Bug fix for handling of beta multiplier

If a model was recreated multiple times during the same software run,
the effect of the beta multiplier was compounded.  A change to
FeaturedSpace fixed this bug.

.gitignore

@@ -1,10 +1,11 @@
-# class files, zip files, emacs backup files, semantic cache and javadoc files
+# class files, zip files, emacs backup files, semantic cache and javadoc files, maxent.jar
 *.class
 *.zip
 *~
 semantic.cache
 html/
 help.html
+maxent.jar
 
 # Windows image file caches
 Thumbs.db

density/FeaturedSpace.java

@@ -294,6 +294,7 @@ public FeaturedSpace(Sample[] samples, Feature[] f, Params params) { //, boolean
 	this.samples = samples;
 	//	this.doClamp = doClamp;
 	numPoints = numPointsForNormalizer = (f.length==0) ? 0 : f[0].n;
+	minDeviation = 0.001;	
 	if (params != null)
 	    minDeviation *= params.getBetamultiplier();
 
@@ -464,8 +465,7 @@ else if (cnt==1)
     }
 
     SampleInfo biasInfo = null;
-    public static double minDeviation = 0.001;
-    // better on NCEAS:  public static double minDeviation = 0.001;
+    public static double minDeviation;
     void setSampleExpectations() {
 	Utils.echoln(numSamples + " samples");
 	biasInfo = getDividedSampleInfo(new ConstFeature(1.0,biasDiv.n), biasDiv);

density/Utils.java

@@ -32,7 +32,7 @@ a copy of this software and associated documentation files (the
 
 public class Utils {
 
-    static String version = "3.4.0";
+    static String version = "3.4.1";
     static boolean interrupt=false, warnings=true;
     public static boolean verbose=false, visible=true;
     static JFrame topLevelFrame = null;

readme.txt

@@ -7,7 +7,7 @@ Miro Dudik          ([email protected])
 Steven Phillips     ([email protected])
 Rob Schapire        ([email protected])
 
-Version 3.4.0, December 2016
+Version 3.4.1, December 2016
 
 This file outlines the steps you should take to begin using maxent to
 model species geographic distributions.  To download the program, or
@@ -118,7 +118,13 @@ click on the maxent.bat file instead.  If this is not the problem,
 click on the "help" button for more advice.
 
 
+Main Changes in Version 3.4.1:
+-----------------------------
+   Fixed bug that caused regularization multiplier to be have increasing effect over multiple runs
+
+
 Main Changes in Version 3.4.0:
+-----------------------------
    Added cloglog output transformation, and made it the default output format
    Threshold features are no longer used in default settings