+}
+\arguments{
+\item{disease}{A disease identifier.}
+}
+\value{
+\itemize{
+\item \code{make_novax_scenario()} returns a tibble with the minimum required column
+names, and entries corresponding to a 'no-vaccination' scenario for
+\code{disease}.
+}
+}
+\description{
+Helper functions for burden diagnostics.
+}
+\keyword{internal}
diff --git a/man/plotting.Rd b/man/plotting.Rd
new file mode 100644
index 0000000..213634f
--- /dev/null
+++ b/man/plotting.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting.R
+\name{plotting}
+\alias{plotting}
+\alias{plot_compare_demography}
+\alias{plot_age_patterns}
+\alias{plot_global_burden_decades}
+\alias{plot_global_burden}
+\alias{plot_coverage_set}
+\alias{plot_fvp}
+\title{Plot burden and impact diagostics}
+\usage{
+plot_compare_demography(d, fig_number)
+
+plot_age_patterns(burden, fig_number)
+
+plot_global_burden_decades(burden, year_max, fig_number)
+
+plot_global_burden(d, outcome, fig_number)
+
+plot_coverage_set(cov, figure_number)
+
+plot_fvp(fvp, year_min, year_max, figure_number)
+}
+\arguments{
+\item{d}{}
+
+\item{fig_number}{}
+
+\item{burden}{}
+
+\item{year_max}{}
+
+\item{outcome}{}
+
+\item{cov}{}
+
+\item{fvp}{}
+
+\item{year_min}{}
+}
+\value{
+A \verb{<ggplot>} object that can be printed to screen in the plot frame
+or saved to an output device (i.e., saved as an image file).
+}
+\description{
+Plotting functions for burden and impact diagnostics. This documentation
+holds all plotting functions for now.
+}
diff --git a/man/plotting_theme.Rd b/man/plotting_theme.Rd
new file mode 100644
index 0000000..80fcf2e
--- /dev/null
+++ b/man/plotting_theme.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting.R
+\name{plotting_theme}
+\alias{plotting_theme}
+\alias{theme_vimc}
+\title{Plotting theme for vimcheck}
+\usage{
+theme_vimc(x_text_angle = 45, y_text_angle = 0, ...)
+}
+\arguments{
+\item{x_text_angle}{}
+
+\item{y_text_angle}{}
+
+\item{...}{<\code{\link[rlang:dyn-dots]{dynamic-dots}}> Other arguments passed to
+\code{\link[ggplot2:theme]{ggplot2::theme()}}.}
+}
+\value{
+A \code{ggplot2} theme that can be added to \code{ggplot2} plots or objects.
+}
+\description{
+A simple plotting theme building on \code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}.
+}
diff --git a/man/validate_complete_incoming_files.Rd b/man/validate_complete_incoming_files.Rd
new file mode 100644
index 0000000..9a1ecd8
--- /dev/null
+++ b/man/validate_complete_incoming_files.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/burden_diagnositics.R
+\name{validate_complete_incoming_files}
+\alias{validate_complete_incoming_files}
+\title{Validate files in a burden estimate}
+\usage{
+validate_complete_incoming_files(path_burden = "incoming_burden_estimates")
+}
+\arguments{
+\item{path_burden}{A directory with burden estimate data.}
+}
+\value{
+A \verb{<tibble>} of the scenario file dictionary in \code{path_burden} if all
+checks pass. Otherwise, exits with informative errors on failed checks.
+}
+\description{
+Check that incoming data files in a burden estimate are complete, and that
+no extra files have been included.
+This function expects that incoming burden files are in the
+directory given by \code{path_burden}, which holds a file dictionary which maps
+each data file to a specific scenario.
+}
+\keyword{diagnostics}
diff --git a/man/validate_file_dict_template.Rd b/man/validate_file_dict_template.Rd
new file mode 100644
index 0000000..525b4a5
--- /dev/null
+++ b/man/validate_file_dict_template.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/burden_diagnositics.R
+\name{validate_file_dict_template}
+\alias{validate_file_dict_template}
+\title{Validate file dictionary template}
+\usage{
+validate_file_dict_template(disease, path_burden = "incoming_burden_estimates")
+}
+\arguments{
+\item{disease}{A disease identifier.}
+
+\item{path_burden}{A directory with burden estimate data.}
+}
+\value{
+Nothing; called primarily for its side-effets.
+If the file \code{path_burden/file_dictionary.csv} does not exist, a file
+dictionary CSV file is written to the same location.
+Prints a message to screen informing the user whether any action has been
+taken.
+}
+\description{
+Function to create a \code{file_dictionary} template.
+It maps to touchstone disease scenarios and you will see expected number of
+scenarios i.e. the number of files that we expect from a model.
+Users should populate the file column to match the scenario-file.
+This function will run if a \code{file_dictionary.csv} file does not exist
+}
+\keyword{diagnostics}
diff --git a/man/vimcheck-package.Rd b/man/vimcheck-package.Rd
index c26fbd9..c8369de 100644
--- a/man/vimcheck-package.Rd
+++ b/man/vimcheck-package.Rd
@@ -33,4 +33,4 @@ Other contributors:
 }
 
 }
-\keyword{internal}
+\keyword{package_doc}