Merge pull request #130 from LAPKB/v2_dev

Release 4.0.2

DESCRIPTION

@@ -25,10 +25,10 @@ Authors@R: c(
   person("David", "Bayard", email = "", role = "ctb"),
   person("Robert", "Leary", email = "", role = "ctb")
     )
-Version: 2.0.1
+Version: 2.0.2
 URL: https://lapkb.github.io/Pmetrics/
 BugReports: https://github.com/LAPKB/Pmetrics/issues
-Date: 2022-09-30
+Date: 2023-01-05
 Depends: 
     R (>= 4.0.0)
 Imports:
@@ -45,7 +45,6 @@ Imports:
     Matrix,
     mclust,
     methods,
-    npde,
     openxlsx,
     parallel,
     plyr,
@@ -61,6 +60,7 @@ Imports:
     xtable,
     readr,
     trelliscopejs,
+    npde,
     lubridate,
     mvtnorm,
     tidyverse,

NAMESPACE

@@ -99,6 +99,7 @@ export(SIMrun)
 export(ab)
 export(ab_line)
 export(add_shapes)
+export(add_smooth)
 export(additive)
 export(combination)
 export(fixed)
@@ -118,6 +119,7 @@ export(makePost)
 export(makeValid)
 export(make_NCA)
 export(make_valid)
+export(modelLibrary)
 export(msd)
 export(proportional)
 export(qgrowth)

R/Deprecated.R

@@ -1,65 +1,68 @@
 #' The following functions are deprecated in Pmetrics.
-#' 
-#' 
+#'
+#'
 #' @title Deprecated functions.
-#' @aliases PMcheckMatrix, PMfixMatrix, NPload, ITload, NPreport, ITreport, 
+#' @aliases PMFortranConfig, PMcheckMatrix, PMfixMatrix, NPload, ITload, NPreport, ITreport,
 #' PMdiag, PMreadDefaults, PMwriteDefaults, makeNPDE, PMupdate
 #' @author Michael Neely
 #' @export
 
+#' @export
+PMFortranConfig <- function(...) {
+  cat("\nPMFortranConfig is deprecated.  Use setPMoptions instead to change the compilation arguments.\n")
+}
 
-
-PMcheckMatrix <- function(...){
+#' @export
+PMcheckMatrix <- function(...) {
   cat("\nPMcheckMatrix is deprecated.  Use PMcheck() instead to check data and model files.\n")
 }
 
 #' @export
-PMfixMatrix <- function(...){
+PMfixMatrix <- function(...) {
   cat("\nPMfixMatrix is deprecated.  Use PMcheck(...,fix=T) instead to fix data files.\n")
 }
 
 #' @export
-NPload <- function(...){
+NPload <- function(...) {
   cat("\nNPload is deprecated.  Use PMload() instead to load results of NPAG or IT2B runs.\n")
 }
 
 #' @export
-ITload <- function(...){
+ITload <- function(...) {
   cat("\nITload is deprecated.  Use PMload() instead to load results of NPAG or IT2B runs.\n")
 }
 
 #' @export
-NPreport <- function(...){
+NPreport <- function(...) {
   cat("\nNPreport is deprecated.  Use PMreport() instead to process completed NPAG or IT2B runs.\n")
 }
 
 #' @export
-ITreport <- function(...){
+ITreport <- function(...) {
   cat("\nITreport is deprecated.  Use PMreport() instead to process completed NPAG or IT2B runs.\n")
 }
 
 #' @export
-PMdiag <- function(...){
+PMdiag <- function(...) {
   cat("\nPMdiag is deprecated.  Use makeNPDE() instead to internally validate a model.\n")
 }
 
 #' @export
-PMreadDefaults <- function(...){
+PMreadDefaults <- function(...) {
   cat("\nPMreadDefaults is deprecated.  Use getPMoptions() instead to read Pmetrics options.\n")
 }
 
 #' @export
-PMwriteDefaults <- function(...){
+PMwriteDefaults <- function(...) {
   cat("\nPMwriteDefaults is deprecated.  Use setPMoptions() instead to set Pmetrics options.\n")
 }
 
 #' @export
-makeNPDE <- function(...){
+makeNPDE <- function(...) {
   cat("\nmakeNPDE is deprecated.  Use $validate() on a PM_result object or makeValid() instead.\n")
 }
 
