more calculator edits and added coverage and whittaker

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1c8df765aba58235fdb4c557be80834880aa1da0..6fd4a0656cc57fa33f0f78be7819368044d31d22 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -115,6 +115,8 @@
                7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412F480F8D21B600381DD0 /* slibshuff.cpp */; };
                7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */; };
                7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */; };
+               7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */; };
+               7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; };
                8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
                A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; };
                A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
@@ -123,7 +125,6 @@
                EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; };
                EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; };
                EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB6E68180F5F1C780044E17B /* qstat.cpp */; };
-               EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */; };
                EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303EA0F534D9400E8EF26 /* logsd.cpp */; };
                EB9303F90F53517300E8EF26 /* geom.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303F80F53517300E8EF26 /* geom.cpp */; };
 /* End PBXBuildFile section */
@@ -369,6 +370,11 @@
                7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = "<group>"; };
                7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = "<group>"; };
                7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = "<group>"; };
+               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = "<group>"; };
+               7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
+               7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = "<group>"; };
+               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
+               7EC3D4540FA0FFF900338DA5 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
                8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = "<group>"; };
                A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
@@ -385,8 +391,6 @@
                EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
                EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
                EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
-               EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = "<group>"; };
-               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = "<group>"; };
                EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
                EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
                EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
@@ -537,10 +541,13 @@
                                37D928220F21331F001D4494 /* sharedace.cpp */,
                                37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
                                37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
+                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
+                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
+                               7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
+                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
+                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
                                375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
                                375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
-                               EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
-                               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
                                37D928250F21331F001D4494 /* sharedchao1.h */,
                                37D928240F21331F001D4494 /* sharedchao1.cpp */,
                                37D928290F21331F001D4494 /* sharedjabund.h */,
@@ -851,7 +858,6 @@
                                EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
                                EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
                                EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
-                               EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
                                375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
                                375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
                                375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
@@ -877,6 +883,8 @@
                                375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
                                375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */,
                                375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
+                               7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */,
+                               7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 56611a8f1e5af0eea6b64eef76e3ec1588b7298f..5c2e1714d97612bb595044fc566d61bd47c540ec 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -35,7 +35,7 @@ BootSharedCommand::BootSharedCommand(){
                        if (validCalculator->isValidCalculator("boot", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "jabund") {    
                                        treeCalculators.push_back(new JAbund());
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        treeCalculators.push_back(new SorAbund());
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        treeCalculators.push_back(new Jclass());

diff --git a/bstick.cpp b/bstick.cpp
index 7f12d1d826fa0baf28b4726c3dbd0abf0c9b660c..eabf087ba0b7def92129c52e1f60257b93ca8b7f 100644 (file)
--- a/bstick.cpp
+++ b/bstick.cpp
@@ -46,7 +46,7 @@ RAbundVector BStick::getRAbundVector(SAbundVector* rank){
 /***************************************************************************/
 EstOutput BStick::getValues(SAbundVector* rank){
        try {
-               data.resize(2,0);
+               data.resize(3,0);
                rdata = getRAbundVector(rank);
                double numInd = (double)rdata.getNumSeqs();
                double numSpec = (double)rdata.getNumBins();
@@ -64,27 +64,16 @@ EstOutput BStick::getValues(SAbundVector* rank){
                                maxDiff = diff;
                }
                
-               double DStatistic = maxDiff/numInd;
-               double critVal = 0;
-               /*cout << "BStick:\n";
-               cout << "D-Statistic = " << DStatistic << "\n";
-               cout << "Critical value for 95% confidence interval = ";*/
-               if(rdata.size() > 20)
-               {
-                       critVal = .886/sqrt(rdata.size());
-               }
-               else
-               {
-                       KOSTable table;
-                       critVal = table.getConfLimit(numSpec);
-               }
+               data[0] = maxDiff/numInd;
+               data[1] = 0.886/sqrt(rdata.size());
+               data[2] = 1.031/sqrt(rdata.size());
+
                /*cout << critVal << "\n";
                cout << "If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n\n";*/
                
