From 75d119e709eff6fb634cec9fdf2cef36665f25d8 Mon Sep 17 00:00:00 2001
From: mrmaxent <mrmaxent@gmail.com>
Date: Fri, 17 Jul 2020 18:54:19 -0600
Subject: [PATCH 1/5] Update Project.java

---
 density/Project.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/density/Project.java b/density/Project.java
index 47834fc..9debf32 100644
--- a/density/Project.java
+++ b/density/Project.java
@@ -291,6 +291,7 @@ boolean wouldExtrapolate(int r, int c) {
 		}
 
 		public float eval(int r, int c) {
+		    doClamp = is("doClamp");
 		    double pred = predclamp = pred(r, c, true);
 		    if (doClamp) {
 			doClamp = false;

From 234b3ab50c54dae704558b751fb7f349535c5b0e Mon Sep 17 00:00:00 2001
From: mrmaxent <mrmaxent@gmail.com>
Date: Fri, 17 Jul 2020 19:00:49 -0600
Subject: [PATCH 2/5] Update readme.txt

Add description of changes for version 3.4.2
---
 readme.txt | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/readme.txt b/readme.txt
index 8fa3f26..23b8bc3 100644
--- a/readme.txt
+++ b/readme.txt
@@ -7,7 +7,7 @@ Miro Dudik          (mdudik@microsoft.com)
 Steven Phillips     (mrmaxent@gmail.com)
 Rob Schapire        (schapire@microsoft.com)
 
-Version 3.4.1, April 2017
+Version 3.4.2, April 2017
 
 This file outlines the steps you should take to begin using maxent to
 model species geographic distributions.  To download the program, or
@@ -118,6 +118,11 @@ 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 3.4.2:
+-----------------------------
+   Fixed bug that causes nodoclamp flag not to work for dismo's predict method for MaxEnt objects
+   
+   
 Main Changes in Version 3.4.1:
 -----------------------------
    Fixed bug that caused regularization multiplier to be have increasing effect over multiple runs

From bad787e152e113dbd351464d046eed501a3a3457 Mon Sep 17 00:00:00 2001
From: mrmaxent <mrmaxent@gmail.com>
Date: Fri, 17 Jul 2020 19:16:24 -0600
Subject: [PATCH 3/5] Update Utils.java

Change version to 3.4.2.
---
 density/Utils.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/density/Utils.java b/density/Utils.java
index ac21949..161a2fb 100644
--- a/density/Utils.java
+++ b/density/Utils.java
@@ -32,7 +32,7 @@ a copy of this software and associated documentation files (the
 
 public class Utils {
 
-    static String version = "3.4.1";
+    static String version = "3.4.2";
     static boolean interrupt=false, warnings=true;
     public static boolean verbose=false, visible=true;
     static JFrame topLevelFrame = null;

From 8fc06198e089eb1ca0c3cf158322f28107cebcbc Mon Sep 17 00:00:00 2001
From: mrmaxent <mrmaxent@gmail.com>
Date: Mon, 9 Nov 2020 11:45:16 -0700
Subject: [PATCH 4/5] Bug fix for floating point data inconsistencies

Floating point (non-integer) environmental data was being treated differently for presence and background points, resulting in the "add samples to background" option not working correctly.  This caused some response curves to have abrupt changes, typically at the edge of the predictor range.
---
 density/CachedFeature.java | 6 +++---
 density/Runner.java        | 4 ++--
 density/SampleSet2.java    | 6 +++---
 density/Utils.java         | 2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/density/CachedFeature.java b/density/CachedFeature.java
index 32f7a8d..4c91e2f 100644
--- a/density/CachedFeature.java
+++ b/density/CachedFeature.java
@@ -24,16 +24,16 @@ a copy of this software and associated documentation files (the
 package density;
 
 class CachedFeature extends Feature {
-    float[] vals=null;
+    double[] vals=null;
     Feature f;
 
     public CachedFeature(Feature f) {
 	this.f = f;
 	name = f.name;
 	n = f.n;
-	vals = new float[n];
+	vals = new double[n];
 	for (int p=0; p<n; p++)
-	    vals[p] = (float) f.eval(p);
+	    vals[p] = f.eval(p);
     }
 
