Updating documentation.

NAMESPACE

@@ -63,6 +63,7 @@ export(mk_table_nca_params)
 export(nca_builder)
 export(plot_sr_tc)
 export(ruminate)
+export(ruminate_check)
 export(run_nca_components)
 export(simulate_rules)
 import(dplyr)

R/CTS_Server.R

@@ -1709,7 +1709,7 @@ CTS_fetch_state = function(id, id_ASM, id_MB, input, session, FM_yaml_file, MOD_
 
     #browser()
 
-    if(current_ele[["cares"]][["COV_GOOD"]]){
+    if(current_ele[["cares"]][["COV_IS_GOOD"]]){
       state = formods::FM_set_notification(state,
         notify_text = paste0("Covariate ", selected_covariate, " Added"),
         notify_id   = "COV_IS_GOOD",
@@ -2150,30 +2150,24 @@ element}
 #'@description Takes the ui elements in the module state and processes the covariate elements for addition.
 #'@param state CTS state from \code{CTS_fetch_state()}
 #'@param element Element list from \code{CTS_fetch_current_element()}
-#'@return Element with the results of adding the rule. The \code{cares} list
+#'@return Element with the results of adding the covariate. The \code{cares} list
 #'element can be used to determine the exit status of the function.
 #'\itemize{
-#'  \item{RULE_IS_GOOD}  If true it indicates that the pieces of the rule from
-#'  the UI check out.
-#'  \item{RULE_UPDATED}  If RULE_IS_GOOD and RULE_UPDATED is true then a
-#'  previous rule definition was overwritten. If RULE_IS_GOOD is TRUE and
-#'  RULE_UPDATED is FALSE then a new rule was added.
-#' \item{notify_text}  Text for notify message
-#' \item{notify_id}    Notification ID
-#' \item{notify_type}  Notification type
-#' \item{msgs}         Vector of messages.
+#'  \item{COV_IS_GOOD}  If TRUE if the covariate was good and added, and FALSE if
+#'  there were any issues.
+#' \item{msgs}     Vector of messages.
 #'}
 #'@details This depends on the following UI values in the state
 #'\itemize{
-#'  \item{}  state[["CTS"]][["ui"]][["covariate_value"]]
-#'  \item{}  state[["CTS"]][["ui"]][["covariate_type_selected"]]
-#'  \item{}  state[["CTS"]][["ui"]][["selected_covariate"]]
+#'  \item{} state[["CTS"]][["ui"]][["covariate_value"]]
+#'  \item{} state[["CTS"]][["ui"]][["covariate_type_selected"]]
+#'  \item{} state[["CTS"]][["ui"]][["selected_covariate"]]
 #'}
 #'@example inst/test_apps/CTS_funcs.R
 CTS_add_covariate   = function(state, element){
 
   msgs         = c()
-  COV_GOOD = TRUE
+  COV_IS_GOOD = TRUE
 
   covariate_value    = state[["CTS"]][["ui"]][["covariate_value"]]
   covariate_type     = state[["CTS"]][["ui"]][["covariate_type_selected"]]
@@ -2182,7 +2176,7 @@ CTS_add_covariate   = function(state, element){
     tmp_msg = paste0("No value specified for covariate: ", selected_covariate, ".")
     FM_le(state, tmp_msg)
     msgs = c(msgs, tmp_msg)
-    COV_GOOD = FALSE
+    COV_IS_GOOD = FALSE
   }else{
     covariate_value = paste0("c(", covariate_value, ")")
     cmd = paste0("cvval = ", covariate_value)
@@ -2205,13 +2199,13 @@ CTS_add_covariate   = function(state, element){
       msgs = c(msgs, tmp_msg)
       msgs = c(msgs, paste0("  -> ", covariate_value))
       msgs = c(msgs, tcres[["msgs"]])
-      COV_GOOD = FALSE
+      COV_IS_GOOD = FALSE
     }
   }
 
   # Appending results
   element[["cares"]] = list(
-    COV_GOOD     = COV_GOOD,
+    COV_IS_GOOD  = COV_IS_GOOD,
     msgs         = msgs
   )
 element}

R/ruminate.R

@@ -38,21 +38,70 @@
   }
 
   Sys.setenv(ruminate_rxfamily_found = suggested_found)
+}
+
+#'@export
+#'@title Checks `ruminate` Dependencies
+#'@description  Looks at the suggested dependencies and checks to make sure
+#'they are installed.
+#'@param verbose Logical indicating if messages should be displayed
+#'@return List with the following elements:
+#' \itemize{
+#'   \item{all_found:}    Boolean indicating if all packages were found
+#'   \item{found_pkgs:}   Character vector of found packages
+#'   \item{missing_pkgs:} Character vector of missing packages
+#'}
+#'@examples
+#' fcres =ruminate_check()
+ruminate_check <- function(verbose=TRUE){
 
-  #mr = FM_message("Checking for other suggested packages", entry_type="h2")
+  #------------------------------------
+  # Checking for rxpackages
+  # If all the suggested packages are found this will be true:
+  suggested_found = TRUE
+  if(verbose){
+    mr = FM_message("Checking ruminate for suggested packages", entry_type="h1")
+  }
 
-  other_pkgs = c(
-    "clipr",       "gridExtra", "prompter",
-    "rmarkdown",   "readxl",    "shinydashboard",
-    "ubiquity")
-  for(pkg in other_pkgs){
+  pkgs = c(
+   "clipr",
+   "gridExtra",
+   "knitr",
+   "nlmixr2lib",
+   "nonmem2rx",
+   "prompter",
+   "rmarkdown",
+   "readxl",
+   "rxode2et",
+   "shinydashboard",
+   "testthat",
+   "ubiquity")
+
+  pkg_found   = c()
+  pkg_missing =  c()
+  for(pkg in pkgs){
     if(!requireNamespace(pkg, quietly=TRUE)){
-      #mr = FM_message(paste0("missing ", pkg), entry_type="danger")
+      if(verbose){
+        mr = FM_message(paste0("missing ", pkg), entry_type="danger")
+      }
+      pkg_missing = c(pkg_missing, pkg)
+      suggested_found = FALSE
     } else {
-      #mr = FM_message(paste0("found ", pkg), entry_type="success")
+      if(verbose){
+        mr = FM_message(paste0("found ", pkg), entry_type="success")
+      }
+      pkg_found   = c(pkg_found  , pkg)
     }
   }
-}
+
+  res = list(
+    all_found     = suggested_found,
+    found_pkgs    = pkg_found,
+    missing_pkgs  = pkg_missing
+  )
+res}
+
+
 
 #'@export
 #'@title Run the {ruminate} Shiny App

_pkgdown.yml

@@ -19,6 +19,9 @@ reference:
    - title: "Running ruminate"
    - contents:
      - ruminate
+   - title: "Helper functions"
+   - contents:
+     - ruminate_check
    - title: "CTS Module functions"
    - contents:
      - starts_with("CTS_")

docs/pkgdown.yml

@@ -7,5 +7,5 @@ articles:
   model_builder: model_builder.html
   noncompartmental_analysis: noncompartmental_analysis.html
   simulate_rules: rmdhunks/simulate_rules.html
-last_built: 2024-03-12T14:14Z
+last_built: 2024-03-17T18:18Z