-               data[0] = DStatistic;
-               data[1] = critVal;
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+               if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
                
                return data;
        }

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index ad392e7535ece7e6617f63e5573c7e577cfe47da..bc0609ef539e119addffbb531d7f8f54f44f747b 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -20,7 +20,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
 #include "sharednseqs.h"
 #include "sharedochiai.h"
 #include "sharedanderbergs.h"
@@ -54,7 +54,7 @@ CollectSharedCommand::CollectSharedCommand(){
                                        cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
                                }else if (globaldata->Estimators[i] == "jabund") {      
                                        cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
@@ -70,8 +70,8 @@ CollectSharedCommand::CollectSharedCommand(){
                                        cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
                                }else if (globaldata->Estimators[i] == "kstest") { 
                                        cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
-                               }else if (globaldata->Estimators[i] == "bdiversity") { 
-                                       cDisplays.push_back(new CollectDisplay(new BDiversity(), new SharedOneColumnFile(fileNameRoot+"bdiversity")));
+                               }else if (globaldata->Estimators[i] == "whittaker") { 
+                                       cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
                                }else if (globaldata->Estimators[i] == "sharednseqs") { 
                                        cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
                                }else if (globaldata->Estimators[i] == "ochiai") { 

diff --git a/coverage.cpp b/coverage.cpp
new file mode 100644 (file)
index 0000000..a93cbf3
--- /dev/null
+++ b/coverage.cpp
@@ -0,0 +1,33 @@
+/*
+ *  coverage.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/22/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "coverage.h"
+
+/***********************************************************************/
+EstOutput Coverage::getValues(SAbundVector* rank){
+
+       try {
+               data.resize(1,0);
+
+               data[0] = 1. - rank->get(1) / (double)rank->getNumSeqs();
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+};
+
+
+/***********************************************************************/

diff --git a/coverage.h b/coverage.h
new file mode 100644 (file)
index 0000000..c17f8e7
--- /dev/null
+++ b/coverage.h
@@ -0,0 +1,31 @@
+#ifndef COVERAGE_H
+#define COVERAGE_H
+
+/*
+ *  coverage.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/22/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/* This class implements the coverage estimator on single group. 
+ It is a child of the calculator class. */
+
+/***********************************************************************/
+
+class Coverage : public Calculator  {
+       
+public: 
+       Coverage() : Calculator("coverage", 1) {};
+       EstOutput getValues(SAbundVector*);     
+       EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
+};
+
+
+/***********************************************************************/
+
+#endif

diff --git a/geom.cpp b/geom.cpp
index 31580db15b7bbb08b648cd10ff3c0bcf4cd98a10..755c1ec81cd282224ad44f574ec13627a9fd1408 100644 (file)
--- a/geom.cpp
+++ b/geom.cpp
@@ -75,26 +75,18 @@ EstOutput Geom::getValues(SAbundVector* rank){
                        
                }
 
-               double DStatistic = maxDiff/numInd;
-               double critVal = 0;
+
                /*cout << "Geom:\n";
                cout << "D-Statistic = " << DStatistic << "\n";
                cout << "Critical value for 95% confidence interval = ";*/
-               if(rdata.size() > 20)
-               {
-                       data[1] = 1.031/sqrt(rdata.size());
-                       data[2] = 0.886/sqrt(rdata.size());
-               }
-               else
-               {
-                       KOSTable table;
-                       critVal = table.getConfLimit(numSpec);
-               }
+
+               data[0] = maxDiff/numInd;
+               data[1] = 0.886/sqrt(numSpec);
+               data[2] = 1.031/sqrt(numSpec);
+
                /*cout << critVal << "\n";
                cout << "If D-Statistic is less than the critical value then the data fits the Geometric Series model w/ 95% confidence.\n\n";*/
-               
-               data[0] = DStatistic;
-               
+                               
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
                if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }

diff --git a/geom.h b/geom.h
index 05fc0d76d3e6cd89b1c8b53b3875fcd2634c6f60..f88cb4acb33d2cf4027062f309329f3bc9f9aaf6 100644 (file)
--- a/geom.h
+++ b/geom.h
@@ -11,7 +11,7 @@
  */
 #include "calculator.h"
 
-/* This class implements the LogSD estimator on single group. 
+/* This class implements the geometric estimator on single group. 
 It is a child of the calculator class. */
 
