Merge pull request #8 from ukhsa-collaboration/crancomments-feb

Cran comments addressed

Author: harshana-ukhsa

.Rbuildignore

@@ -4,6 +4,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README\.Rmd$
+^README\.html$
 ^cran-comments\.md$
 ^pkgdown$
 ^_pkgdown\.yml$

DESCRIPTION

@@ -17,7 +17,11 @@ Authors@R:
     person(given="Frederick", family="Sloots", email="Frederick.Sloots@ukhsa.gov.uk", role = c("ctb")),
     person(given="Charlie", family="Turner", email="Charlie.Turner@ukhsa.gov.uk", role = c("ctb"))
     )
-Description: Tools for making epidemiological reporting easier with consistent static and dynamic charts and maps.
+Description: Tools for making epidemiological reporting easier with consistent 
+    static and dynamic charts and maps. Builds on 'ggplot2' for static 
+    visualizations as described in Wickham (2016) <doi:10.1007/978-3-319-24277-4> 
+    and 'plotly' for interactive visualizations as described in 
+    Sievert (2020) <doi:10.1201/9780429447273>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -30,7 +34,8 @@ Suggests:
     withr,
     yarrr,
     knitr,
-    rmarkdown
+    rmarkdown,
+    shiny
 Config/testthat/edition: 3
 Imports: 
     grDevices,

NEWS.md

@@ -3,9 +3,11 @@
 
 ## CRAN submission fixes
 
-* Added `on.exit()` calls to properly restore user options in `.onLoad()`
-* Replaced `\dontrun{}` with `\donttest{}` or unwrapped examples where appropriate
-* Resubmission addressing CRAN reviewer feedback
+* Added references to DESCRIPTION field (ggplot2 and plotly DOIs)
+* Replaced all `\dontrun{}` with `\donttest{}` in examples
+* Simplified examples to execute in < 5 seconds
+* Added `@seealso` references to vignettes for additional examples
+* Verified `on.exit()` is correctly used in `.onLoad()` for option changes
 
 # epiviz 0.1.1
 

R/age_sex_pyramid.R

@@ -52,31 +52,14 @@
 #' \donttest{
 #' # Example using a line list
 #' df <- epiviz::lab_data
-#' age_sex_pyramid(
+#' result <- age_sex_pyramid(
 #'   dynamic = FALSE,
 #'   params = list(
 #'     df = df,
-#'     var_map = list(age_var = 'age', dob_var = 'date_of_birth', sex_var = 'sex'),
+#'     var_map = list(dob_var = 'date_of_birth', sex_var = 'sex'),
 #'     grouped = FALSE
 #'   )
 #' )
-#'
-#' # Example using pre-grouped data
-#' grouped_df <- data.frame(
-#'   age_group = c("0-4", "5-18", "19-64", "65+"),
-#'   sex = c("Male", "Female"),
-#'   value = c(100, 120, 150, 80),
-#'   ci_lower = c(90, 110, 140, 70),
-#'   ci_upper = c(110, 130, 160, 90)
-#' )
-#' age_sex_pyramid(
-#'   dynamic = FALSE,
-#'   params = list(
-#'     df = grouped_df,
-#'     var_map = list(age_group_var = 'age_group', sex_var = 'sex', value = 'value'),
-#'     grouped = TRUE
-#'   )
-#' )
 #' }
 #'
 #' @import ggplot2
@@ -112,9 +95,6 @@ age_sex_pyramid <- function(
     )
 ) {
 
-  # Solve warnings regarding font family not found using utils/set_Arial() function
-  set_Arial()
-
   # Where relevant, assign defaults to any parameters not specified by the user
   if(!exists('mf_colours',where=params)) params$mf_colours <- c("#440154", "#2196F3")
   if(!exists('x_breaks',where=params)) params$x_breaks <- 10
@@ -251,6 +231,9 @@ age_sex_pyramid <- function(
   }else{
     # plotly implementation of dynamic age-sex-pyramid
 
+    # Solve warnings regarding font family not found using utils/set_Arial() function
+    set_Arial()
+
     # Process data similarly to static version
 # plotly implementation of dynamic age-sex-pyramid
   var_map <- params$var_map
@@ -422,7 +405,7 @@ age_sex_pyramid <- function(
                 linecolor = "black"
               ),
               barmode = 'overlay',
-              font = list(family = "Arial"),
+              font = list(family = "sans"),
               hoverlabel = list(bgcolor = "white", font = list(size = 12)),
               showlegend = TRUE,
               legend = list(orientation = "h",

R/agesex_pyramid_grouped.R

@@ -118,12 +118,12 @@ agesex_pyramid_grouped <- function(df,
     # customisations to minimal theme
     theme(
       panel.grid = element_blank(),
-      axis.title.y = element_text(family="Arial", margin = margin(0, 20, 0, 0, "mm"), face="bold"),
+      axis.title.y = element_text(family="sans", margin = margin(0, 20, 0, 0, "mm"), face="bold"),
       axis.title.x = element_text(face="bold"),
       legend.position = "bottom",
       legend.title = element_blank(),
-      text = element_text(size = text_size, family="Arial"),
-      plot.title = element_text(hjust = 0.5, family="Arial"),
+      text = element_text(size = text_size, family="sans"),
+      plot.title = element_text(hjust = 0.5, family="sans"),
       plot.margin = margin(1, 1.2, 1, 1.2, "cm"),
       axis.line.x = element_line(color = "black"),
       axis.ticks.x = element_line(color = "black")

R/base_gg.R

@@ -15,6 +15,7 @@ base_gg <- function() {
 
 
   # Ensure that unused variables exist
+  if(!exists("chart_font")) {chart_font <- "sans"}
   if(!exists("x_time_series")) {x_time_series <- FALSE}
   if(!exists("axis_flip")) {axis_flip <- FALSE}
 

R/base_plotly.R

@@ -14,6 +14,7 @@ base_plotly <- function() {
 
 
     # Ensure that unused variables exist
+  if(!exists("chart_font")) {chart_font <- "sans"}
     if(!exists("x_time_series")) {x_time_series <- FALSE}
     if(!exists("axis_flip")) {axis_flip <- FALSE}