Minor fixes

Author: pratikunterwegs

NAMESPACE

@@ -34,3 +34,4 @@ importFrom(ggplot2,scale_fill_distiller)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,vars)
+importFrom(rlang,.data)

NEWS.md

@@ -4,6 +4,10 @@
 
 - Added tests for plotting preparation and plotting functions.
 
+- Removed impact and FVPs checker functions.
+
+- Importing `rlang::.data` data pronoun in plotting function; works overall.
+
 # vimcheck 0.0.2
 
 - Added initial data validation functions and some tests.

R/burden_diagnositics.R

@@ -31,7 +31,6 @@ validate_file_dict_template <- function(
   template <- file.path(path_burden, "file_dictionary.csv")
 
   if (file.exists(template)) {
-    # TODO: check that file_dictionary entries are acceptable?
     data_dict <- readr::read_csv(
       template,
       show_col_types = FALSE
@@ -349,7 +348,6 @@ check_demography_alignment <- function(
 #'
 #' @export
 basic_burden_sanity <- function(burden) {
-  # TODO: expectations on burden
   mes_start <- "Basic sanity check for burden estimates:"
   mes <- mes_start
 

R/plotting.R

@@ -72,6 +72,8 @@ theme_vimc_noxaxis <- function() {
 #' scale_fill_distiller scale_x_continuous scale_y_continuous labs vars
 #' labeller label_wrap_gen
 #'
+#' @importFrom rlang .data
+#'
 #' @description
 #' Plotting functions for burden and impact diagnostics. All functions operate
 #' on data prepared for plotting by a corresponding
@@ -98,7 +100,6 @@ plot_compare_demography <- function(data, fig_number) {
   n_cols_allowed <- 3
   num_countries <- length(unique(data$country))
 
-  # TODO: use .data and .vars, import or namespace functions
   g <- ggplot(
     data,
     aes(.data$year, .data$value_millions, fill = .data$age)
@@ -246,7 +247,6 @@ plot_coverage_set <- function(coverage_set, fig_number) {
     aes(.data$year, .data$coverage, fill = .data$delivery)
   ) +
     geom_col(
-      # TODO: check if dodging is really needed
       position = ggplot2::position_dodge(dodge_width),
       alpha = col_opacity
     ) +

R/plotting_prep.R

@@ -162,7 +162,6 @@ prep_plot_burden_decades <- function(burden, year_max) {
 #'
 #' @export
 prep_plot_global_burden <- function(burden) {
-  # TODO: add colnames check
   checkmate::assert_tibble(burden)
 
   nesting_cols <- "burden_outcome"
@@ -267,7 +266,6 @@ prep_plot_fvp <- function(fvp, year_min, year_max) {
     ) # convert characters to factors and set first level
   )
 
-  # TODO: need to see an example to figure this out
   fvp_final$scenario <- gsub(tolower(fvp$disease[1L]), "", fvp_final$scenario)
   fvp_final$scenario <- gsub("-", " ", fvp_final$scenario, fixed = TRUE)
 

vignettes/vimcheck.Rmd

@@ -18,15 +18,6 @@ knitr::opts_chunk$set(
 library(vimcheck)
 ```
 
-This is a special vignette, which shares the same name as the package.
-It will render as the "Get started" page in the navigation bar of _pkgdown_ websites.
-
-To develop it further:
-
-1. Rename the file to your package name;
-
-2. Add code and explainers to help users get started with using your package in this vignette;
-
-3. Remember to add and link references if needed.
+This vignette is a work in progress, please see the [vignette on plotting and preparing data for plotting](plotting_and_plotting_prep.html) instead.
 
 ## References