 /***********************************************************************/

diff --git a/globaldata.cpp b/globaldata.cpp
index 714b5ad2e447a579872f9f5b8d8c7886303a8391..312b314120adf6eef3beb5d09bf21517e103c5cc 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -173,7 +173,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "collect.shared") {
-                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -183,7 +183,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "summary.shared") {
-                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 6cf2134451e97369bab550382845a056387491d3..ac013303de6e837847416e343295ee613593f12e 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -86,8 +86,8 @@ int HelpCommand::execute(){
                cout << "The collect.shared command parameters are label, line, freq, jumble, calc and groups.  No parameters are required, but you may not use " << "\n";
                cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
                cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
-               cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, jumble=1, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
-               cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n";
+               cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, jumble=1, groups=B-C, calc=sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
+               cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n";
                cout << "The default value for groups is all the groups in your groupfile." << "\n";
                validCalcs->printCalc("shared", cout);
                cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
@@ -150,9 +150,9 @@ int HelpCommand::execute(){
                cout << "The summary.shared command parameters are label, line, jumble and calc.  No parameters are required, but you may not use " << "\n";
                cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
                cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
-               cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
+               cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, groups=B-C, calc=sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
                validCalcs->printCalc("sharedsummary", cout);
-               cout << "The default value for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble) and calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
+               cout << "The default value for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble) and calc is sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
                cout << "The default value for groups is all the groups in your groupfile." << "\n";
                cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
                cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups." << "\n";
@@ -232,7 +232,7 @@ int HelpCommand::execute(){
                cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
                cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
                cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
-               cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorensonabund)." << "\n";
+               cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
                cout << "The default value for groups is all the groups in your groupfile." << "\n";
                cout << "There is no default value for calc." << "\n";
                validCalcs->printCalc("treegroup", cout);
@@ -244,7 +244,7 @@ int HelpCommand::execute(){
                cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
                cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
                cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
-               cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorensonabund, iters=100)." << "\n";
+               cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
                cout << "The default value for groups is all the groups in your groupfile." << "\n";
                cout << "There is no default value for calc. The default for iters is 1000." << "\n";
                validCalcs->printCalc("boot", cout);

diff --git a/logsd.cpp b/logsd.cpp
index 14d2e442fa2bea0a6e153dc310b59d687b51b642..e959ab8cb8c1bcce52350331653903345b89c48b 100644 (file)
--- a/logsd.cpp
+++ b/logsd.cpp
@@ -78,17 +78,21 @@ EstOutput LogSD::getValues(SAbundVector* rank){
                        if(diff > maxDiff)
                                maxDiff = diff;
                }
-               
-               double DStatistic = (maxDiff + .5)/numSpec;
+
+
                /*cout << "LogSD:\n";
                cout << "D Test Statistic = " << DStatistic << "\n";
                cout << ".05 confidence value = " << .89196/sqrt(numSpec) << "\n";
                cout << "If D Test Statistic is greater than the critical value then the data fits the Log Series Distribution model w/ 95% confidence.\n\n";*/
                
-               data[0] = DStatistic;
-               data[1] = .89196/sqrt(numSpec);
+               data[0] = (maxDiff + .5)/numSpec;
+               data[1] = 0.886/sqrt(numSpec);
+               data[2] = 1.031/sqrt(numSpec);
+               
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+               if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
+               
                return data;
        }
        catch(exception& e) {

diff --git a/sharedace.cpp b/sharedace.cpp
index 791b52657859802922d7735d0a52a9144edf368e..87305965d135f8ac6b88c922c100dc0ddac91118 100644 (file)
--- a/sharedace.cpp
+++ b/sharedace.cpp
@@ -77,13 +77,13 @@ EstOutput SharedAce::getValues(SharedRAbundVector* shared1, SharedRAbundVector*
                C12 = 1 - (C12Numerator /(float) t11);
                part1 = S12Rare / (float)C12;
                part2 = 1 / (float)C12;
-       
+
                //calculate gammas
                Gamma1 = ((S12Rare * t21) / (float)((C12 * t10 * t11)) - 1);
                Gamma2 = ((S12Rare * t12) / (float)((C12 * t01 * t11)) - 1);
                Gamma3 = ((S12Rare / C12) * (S12Rare / C12)) * ( t22 / (float)(t10 * t01 * t11));
                Gamma3 = Gamma3 - ((S12Rare * t11) / (float)(C12 * t01 * t10)) - Gamma1 - Gamma2;       
-       
+
                if (isnan(Gamma1) || isinf(Gamma1)) { Gamma1 = 0; }
                if (isnan(Gamma2) || isinf(Gamma2)) { Gamma2 = 0; }
                if (isnan(Gamma3) || isinf(Gamma3)) { Gamma3 = 0; }

