From 7c49fea3dc63ad1596e05b43ec38d1d486a740ef Mon Sep 17 00:00:00 2001
From: k_harling <k_harling>
Date: Fri, 15 Feb 2008 09:07:07 +0000
Subject: [PATCH] changed input options to allow list of alternative models, or
 none. Removed inapplicable options

---
 bin/mcs | 79 ++++++++++++++++++++++++++---------------------------------------
 1 file changed, 32 insertions(+), 47 deletions(-)

diff --git a/bin/mcs b/bin/mcs
index 6e318e9..c9d5db4 100644
--- a/bin/mcs
+++ b/bin/mcs
@@ -22,10 +22,9 @@ Getopt::Long::config("auto_abbrev");
 my %options;
 ## Declare the options
 
-my %required_options = ( 'case_column:s' => 'column_name|column_number',
-			 'samples:i' => '100',
-			 'alternative_model:s' => 'alt.mod' );
-my %optional_options = ( "bins:i" => '',
+my %required_options = ( 'samples:i' => '100');
+my %optional_options = ( 'alternative_model:s' => 'alt1.mod,alt2.mod,...',
+			 "bins:i" => '',
 			 "selection_method:s" => '\'random\'|\'consecutive\'' );
 
 my $res = GetOptions( \%options,
@@ -39,38 +38,11 @@ my %help_text;
 $help_text{Pre_help_message} = <<'EOF';
   mc
 
-    Perl script for Monte-carlo Simulation of Case-Deletion Diagnostics of NONMEM runs.
+    Perl script for Monte-Carlo Simulation of NONMEM runs.
 
   Usage:
 EOF
 
-$help_text{Description} = <<'EOF';
-    Description:
-
-      The Case Deletion Diagnostics tool is run from the command line
-      with a few mandatory arguments. MC is run as a diagnostic after
-      a model is regarded finished or at least mature enough to run
-      validation tool on. You need to specify the NONMEM modelfile
-      with a model that have successful termination. You also have to
-      specify the number or name of the datafile column on which to
-      select for deletion. You do so with the case_column option.
-EOF
-
-$help_text{Examples} = <<'EOF';
-    Example:
-      
-      mc -model=run89.mod -case_column=10
-      
-      This will perform a Case Deletion Diagnostic on the model
-      specified in run89.mod based on the factors in column ten. If,
-      for example, column ten holds the ids of the seven centers
-      included in the study, this command will create seven copies of
-      the dataset, each with individuals included in one specific
-      center deleted. Say that the centers are numbered 1 to 7. Then
-      dataset 1 will have individuals from center 1 excluded, dataset
-      2 individuals from center 2 and so on.
-EOF
-
 $help_text{Options} = <<'EOF';      
     Options:
 
@@ -95,6 +67,14 @@ $help_text{-help} = <<'EOF';
       With -help mc will print this, longer, help message.
 EOF
 
+$help_text{-alternative_model} = <<'EOF';
+      -alternative_model=alt1.mod,alt2.mod,...
+
+      List of one or more alternative models to use for estimation 
+      with simulated datasets. The filenames must be comma-separated,
+      no spaces.
+EOF
+
 $help_text{-bins} = <<'EOF';
       -bins=$number 
 
@@ -115,9 +95,6 @@ $help_text{-selection_method} = <<'EOF';
       Default value = 'consecutive'
 EOF
 
-$help_text{-case_column} = <<'EOF';
-       -case_column=column_name|column_number
-EOF
 
 $help_text{Post_help_message} = <<'EOF';
       Also see 'execute -help' for a description of common options.
@@ -136,11 +113,6 @@ if( scalar(@ARGV) > 1 ){
   exit;
 }
 
-unless ( defined $options{'alternative_model'} ){
-  print "alternative_model must be given\n" ;
-  exit;
-}
-
 unless ( defined $options{'samples'} ){
   print "samples must be given\n" ;
   exit;
@@ -160,18 +132,31 @@ my $model = model -> new ( eval( $eval_string ),
 			   filename                    => $ARGV[0],
 			   ignore_missing_output_files => 1 );
 
-my $alternative_model = model ->
-    new ( eval( $eval_string ),
-	  filename                    => $options{'alternative_model'},
-	  ignore_missing_output_files => 1 );
 
-## Create new Mc object:
+my @alternatives=();
+
+if ( defined $options{'alternative_model'} ){
+    #split string, assume comma separated
+    foreach my $altfile (split(/,/,$options{'alternative_model'})){
+	if (length($altfile)>0){
+	    my $alternative_model = model ->
+		new ( eval( $eval_string ),filename => $altfile,ignore_missing_output_files => 1 );
+	    push(@alternatives,$alternative_model);
+	}
+    }
+    if (scalar(@alternatives)<1){
+	die "Error: Option alternative_model used, but list of filenames could not be parsed.\n";
+    }	
+}else{
+    print "No alternative model given, will only estimate original model.\n" ;
+
+}
+
 my $mc = tool::mc -> 
     new ( eval( $common_options::parameters ),
 	  models	     => [ $model ],
-	  alternative_models => [ $alternative_model ],
+	  alternative_models => \@alternatives,
 	  samples            => $options{'samples'} );
-
 open(CMD, ">", $mc -> directory . "/command.txt");
 print CMD $cmd_line, "\n";
 close(CMD);
-- 
2.11.4.GIT