Restored npde function

DESCRIPTION

@@ -17,9 +17,9 @@ Description: Parametric and non-parametric
     which used to be available on CRAN.
 Authors@R: person("Michael", "Neely",
     email = "[email protected]", role = c("aut", "cre"))
-Version: 1.9.6
+Version: 1.9.7
 URL: http://www.lapk.org
-Date: 2020-06-09
+Date: 2020-06-12
 Depends: 
     R (>= 3.5.0)
 Imports:

NAMESPACE

@@ -86,8 +86,8 @@ export(setPMoptions)
 export(ss.PK)
 export(update_gfortran)
 importFrom(base64enc,base64decode)
-importFrom(dplyr,arrange)
 importFrom(cubelyr,as.tbl_cube)
+importFrom(dplyr,arrange)
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)

R/PMutilities.R

@@ -2005,7 +2005,7 @@ getOSname <- function() {
 
 # check for installed packages --------------------------------------------
 
-checkRequiredPackages <- function(pkg) {
+checkRequiredPackages <- function(pkg, repos="CRAN") {
 
   managePkgs <- function(thisPkg) {
     # if (length(grep(thisPkg, installed.packages()[, 1])) == 0) {
@@ -2014,7 +2014,12 @@ checkRequiredPackages <- function(pkg) {
     if (requireNamespace(thisPkg, quietly = T)) {
       return("ok") #package is installed
     } else { #package is not installed
-      install.packages(thisPkg, dependencies = T, quiet = T) #try to install
+      cat(paste0("The package ",thisPkg," is required and will be installed.\n"))
+      if(repos == "CRAN"){
+        install.packages(thisPkg, dependencies = T, quiet = T) #try to install
+      }else{
+        devtools::install_github(repos)
+      }
       if (requireNamespace(thisPkg, quietly = T)){ #check again
         return("ok") #now it is installed and ok
       } else {return(thisPkg) } #nope, still didn't install

R/makeValid.R

@@ -427,25 +427,28 @@ makeValid <- function(run,input=1,outeq=1,tad=F,binCov,doseC,timeC,tadC,...){
   #NPDE --------------------------------------------------------------------
 
   #temporarily disable NPDE until we can clean code 3/9/2020
-  npdeRes <- NA
-
-  # #prepare data for npde
-  # obs <- tempDF[tempDF$icen=="mean",c("id","time","obs")]
-  # 
-  # #remove missing obs
-  # obs <- obs[obs$obs!=-99,]
-  # names(obs)[3] <- "out"
-  # 
-  # simobs <- simFull$obs
-  # #remove missing simulations
-  # simobs <- simobs[simobs$out!=-99,]
-  # simobs$id <- rep(obs$id,each=nsim)
-  # 
-  # #get NPDE
-  # assign("thisobs",obs,pos=1)
-  # assign("thissim",simobs,pos=1)
-  # npdeRes <- tryCatch(autonpde(namobs=thisobs,namsim=thissim,1,2,3,verbose=T),error=function(e) e)
-  # 
+  #npdeRes <- NA
+
+  #get npde from github
+  checkRequiredPackages("npde", repos = "LAPKB/npde") 
+
+  #prepare data for npde
+  obs <- tempDF[tempDF$icen=="mean",c("id","time","obs")]
+
+  #remove missing obs
+  obs <- obs[obs$obs!=-99,]
+  names(obs)[3] <- "out"
+
+  simobs <- simFull$obs
+  #remove missing simulations
+  simobs <- simobs[simobs$out!=-99,]
+  simobs$id <- rep(obs$id,each=nsim)
+
+  #get NPDE
+  assign("thisobs",obs,pos=1)
+  assign("thissim",simobs,pos=1)
+  npdeRes <- tryCatch(npde::autonpde(namobs=thisobs,namsim=thissim,1,2,3,verbose=T),error=function(e) e)
+
 
 
 

R/plotPMvalid.R

@@ -159,9 +159,10 @@ plot.PMvalid <- function(x,type="vpc",tad=F,icen="median",outeq=1,lower=0.025,up
   }
 
   if(type=="npde"){
-    cat("NPDE temporarily disabled pending code cleaning.\n")
-    # plot(x$npde)
-    # par(mfrow=c(1,1))
+    #cat("NPDE temporarily disabled pending code cleaning.\n")
+    if(is.null(x$npde)) stop("No npde object found.  Re-run makeValid.\n")
+    plot(x$npde)
+    par(mfrow=c(1,1))
   }
 
 }

inst/NEWS.Rd

@@ -1,5 +1,34 @@
 \name{NEWS}
 \title{NEWS file for the Pmetrics package}
+\section{Changes in version 1.9.7}{
+
+\subsection{NEW FEATURES}{
+\itemize{
+\item Restored npde function by creating new git npde repository
+}
+}
+\subsection{BUG FIXES}{
+\itemize{
+\item None
+}
+}
+}
+
+
+\section{Changes in version 1.9.6}{
+
+\subsection{NEW FEATURES}{
+\itemize{
+\item None
+}
+}
+\subsection{BUG FIXES}{
+\itemize{
+\item Fixed error in makePost associated with conversion to tidyverse handling
+}
+}
+}
+
 
 \section{Changes in version 1.9.5}{