diff --git a/sharedbdiversity.cpp b/sharedbdiversity.cpp
deleted file mode 100644 (file)
index ae2753d..0000000
--- a/sharedbdiversity.cpp
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- *  bdiversity.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 3/13/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedbdiversity.h"
-
-/***********************************************************************/
-
-double BDiversity::whitt(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
-       double nz1 = (double)shared1->numNZ();
-       double nz2 = (double)shared2->numNZ();
-       double sum = nz1;
-       for(int i = 1; i < shared1->size(); i++)
-       {
-               if(shared1->get(i).abundance == 0 && shared2->get(i).abundance != 0)
-                       sum++;
-                       }
-       return 2*sum/(nz1+nz2)-1;
-}
-
-/***********************************************************************/
-
-double BDiversity::ms(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
-       double a = 0;
-       double b = 0;
-       double c = 0;
-       for(int i = 1; i < shared1->size(); i++)
-       {
-               int abund1 = shared1->get(i).abundance;
-               int abund2 = shared2->get(i).abundance;
-               
-               if(abund1 > 0 && abund2 > 0)
-                       a++;
-               else if(abund1 > 0 && abund2 == 0)
-                       b++;
-               else if(abund1 == 0 && abund2 > 0)
-                       c++;
-       }
-       return (b+c)/(a+b+c);
-}
-
-/***********************************************************************/
-
-double BDiversity::sor(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
-       double sum = 0;
-       double asum = 0;
-       double bsum = 0;
-       for(int i = 1; i < shared1->size(); i++)
-       {
-               int abund1 = shared1->get(i).abundance;
-               int abund2 = shared2->get(i).abundance;
-               
-               asum += abund1;
-               bsum += abund2;
-               if(abund1 >= abund2)
-                       sum += abund2;
-               else
-                       sum += abund1;
-       }
-       return 2*sum/(asum+bsum);
-}
-
-/***********************************************************************/
-
-double BDiversity::mor(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
-       double multSum = 0;
-       double powSum1 = 0;
-       double powSum2 = 0;
-       double ind1 = 0;
-       double ind2 = 0;
-       for(int i = 1; i < shared1->size(); i++)
-       {
-               double abund1 = (double)shared1->get(i).abundance;
-               double abund2 = (double)shared2->get(i).abundance;
-               multSum += abund1*abund2;
-               powSum1 += pow(abund1, 2);
-               powSum2 += pow(abund2, 2);
-               ind1 += abund1;
-               ind2 += abund2;
-       }
-       return 2*multSum / ((powSum1/pow(ind1, 2) + powSum2/pow(ind2, 2)) * (ind1*ind2));
-}
-/***********************************************************************/
-       
-EstOutput BDiversity::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
-       try {
-               data.resize(4,0);
-               
-               double whitt1 = whitt(shared1, shared2);
-               double jac1 = 1-ms(shared1, shared2);
-               double sor1 = sor(shared1, shared2);
-               double mor1 = mor(shared1, shared2);
-               /*cout << "Whittaker's Measure: " << whitt1 << "\n";
-               cout << "Marczewski-Steinhaus distance: " << jac1 << "\n";
-               cout << "Sorensen index: " << sor1 << "\n";
-               cout << "Morisita-Horn index: " << mor1 << "\n";*/
-               
-               data[0] = whitt1;
-               data[1] = jac1;
-               data[2] = sor1;
-               data[3] = mor1;
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-               if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
-               if (isnan(data[2]) || isinf(data[0])) { data[2] = 0; }
-               if (isnan(data[3]) || isinf(data[1])) { data[3] = 0; }
-               
-               return data;
-       }
-               
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the BDiversity class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-}
-
-/***********************************************************************/
\ No newline at end of file

