version 0.0.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NMsim
 Type: Package
 Title: Seamless 'Nonmem' Simulation Platform
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: c(person("Philip", "Delff", email = "philip@delff.dk",role = c("aut","cre")),
   person("Matthew","Fidler", role = c("ctb"), email = "matt.fidler@novartis.com", comment="Co-author on NMreadCov"))
 Maintainer: Philip Delff <philip@delff.dk>
@@ -17,8 +17,8 @@ BugReports: https://github.com/philipdelff/NMsim/issues
 Language: en-US
 URL: https://philipdelff.github.io/NMsim/
 NeedsCompilation: no
-Packaged: 2023-09-21 00:08:34 UTC; philip
+Packaged: 2023-11-11 03:18:52 UTC; philipde
 Author: Philip Delff [aut, cre],
   Matthew Fidler [ctb] (Co-author on NMreadCov)
 Repository: CRAN
-Date/Publication: 2023-09-21 06:50:13 UTC
+Date/Publication: 2023-11-11 07:03:20 UTC

NAMESPACE

@@ -10,6 +10,7 @@ export(NMsim_known)
 export(NMsim_typical)
 export(addEVID2)
 export(addResVar)
+export(genPhiFile)
 export(inputArchiveDefault)
 import(MASS)
 import(NMdata)

NEWS

@@ -1,7 +1,34 @@
-# Post 0.0.1
+# 0.0.5
 ## New features
 
-* NMsim supports type.sim="typical" which means all OMEGAS will be
+* Full support for models estimated with SAEM. Especially, simulation
+  of "known" subjects, i.e. re-using emperical Bayes estimates, is
+  slightly different with these models.
+
+* Experimental support for windows with PsN. `dir.psn` argument has to
+  point to a directory where executables `execute` and `update_inits`
+  are found. Thanks to Sjoerd Koopman for debugging and testing
+  this. Hopefully in future versions, `PsN` will not be needed on
+  Windows (like it is not needed on Linux).
+
+* The simulation method called NMsim_known now accepts other `.phi`
+  files to use than the .phi file generated by the estimation
+  run. This is useful if one wants to reuse subjects generated in a
+  previous simulation.
+
+## Other/minor improvements
+
+* NMexec now also copies out the shk (shrinkage estimates) file after
+  a run. The files that will by default be copied and reported next to
+  the control streams are now `xml`, `ext`, `cov`, `cor`, `coi`,
+  `phi`, `shk` - in addition to output table files and the archived
+  input data of course.
+
+# 0.0.2
+## New features
+
+* NMsim supports `type.sim="typical"` which means all OMEGAS will be
   fixed to zero. This requires the ext file to be present.
 
-* Experimental support for simulation of estimated subjects using type.sim="known".
+* Experimental support for simulation of estimated subjects using
+  `type.sim="known"`.

R/NMcreateMatLines.R

@@ -8,7 +8,6 @@
 ##' @keywords internal
 
 NMcreateMatLines <- function(omegas,type){
-
     . <- NULL
     j <- NULL
     i <- NULL

R/NMexec.R

@@ -31,7 +31,7 @@
 ##'     to be available for further processing.
 ##' @param args.psn.execute A character string with arguments passed
 ##'     to execute. Default is
-##'     "-model_dir_name -nm_output=xml,ext,cov,cor,coi,phi".
+##'     "-model_dir_name -nm_output=xml,ext,cov,cor,coi,phi,shk".
 ##' @param update.only Only run model(s) if control stream or data
 ##'     updated since last run?
 ##' @param nmquiet Suppress terminal output from `Nonmem`. This is
@@ -69,16 +69,19 @@
 ##'     installed version of PSN).
 ##' @param path.nonmem The path to the nonmem executable. Only used if
 ##'     \code{method.execute="direct"} or
-##'     \code{method.execute="nmsim"} (which is not default). If
-##'     this argument is not supplied, NMexec will try to run nmfe75,
+##'     \code{method.execute="nmsim"} (which is not default). If this
+##'     argument is not supplied, NMexec will try to run nmfe75,
 ##'     i.e. this has to be available in the path of the underlying
 ##'     shell. The default value can be modified using
 ##'     \code{NMdata::NMdataConf}, like
 ##'     \code{NMdataConf(path.nonmem="/path/to/nonmem")}
-##' @param files.needed In case method.execute="nmsim", this
-##'     argument specifies files to be copied into the temporary
-##'     directory before Nonmem is run. Input control stream and
-##'     simulation input data does not need to be specified.
+##' @param files.needed In case method.execute="nmsim", this argument
+##'     specifies files to be copied into the temporary directory
+##'     before Nonmem is run. Input control stream and simulation
+##'     input data does not need to be specified.
+##' @param system.type A charachter string, either \"windows\" or
+##'     \"linux\" - case insensitive. Windows is only experimentally
+##'     supported. Default is to use \code{Sys.info()[["sysname"]]}.
 ##' @details Use this to read the archived input data when retrieving
 ##'     the nonmem results:
 ##'     \code{NMdataConf(file.data=inputArchiveDefault)}
@@ -114,7 +117,7 @@
 NMexec <- function(files,file.pattern,dir,sge=TRUE,input.archive,
                    nc=64,dir.data=NULL,wait=FALSE, args.psn.execute,
                    update.only=FALSE,nmquiet=FALSE,
-                   method.execute="psn",dir.psn,path.nonmem,
+                   method.execute="psn",dir.psn,path.nonmem,system.type,
                    files.needed){
 
