A bunch of stuff related mostly to the initial CTS checkin but aslo s…

…ome updates to MB and the main ruminiate functionality.

DESCRIPTION

@@ -27,6 +27,7 @@ Imports:
   shiny,
   shinyAce,
   shinyWidgets,
+  rxode2,
   stats,
   stringr,
   tidyr,
@@ -41,7 +42,6 @@ Suggests:
   prompter,
   rmarkdown,
   readxl,
-  rxode2,
   rxode2et,
   shinydashboard,
   testthat (>= 3.0.0),

NAMESPACE

@@ -1,5 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
+export(CTS_Server)
+export(CTS_append_report)
+export(CTS_del_current_element)
+export(CTS_fetch_code)
+export(CTS_fetch_current_element)
+export(CTS_fetch_ds)
+export(CTS_fetch_sc_meta)
+export(CTS_fetch_state)
+export(CTS_init_state)
+export(CTS_new_element)
+export(CTS_set_current_element)
+export(CTS_test_mksession)
+export(CTS_update_checksum)
 export(MB_Server)
 export(MB_append_report)
 export(MB_build_code)
@@ -57,6 +70,8 @@ importFrom(digest,digest)
 importFrom(rlang,":=")
 importFrom(shinyAce,aceEditor)
 importFrom(shinyAce,updateAceEditor)
+importFrom(stats,rnorm)
+importFrom(stats,runif)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_split)

R/MB_Server.R

@@ -13,6 +13,7 @@
 #'@param deployed Boolean variable indicating whether the app is deployed or not.
 #'@param react_state Variable passed to server to allow reaction outside of module (\code{NULL})
 #'@return MB Server object
+# JMH Add example
 MB_Server <- function(id,
                id_ASM        = "ASM",
                FM_yaml_file  = system.file(package = "formods", "templates", "formods.yaml"),
@@ -1523,25 +1524,25 @@ MB_test_mksession = function(session, id = "MB", full_session=TRUE){
   input  = list()
   state  = list()
 
-    # Configuration files
-    FM_yaml_file  = system.file(package = "formods", "templates", "formods.yaml")
-    MOD_yaml_file = system.file(package = "ruminate", "templates", "MB.yaml")
-    
-    # Creating an empty state object
-    state = MB_fetch_state(id              = "MB",
-                           input           = input,
-                           session         = session,
-                           FM_yaml_file    = FM_yaml_file,
-                           MOD_yaml_file   = MOD_yaml_file,
-                           react_state     = NULL)
+  # Configuration files
+  FM_yaml_file  = system.file(package = "formods", "templates", "formods.yaml")
+  MOD_yaml_file = system.file(package = "ruminate", "templates", "MB.yaml")
+
+  # Creating an empty state object
+  state = MB_fetch_state(id              = "MB",
+                         input           = input,
+                         session         = session,
+                         FM_yaml_file    = FM_yaml_file,
+                         MOD_yaml_file   = MOD_yaml_file,
+                         react_state     = NULL)
 
   if( Sys.getenv("ruminate_rxfamily_found") == "TRUE"){
     # This will provide a list of the available models
     models = MB_fetch_catalog(state)
 
     #-------------------------------------------------------
     # Simplest model:
-    ridx = which(models[["summary"]][["Name"]] == "PK_1cmt")
+    ridx = which(models[["summary"]][["Name"]] == "PK_1cmt_des")
     model_row  = models[["summary"]][ridx, ]
 
     mk_rx_res = mk_rx_obj(

R/ruminate.R

@@ -16,14 +16,13 @@
 
 .onLoad <- function(libname, pkgname){
 
-
   #------------------------------------
   # Checking for rxpackages
   # If all the suggested packages are found this will be true:
   suggested_found = TRUE
-  #mr = FM_message("Loading ruminate", entry_type="h1")
+  mr = FM_message("Loading ruminate", entry_type="h1")
+  mr = FM_message("Checking for required nlmixr2 family of tools", entry_type="h2")
 
-  mr = FM_message("Checking for required nlmixr2 family of tools", entry_type="alert")
   pkgs = c("rxode2", "nonmem2rx", "nlmixr2lib", "rxode2et")
   for(pkg in pkgs){
     pkg_var = paste0("ruminate_", pkg, "_found")
@@ -39,6 +38,20 @@
   }
 
   Sys.setenv(ruminate_rxfamily_found = suggested_found)
+
+  mr = FM_message("Checking for other suggested packages", entry_type="h2")
+
+  other_pkgs = c(
+    "clipr",       "gridExtra", "prompter",
+    "rmarkdown",   "readxl",    "shinydashboard",
+    "ubiquity")
+  for(pkg in other_pkgs){
+    if(!requireNamespace(pkg, quietly=TRUE)){
+      mr = FM_message(paste0("missing ", pkg), entry_type="danger")
+    } else {
+      mr = FM_message(paste0("found ", pkg), entry_type="success")
+    }
+  }
 }
 
 #'@export