diff --git a/sharedbdiversity.h b/sharedbdiversity.h
deleted file mode 100644 (file)
index 07b4fe0..0000000
--- a/sharedbdiversity.h
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef BDIVERSITY_H
-#define BDIVERSITY_H
-/*
- *  bdiversity.h
- *  Mothur
- *
- *  Created by Thomas Ryabin on 3/13/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-#include "calculator.h"
-
-/*This class implements the BDiversity estimator on 2 groups. 
-It is a child of the calculator class.*/ 
-
-/***********************************************************************/
-
-class BDiversity : public Calculator  {
-       
-public:
-       BDiversity() : Calculator("bdiversity", 3) {};
-       EstOutput getValues(SAbundVector*) {return data;};
-       EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
-private:
-       double whitt(SharedRAbundVector*, SharedRAbundVector*);
-       double ms(SharedRAbundVector*, SharedRAbundVector*);
-       double sor(SharedRAbundVector*, SharedRAbundVector*);
-       double mor(SharedRAbundVector*, SharedRAbundVector*);
-};
-
-/***********************************************************************/
-
-#endif
\ No newline at end of file

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 824115f0f856e47278f7f06c6c2d64b40f3c09a0..02e241180d2d4855309a8f8aa01a279963b506e5 100644 (file)
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -39,6 +39,7 @@ EstOutput SharedChao1::getValues(SharedRAbundVector* sharedA, SharedRAbundVector
                                //does B have one or two
                                if (tempB == 1)                 { f1B++; }
                                else if (tempB == 2)    { f2B++; }
+
                        }
                }
                

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index eea7b25c4ade2bd6a98f5cea0eaabd9b1787ede8..e6a7d9a7363a5d9a71d32fad38d6172248b0934a 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -21,7 +21,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
 #include "sharedochiai.h"
 #include "sharedanderbergs.h"
 #include "sharedkulczynski.h"
@@ -53,7 +53,7 @@ SummarySharedCommand::SummarySharedCommand(){
                                        sumCalculators.push_back(new SharedAce());
                                }else if (globaldata->Estimators[i] == "jabund") {      
                                        sumCalculators.push_back(new JAbund());
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        sumCalculators.push_back(new SorAbund());
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        sumCalculators.push_back(new Jclass());
@@ -86,8 +86,8 @@ SummarySharedCommand::SummarySharedCommand(){
                                }else if (globaldata->Estimators[i] == "braycurtis") { 
                                        sumCalculators.push_back(new BrayCurtis());
                                }
-                               else if (globaldata->Estimators[i] == "bdiversity") { 
-                                       sumCalculators.push_back(new BDiversity());
+                               else if (globaldata->Estimators[i] == "whittaker") { 
+                                       sumCalculators.push_back(new Whittaker());
                                }
                                
                        }

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 6393684f2e79380788553e978504d0f0d306253f..7791d5ecd913c431114a9de5afb2ca651ec1232c 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -33,7 +33,7 @@ TreeGroupCommand::TreeGroupCommand(){
                        if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "jabund") {    
                                        treeCalculators.push_back(new JAbund());
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        treeCalculators.push_back(new SorAbund());
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        treeCalculators.push_back(new Jclass());

