Load custom models (#20)

* Create .devcontainer and update Dockerfile

* Update gitignore and Makefile with dev command

* Enable passing filepath to custom models

* Prepend (custom) label to custom models

* Add reading model description .md file to app.R

* Delete .DS_Store

* Update actions/upload-artifact version to v3

* Update getting_started vignette to include newest changes

* Update actions/upload-artifact version to v4

* Update docs

* Add devcontainer to Rbuildignore

* Add default value to models_setup input

* Update DESCRIPTION version num and date, add Andrew as author

* Add details on custom_models_path to both app.R and functions-ui.R

* Update failed examples

* Remove failing examples

.Rbuildignore

@@ -11,6 +11,7 @@ README.html
 Dockerimage
 epishiny
 Dockerfile
+.devcontainer
 
 # Adding the vignettes as these are heavy
 vignettes/

Dockerfile → .devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.3.3
+FROM rocker/tidyverse:4.4.1
 
 # Installing only packages that are not already installed in the base image
 RUN install2.r -s \

.devcontainer/devcontainer.json

@@ -0,0 +1,24 @@
+{
+	// Dev container name
+	"name": "epiworldRShiny",
+	// Build image from Dockerfile
+	"build": {
+			// Path is relative to the devcontainer.json file.
+			"dockerfile": "Dockerfile"
+	}
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "uname -a",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.gitignore

@@ -1,3 +1,5 @@
 .Rproj.user
 .Rhistory
-.secrets.R
+.secrets.R
+
+*.DS_Store

DESCRIPTION

@@ -1,13 +1,15 @@
 Package: epiworldRShiny
 Type: Package
 Title: A 'shiny' Wrapper of the R Package 'epiworldR'
-Version: 0.1-1
-Date: 2025-01-30
+Version: 0.1-2
+Date: 2025-02-18
 Authors@R: c(
   person("George", "Vega Yon", role=c("aut"),
   email="[email protected]", comment = c(ORCID = "0000-0002-3171-0844")),
   person("Derek", "Meyer", role=c("aut","cre"), 
   email="[email protected]", comment = c(ORCID = "0009-0005-1350-6988")),
+  person("Andrew", "Pulsipher", role=c("aut"),
+  email="[email protected]", comment = c(ORCID = "0000-0002-0773-3210")),
   person("Centers for Disease Control and Prevention", role="fnd", comment = "Award number 1U01CK000585; 75D30121F00003"
   ),
   person("Lindsay", "Keegan", role=c("ctb"), email="[email protected]", comment = c(ORCID = "0000-0002-8526-3007")),
@@ -22,7 +24,7 @@ URL: https://github.com/UofUEpiBio/epiworldRShiny/,
     https://uofuepibio.github.io/epiworldRShiny/,
 BugReports: https://github.com/UofUEpiBio/epiworldRShiny/issues/
 License: MIT + file LICENSE
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Suggests:

Makefile

@@ -21,6 +21,8 @@ install:
 run:
 	Rscript --vanilla -e 'epiworldRShiny::epiworldRShiny()'
 
+dev: build install run
+
 check:
 	cd .. && R CMD check $(PKG_NAME)_$(PKG_VERSION).tar.gz
 

R/app.R

@@ -33,22 +33,30 @@ epiworldRenv <- function() {
 }
 
 #' @export
+#' @param custom_models_path Optional path to custom model files (see details).
+#' @details
+#' When `custom_models_path` is specified, the function will look for valid model files
+#' at the specified path. These will be added to the list of available models.
+#' The function expects R files named `shiny_<model_name>.R` which contain the model.
+#' The function will also look for optional Markdown files named `shiny_<model_name>.md`
+#' which contain the model description.
 #' @rdname epiworldRShiny
-epiworldRShiny <- function(...) {
+epiworldRShiny <- function(custom_models_path = NULL, ...) {
 
   # If the package is not loaded, load it
   if (!"epiworldRShiny" %in% search()) {
     library(epiworldRShiny)
   }
 
-  models_setup()
+  models_setup(custom_models_path)
 
   header <- shinydashboard::dashboardHeader(
     title = shiny::HTML(
       'epiworldR <text style="color: gray; font-size:50%">(beta)</text>'
       )
   )
 
+  # Sets CSS cursor style for headers
   cursor_header_pointer <-
     sprintf(
       "#npis_header_%1$s, #network_header_%1$s, #population_header_%1$s",
@@ -148,11 +156,17 @@ epiworldRShiny <- function(...) {
     output$model_description <- shiny::renderText({
 
       # Reading the model description from the package
+      # - First check the prebuilt models
       fn <- system.file(
         "models", paste0("shiny_", model_id(), ".md"),
         package = "epiworldRShiny"
       )
 
+      # If the model is not found in the prebuilt models, check the custom models
+      if (!file.exists(fn)) {
+        fn <- paste0(custom_models_path, paste0("/shiny_", model_id(), ".md"))
+      }
+
       contents <- if (file.exists(fn))
         readLines(fn, warn = FALSE)
       else

R/functions-ui.R

@@ -299,12 +299,20 @@ seed_input <- function(model_name) {
 }
 
 #' @export
+#' @param custom_models_path Optional path to custom model files (see details).
+#' @details
+#' When `custom_models_path` is specified, the function will look for valid model files
+#' at the specified path. These will be added to the list of available models.
+#' The function expects R files named `shiny_<model_name>.R` which contain the model.
 #' @return
 #' - `models_setup` returns an object of class list.
 #' @rdname epiworldrshiny-ui
 #' @examples
+#' # Setup with default models only:
 #' models_setup()
-models_setup <- function() {
+#' # Setup with default and custom models:
+#' \dontrun{models_setup(custom_models_path = "path/to/custom/models")}
+models_setup <- function(custom_models_path = NULL) {
 
   # Getting the environment
   env <- parent.frame()
@@ -318,6 +326,20 @@ models_setup <- function() {
       full.names = TRUE
       )
 
+
+    # Read in custom models
+    num_custom_models <- 0
+    if (!is.null(custom_models_path)) {
+      custom_models <- list.files(
+        custom_models_path,
+        pattern = "shiny_[a-z]+\\.R$",
+        full.names = TRUE
+        )
+
+      num_custom_models <- length(custom_models)
+      models <- c(custom_models, models)
+    }
+
     # Source each model file
     for (f in models) {
       source(f, local = epiworldRenv())
@@ -340,6 +362,12 @@ models_setup <- function() {
 
     })
 
+    # If model is custom (user-defined), prepend "(custom)"
+    if (num_custom_models > 0) {
+      for (i in 1:num_custom_models) 
+        models_names[i] <- paste("(custom)", models_names[i], sep = " ")
+    }    
+
     # Get the model names from the file names
     models <- gsub("^.+shiny_([^.]+).R$", "\\1", models)
 

vignettes/getting_started.Rmd

@@ -34,6 +34,12 @@ library(epiworldRShiny)
 # epiworldRShiny()
 ```
 
+The application comes with many pre-built models (SIR, SEIR, etc.), but you can use the app with custom-built models by passing a path to your models when running the app
+```
+# epiworldRShiny("path/to/custom/models")
+```
+Custom models will be added to the top of the list of available models (above the pre-built options) and tagged as "(custom)".
+
 ## Model set-up
 
 After launching the application, notice the sidebar contains many disease and model parameters which can be modified. Altering these parameters will affect the spread of the infectious disease in the simulated population. Name the disease