     public double eval(int p) { return vals[p]; }
diff --git a/density/Runner.java b/density/Runner.java
index ba55421..54c0844 100644
--- a/density/Runner.java
+++ b/density/Runner.java
@@ -1238,14 +1238,14 @@ Feature[] featuresWithSamples(Feature[] f, Sample[] ss) {
 	double[] backgroundHash = new double[f[0].n];
 	for (int i=0; i<f[0].n; i++)
 	    for (int j=0; j<f.length; j++) 
-		backgroundHash[i] += rnd[j] * (float) f[j].eval(i);
+		backgroundHash[i] += rnd[j] * f[j].eval(i);
 	Arrays.sort(backgroundHash);
 	ArrayList samplesToAdda = new ArrayList();
 	for (int i=0; i<ss.length; i++) {
 	    double r = 0.0;
 	    for (int j=0; j<f.length; j++)
 		if (f[j].hasData(ss[i]))
-		    r += rnd[j] * (float) f[j].eval(ss[i]);
+		    r += rnd[j] * f[j].eval(ss[i]);
 	    if (is("addAllSamplesToBackground") || Arrays.binarySearch(backgroundHash, r) < 0)  // not found
 		samplesToAdda.add(ss[i]);
 	}
diff --git a/density/SampleSet2.java b/density/SampleSet2.java
index 0fef95a..ad4adbe 100644
--- a/density/SampleSet2.java
+++ b/density/SampleSet2.java
@@ -162,12 +162,12 @@ public void process() {
 		    Sample s = new Sample(-1, r, c, y, x, spid, null);
 		    
 		    int goodvals = 0;
-		    float[] data = new float[n];
+		    double[] data = new double[n];
 		    for (int j=0; j<n; j++) {
 			int idx = layerToColumn[j];
 			data[j] = NODATA_value;
 			if (idx!=-1 && idx<fields.length && !fields[SampleSet.firstEnvVar+idx].trim().equals("")) 
-			    data[j] = Float.parseFloat(fields[SampleSet.firstEnvVar+idx]);
+			    data[j] = Double.parseDouble(fields[SampleSet.firstEnvVar+idx]);
 			if (data[j] == NODATA_value && idx!=-1) {
 			    warnPartialData(x,y,sampleFileName,layers[j].name);
                             if (!params.allowpartialdata())
@@ -204,7 +204,7 @@ static void warnPartialData(double x, double y, String sampleFileName, String fi
     public void createMaps() {
 	Sample[] s = getSamples();
 	for (int i=0; i<s.length; i++) {
-	    float[] data = (float[]) datamap.get(s[i]);
+	    double[] data = (double[]) datamap.get(s[i]);
 	    HashMap map = new HashMap();
 	    for (int j=0; j<n; j++)
 		map.put(layers[j].getName(), (data[j]==SampleSet.NODATA_value) ? null : new Double(data[j]));
diff --git a/density/Utils.java b/density/Utils.java
index 161a2fb..a18cc95 100644
--- a/density/Utils.java
+++ b/density/Utils.java
@@ -32,7 +32,7 @@ a copy of this software and associated documentation files (the
 
 public class Utils {
 
-    static String version = "3.4.2";
+    static String version = "3.4.3";
     static boolean interrupt=false, warnings=true;
     public static boolean verbose=false, visible=true;
     static JFrame topLevelFrame = null;

From 2944fb58ec89fea2b4946fa09854c71e7fe341c3 Mon Sep 17 00:00:00 2001
From: mrmaxent <mrmaxent@gmail.com>
Date: Mon, 9 Nov 2020 11:52:54 -0700
Subject: [PATCH 5/5] Update readme.txt for version 3.4.3

---
 readme.txt | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/readme.txt b/readme.txt
index 23b8bc3..46f6c7e 100644
--- a/readme.txt
+++ b/readme.txt
@@ -7,7 +7,7 @@ Miro Dudik          (mdudik@microsoft.com)
 Steven Phillips     (mrmaxent@gmail.com)
 Rob Schapire        (schapire@microsoft.com)
 
-Version 3.4.2, April 2017
+Version 3.4.3, November 2020
 
 This file outlines the steps you should take to begin using maxent to
 model species geographic distributions.  To download the program, or
@@ -118,6 +118,11 @@ 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 3.4.3:
+-----------------------------
+   Fixed a bug that was causing abrupt changes in response curves for some floating -point predictor variables,
+     due to the "add samples to background" option not adding all samples for floating-point predictors.
+
 Main Changes in Version 3.4.2:
 -----------------------------
    Fixed bug that causes nodoclamp flag not to work for dismo's predict method for MaxEnt objects