Various additions per recommendations

Author: gjanee

.gitignore

@@ -3,5 +3,8 @@
 .RData
 .Ruserdata
 
+# Ignore cache file
+data/cache.Rdata
+
 # Mac OS
 **.DS_Store

README.md

@@ -1,13 +1,32 @@
 ## Developing a reproducible Shiny app
 
-Shiny application example adopting the recommendations of the "10 Quick Tips for Developing a Reproducible Shiny Application", Brun et al., 2025, PLOS Computational Biology
+Example Shiny application adopting the recommendations of "10 Quick Tips for Developing a Reproducible Shiny Application", Brun et al, 2025, PLOS Computational Biology.
 
-In this example, we are reusing the Faithful Shiny app example (https://shiny.posit.co/r/gallery/start-simple/faithful/) provided as part of the R ***shiny*** package.
-This Shiny application displays eruption data for the Old Faithful geyser.
+In this example, we are reusing the Faithful Shiny app example (<https://shiny.posit.co/r/gallery/start-simple/faithful/>) provided as part of the R `shiny` package. This Shiny application displays eruption data for the Old Faithful geyser.
 
-## Contributors
+Tips demonstrated:
 
-## Where to start
+-   Set up your computing environment
+    -   Use git and GitHub
+    -   Use `renv` to record package versions
+    -   Record the output of `sessionInfo()`
+-   Document and develop incrementally
+    -   Comment UI elements
+-   Make your Shiny application portable and easy to maintain
+    -   Organize code and data
+    -   Use relative paths and `file.path`
+-   Preprocess and cache data for performance
+    -   Cache processed data in a local file
+-   Make underlying data accessible
+    -   Cite the original data
+-   License code and data appropriately
+    -   Add a LICENSE file
+    -   Respect the license of the original data
+-   Make you data and source code citable
+    -   Add README and CITATION.cff files
+-   Publish your app
+    -   Publish on shinyapps.io and archive in Zenodo
 
-## Acknowledgements
+The underlying data is available as part of R package X. The original source is...
 
+Cite this work as: Brun, J., Janée, G., & Curty, R. G. (2025). Example Shiny application adopting the recommendations from "10 Quick Tips for Developing a Reproducible Shiny Application" [Computer software]. <https://github.com/UCSB-Library-Research-Data-Services/shiny-qt-examples>

global.R

@@ -2,6 +2,16 @@ library(shiny)
 library(readr)
 
 data_path <- "data"
-csv_old_faithful <- "faithful_data.csv"
+csv_file <- file.path(data_path, "faithful_data.csv")
 
-old_faithful <- read_csv(file.path(data_path, csv_old_faithful))
+# Below is an example of employing a local cache... not necessary in this case,
+# but useful if more processing is involved in preparing the data.
+
+cache_file <- file.path(data_path, "cache.Rdata")
+
+if (file.exists(cache_file) && file.info(cache_file)$mtime > file.info(csv_file)$mtime) {
+  load(cache_file)
+} else {
+  old_faithful <- read_csv(csv_file)
+  save(old_faithful, file=cache_file)
+}

server.R

@@ -1,4 +1,3 @@
-
 function(input, output) {
 
   output$main_plot <- renderPlot({
@@ -20,4 +19,4 @@ function(input, output) {
     }
 
   })
-}
+}

sessionInfo.txt

@@ -0,0 +1,31 @@
+R version 4.4.1 (2024-06-14)
+Platform: aarch64-apple-darwin20
+Running under: macOS Monterey 12.7.6
+
+Matrix products: default
+BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
+LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
+
+locale:
+[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
+
+time zone: America/Los_Angeles
+tzcode source: internal
+
+attached base packages:
+[1] stats     graphics  grDevices datasets  utils     methods   base     
+
+other attached packages:
+[1] readr_2.1.5  shiny_1.10.0
+
+loaded via a namespace (and not attached):
+ [1] crayon_1.5.3        vctrs_0.6.5         cli_3.6.5           rlang_1.1.6        
+ [5] renv_1.1.4          promises_1.3.3      jsonlite_2.0.0      xtable_1.8-4       
+ [9] glue_1.8.0          bit_4.6.0           htmltools_0.5.8.1   httpuv_1.6.16      
+[13] sass_0.4.10         hms_1.1.3           jquerylib_0.1.4     tibble_3.3.0       
+[17] tzdb_0.5.0          fastmap_1.2.0       sourcetools_0.1.7-1 lifecycle_1.0.4    
+[21] memoise_2.0.1       compiler_4.4.1      Rcpp_1.0.14         pkgconfig_2.0.3    
+[25] later_1.4.2         digest_0.6.37       R6_2.6.1            tidyselect_1.2.1   
+[29] parallel_4.4.1      vroom_1.6.5         pillar_1.10.2       magrittr_2.0.3     
+[33] bslib_0.9.0         tools_4.4.1         withr_3.0.2         bit64_4.6.0-1      
+[37] mime_0.13           cachem_1.1.0

ui.R

@@ -1,25 +1,34 @@
 bootstrapPage(
 
-  selectInput(inputId = "n_breaks",
+  selectInput( # bins selector
+      inputId = "n_breaks",
       label = "Number of bins in histogram (approximate):",
       choices = c(10, 20, 35, 50),
-      selected = 20),
+      selected = 20
+  ), # end of bins selector
 
-  checkboxInput(inputId = "individual_obs",
+  checkboxInput( # individual checkbox
+      inputId = "individual_obs",
       label = strong("Show individual observations"),
-      value = FALSE),
+      value = FALSE
+  ), # end of individual checkbox
 
-  checkboxInput(inputId = "density",
+  checkboxInput( # density checkbox
+      inputId = "density",
       label = strong("Show density estimate"),
-      value = FALSE),
+      value = FALSE
+  ), # end of density checkbox
 
+  # main plot area
   plotOutput(outputId = "main_plot", height = "300px"),
 
   # Display this only if the density is shown
   conditionalPanel(condition = "input.density == true",
-    sliderInput(inputId = "bw_adjust",
+    sliderInput( # bandwidth slider
+        inputId = "bw_adjust",
         label = "Bandwidth adjustment:",
-        min = 0.2, max = 2, value = 1, step = 0.2)
+        min = 0.2, max = 2, value = 1, step = 0.2
+    ) # end of bandwidth slider
   )
 
 )