 #' @export
-PMupdate <- function(...){
+PMupdate <- function(...) {
   cat("\nPMupdate is deprecated. Please restart Rstudio and do not load Pmetrics.  Then use the command devtools::install_github(\"LAPKB/Pmetrics\")")
 }
-

R/PM_fit.R

@@ -1,13 +1,13 @@
 #' @title
 #' Object to define and run a model and data in Pmetrics
-#' 
-#' @description 
+#'
+#' @description
 #' `PM_fit` objects comprise a `PM_data` and `PM_model` object ready for analysis
-#' 
-#' @details 
+#'
+#' @details
 #' Data and model objects can be previously created as [PM_data] or [PM_model] objects,
 #' or created on the fly when making a new PM_fit object. PM_fit objects contain
-#' methods to cross-check data and model objects for compatibility, as well as to 
+#' methods to cross-check data and model objects for compatibility, as well as to
 #' run the analysis.
 #' @export
 
@@ -19,7 +19,7 @@ PM_fit <- R6::R6Class("PM_fit",
     #' @param data Either the name of a  [PM_data]
     #' object in memory or the quoted name of a Pmetrics
     #' data file in the current working directory, which will crate a `PM_data`
-    #' object on the fly. However, if created on the fly, this object 
+    #' object on the fly. However, if created on the fly, this object
     #' will not be available to other
     #' methods or other instances of `PM_fit`.
     #' @param model Similarly, this is either the name of a [PM_model]
@@ -44,28 +44,36 @@ PM_fit <- R6::R6Class("PM_fit",
     #' @description Fit the model to the data
     #' @param ... Other arguments passed to [NPrun]
     #' @param engine "NPAG" (default) or "IT2B"
-    run = function(..., engine = "NPAG") {
+    #' @param rundir This argument specifies an *existing* folder that will store the run inside.
+    run = function(..., engine = "NPAG", rundir = getwd()) {
+      wd <- getwd()
+      if (!dir.exists(rundir)) {
+          stop("You have specified a directory that does not exist, please create it first.")
+       }
+      setwd(rundir)
       engine <- tolower(engine)
       if (inherits(private$model, "PM_model_legacy")) {
         cat(sprintf("Runing Legacy"))
-        if(engine=="npag"){
+        if (engine == "npag") {
           Pmetrics::NPrun(private$model$legacy_file_path, private$data$standard_data, ...)
-        } else if(engine=="it2b") {
+        } else if (engine == "it2b") {
           Pmetrics::ITrun(private$model$legacy_file_path, private$data$standard_data, ...)
-        } else{
-          endNicely(paste0("Unknown engine: ",engine,". \n"))
+        } else {
+          endNicely(paste0("Unknown engine: ", engine, ". \n"))
         }
       } else if (inherits(private$model, "PM_model_list")) {
         engine <- tolower(engine)
         model_path <- private$model$write(engine = engine)
         cat(sprintf("Creating model file at: %s\n", model_path))
-        if(engine == "npag"){
+        if (engine == "npag") {
           Pmetrics::NPrun(model_path, private$data$standard_data, ...)
         } else {
           Pmetrics::ITrun(model_path, private$data$standard_data, ...)
         }
       } else if (inherits(private$model, "PM_model_julia")) {
-        if(engine != "npag") {stop("Julia is only for NPAG currently.")}
+        if (engine != "npag") {
+          stop("Julia is only for NPAG currently.")
+        }
         cat(sprintf("Runing Julia: %s-%s\n", private$data, private$model$name))
         return(
           julia_call(
@@ -81,6 +89,7 @@ PM_fit <- R6::R6Class("PM_fit",
           )
         )
       }
+      setwd(wd)
     },
     #' @description
     #' Save the current PM_fit object to a .rds file.
@@ -96,10 +105,10 @@ PM_fit <- R6::R6Class("PM_fit",
     #' function.
     #' @param file_name Name of the file to be read, the default is "PMfit.rds".
     #' @return A `PM_fit` object.
-    load = function(file_name){
+    load = function(file_name) {
       return(invisible())
     },
-    #' @description 
+    #' @description
     #' Checks for errors in data and model objects and agreement between them.
     check = function() {
       if (inherits(private$model, "PM_model_list")) {
@@ -122,4 +131,4 @@ PM_fit <- R6::R6Class("PM_fit",
 #' @export
 PM_fit$load <- function(file_name = "PMfit.rds") {
   readRDS(file_name)
-}
+}