 
@@ -162,11 +165,14 @@ NMexec <- function(files,file.pattern,dir,sge=TRUE,input.archive,
         input.archive <- function(file) FALSE
     }
 
+    if(missing(system.type)) system.type <- NULL
+    system.type <- getSystemType(system.type)
+
     ## args.psn.execute
     if(missing(args.psn.execute)) args.psn.execute <- NULL
     args.psn.execute <- simpleCharArg("args.psn.execute"
                                      ,args.psn.execute
-                                     ,default="-model_dir_name -nm_output=xml,ext,cov,cor,coi,phi"
+                                     ,default="-model_dir_name -nm_output=xml,ext,cov,cor,coi,phi,shk"
                                      ,accepted=NULL
                                      ,clean=FALSE
                                      ,lower=FALSE)
@@ -187,6 +193,8 @@ NMexec <- function(files,file.pattern,dir,sge=TRUE,input.archive,
                                  ,accepted=NULL
                                  ,clean=FALSE
                                  ,lower=FALSE)
+
+
 
     if(is.null(files) && is.null(file.pattern)) file.pattern <- ".+\\.mod"
     files.all <- NMdata:::getFilePaths(files=files,file.pattern=file.pattern,dir=dir,quiet=TRUE)
@@ -222,9 +230,15 @@ NMexec <- function(files,file.pattern,dir,sge=TRUE,input.archive,
             saveRDS(dat.inp,file=file.path(rundir,basename(fn.input)))
         }
 
+
         if(method.execute=="psn"){
-            ## string.cmd <- paste0("cd ",rundir,"; ",cmd.execute ,args.execute)
-            string.cmd <- sprintf("cd %s; %s %s",rundir,cmd.execute ,args.psn.execute)
+            ##if(system.tpe=="linux"){
+
+            string.cmd <- sprintf('cd "%s"; "%s" %s',rundir,cmd.execute ,args.psn.execute)
+            ##}
+            ## if(system.type=="windows"){
+            ##     pas
+            ## }
             if(sge){
                 string.cmd <- paste0(string.cmd," -run_on_sge")
                 if(nc>1){
@@ -249,8 +263,8 @@ NMexec <- function(files,file.pattern,dir,sge=TRUE,input.archive,
             if(sge) {
 
                 ## string.cmd <- sprintf("cd %s; qsub -terse -wd \'%s\' %s",getwd(),dirname(string.cmd),string.cmd)
-#### I am not sure if absolute path is needed here.
-                string.cmd <- sprintf("cd %s; qsub -terse -wd \'%s\' %s",
+                ## I am not sure if absolute path is needed here.
+                string.cmd <- sprintf('cd "%s"; qsub -terse -wd \'%s\' %s',
                                       getwd(),getAbsolutePath(dirname(string.cmd)),string.cmd)
                 ## string.cmd <- paste0("CURWD=",getwd()," ",string.cmd)
                 wait <- TRUE
@@ -259,11 +273,23 @@ NMexec <- function(files,file.pattern,dir,sge=TRUE,input.archive,
             }
         }
 
-        if(nmquiet) string.cmd <- paste(string.cmd, ">/dev/null 2>&1")
-
-        if(!wait) string.cmd <- paste(string.cmd,"&")
-
-        system(string.cmd,ignore.stdout=nmquiet)
+        if(system.type=="windows"){
+
+            ## contents.bat <- gsub(";","\n",string.cmd)
+            ## cat(contents.bat,file=path.script)
+            path.script <- file.path(dirname(file.mod),"NMsim_exec.bat")
+            contents.bat <-
+                strsplit(string.cmd,split=";")[[1]]
+            writeTextFile(contents.bat,file=path.script)
+
+            shell(shQuote(path.script,type="cmd") )
+        }
+        if(system.type=="linux"){
+            if(nmquiet) string.cmd <- paste(string.cmd, ">/dev/null 2>&1")
+            if(!wait) string.cmd <- paste(string.cmd,"&")
+
+            system(string.cmd,ignore.stdout=nmquiet)
+        }
     }
 
     return(invisible(NULL))

R/NMexecDirectory.R

@@ -106,7 +106,7 @@ NMexecDirectory <- function(file.mod,path.nonmem,files.needed,dir.data=".."){
     meta.tables <- NMscanTables(file.mod.tmp,meta.only=TRUE,as.fun="data.table")
 
 ### execute nonmem
-    exts.cp <- c("lst","xml","ext","cov","cor","coi","phi","msf","msfi","msfo" )
+    exts.cp <- c("lst","xml","ext","cov","cor","coi","phi","msf","msfi","msfo","shk" )
 
     dir.mod.abs <- getAbsolutePath(dir.mod)
     lines.bash <- c(
@@ -123,9 +123,10 @@ NMexecDirectory <- function(file.mod,path.nonmem,files.needed,dir.data=".."){
     )
 
     path.script <- file.path(dir.tmp,"run_nonmem.sh")
-    con.newfile <- file(path.script,"wb")
-    writeLines(lines.bash,con=con.newfile)
-    close(con.newfile)
+    ## con.newfile <- file(path.script,"wb")
+    ## writeLines(lines.bash,con=con.newfile)
+    ## close(con.newfile)
+    writeTextFile(lines.bash,path.script)
     Sys.chmod(path.script,mode="0577")
 
     ## system(path.script)

R/NMreadPhi.R

@@ -1,4 +1,4 @@
-##' Read information from Nonmem ext files
+##' Read information from Nonmem phi files
 ##'
 ##' @param file Path to the phi file
 ##'