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 25cc5c5868e46a9659fc88e924a6f03baf48b7da..72d404147a3b71bf9a6b1efe82098f943558adf4 100644 (file)
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -208,7 +208,7 @@ void ValidCalculators::initialShared() {
                shared["sharedchao"]                    = "sharedchao";
                shared["sharedace"]                             = "sharedace";
                shared["jabund"]                                = "jabund";
-               shared["sorensonabund"]                 = "sorensonabund";
+               shared["sorabund"]                      = "sorabund";
                shared["jclass"]                                = "jclass";
                shared["sorclass"]                              = "sorclass";
                shared["jest"]                                  = "jest";
@@ -216,7 +216,7 @@ void ValidCalculators::initialShared() {
                shared["thetayc"]                               = "thetayc";
                shared["thetan"]                                = "thetan";
                shared["kstest"]                                = "kstest";
-               shared["bdiversity"]                    = "bdiversity";
+               shared["whittaker"]                         = "whittaker";
                shared["sharednseqs"]                   = "sharednseqs";
                shared["ochiai"]                                = "ochiai";
                shared["anderberg"]                             = "anderberg";
@@ -276,7 +276,7 @@ void ValidCalculators::initialSummary() {
                summary["bergerparker"] = "bergerparker";
                summary["geometric"]    = "geometric";
                summary["bootstrap"]    = "bootstrap";
-               summary["logsd"]        = "logsd";
+               summary["logseries"]    = "logseries";
                summary["qstat"]        = "qstat";
                summary["bstick"]       = "bstick";
                summary["nseqs"]                = "nseqs";
@@ -300,7 +300,7 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["sharedchao"]                             = "sharedchao";
                sharedsummary["sharedace"]                              = "sharedace";
                sharedsummary["jabund"]                                 = "jabund";
-               sharedsummary["sorensonabund"]                  = "sorensonabund";
+               sharedsummary["sorabund"]                       = "sorabund";
                sharedsummary["jclass"]                                 = "jclass";
                sharedsummary["sorclass"]                               = "sorclass";
                sharedsummary["jest"]                                   = "jest";
@@ -308,7 +308,7 @@ void ValidCalculators::initialSharedSummary() {
                sharedsummary["thetayc"]                                = "thetayc";
                sharedsummary["thetan"]                                 = "thetan";
                sharedsummary["kstest"]                                 = "kstest";
-               sharedsummary["bdiversity"]                             = "bdiversity";
+               sharedsummary["whittaker"]                              = "whittaker";
                sharedsummary["sharednseqs"]                    = "sharednseqs";
                sharedsummary["ochiai"]                                 = "ochiai";
                sharedsummary["anderberg"]                              = "anderberg";
@@ -390,7 +390,7 @@ void ValidCalculators::initialVennShared() {
 void ValidCalculators::initialTreeGroups() {
        try {   
                treegroup["jabund"]                                     = "jabund";
-               treegroup["sorensonabund"]                      = "sorensonabund";
+               treegroup["sorabund"]                   = "sorabund";
                treegroup["jclass"]                                     = "jclass";
                treegroup["sorclass"]                           = "sorclass";
                treegroup["jest"]                                       = "jest";
@@ -412,7 +412,7 @@ void ValidCalculators::initialTreeGroups() {
 void ValidCalculators::initialBoot() {
        try {   
                boot["jabund"]                          = "jabund";
-               boot["sorensonabund"]           = "sorensonabund";
+               boot["sorabund"]                = "sorabund";
                boot["jclass"]                          = "jclass";
                boot["sorclass"]                        = "orclass";
                boot["jest"]                            = "jest";

diff --git a/whittaker.cpp b/whittaker.cpp
new file mode 100644 (file)
index 0000000..95f1c9c
--- /dev/null
+++ b/whittaker.cpp
@@ -0,0 +1,39 @@
+/*
+ *  whittaker.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/23/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "whittaker.h"
+
+/***********************************************************************/
+
+EstOutput Whittaker::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+       try{
+               data.resize(1);
+
+               int countA = 0;
+               int countB = 0;
+               int sTotal = shared1->getNumBins();
+               for(int i=0;i<sTotal;i++){
+                       if(shared1->getAbundance(i) != 0){      countA++;       }
+                       if(shared2->getAbundance(i) != 0){      countB++;       }               
+               }
+               
+               data[0] = 2*sTotal/(float)(countA+countB)-1;
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Whittaker class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Whittaker class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/
\ No newline at end of file

diff --git a/whittaker.h b/whittaker.h
new file mode 100644 (file)
index 0000000..22bf788
--- /dev/null
+++ b/whittaker.h
@@ -0,0 +1,29 @@
+#ifndef WHITTAKER_H
+#define WHITTAKER_H
+/*
+ *  whittaker.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 3/13/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/*This class implements the Whittaker estimator on 2 groups. 
+ It is a child of the calculator class.*/ 
+
+/***********************************************************************/
+
+class Whittaker : public Calculator  {
+       
+public:
+       Whittaker() : Calculator("whittaker", 3) {};
+       EstOutput getValues(SAbundVector*) {return data;};
+       EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+
+};
+
+/***********************************************************************/
+
+#endif
\ No newline at end of file