--- /dev/null
+/*
+ * cooccurrencecommand.cpp
+ * Mothur
+ *
+ * Created by kiverson on 1/2/12.
+ * Copyright 2012 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "cooccurrencecommand.h"
+
+//**********************************************************************************************************************
+vector<string> CooccurrenceCommand::setParameters() {
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "",false,false); parameters.push_back(pmetric);
+ CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "",false,false); parameters.push_back(pmatrix);
+ CommandParameter pruns("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pruns);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string CooccurrenceCommand::getHelpString(){
+ try {
+ string helpString = "help!";
+
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CooccurrenceCommand::CooccurrenceCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "CooccurrenceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CooccurrenceCommand::CooccurrenceCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); }
+
+
+ metric = validParameter.validFile(parameters, "metric", false); if (metric == "not found") { metric = "cscore"; }
+
+ if ((metric != "cscore") && (metric != "checker") && (metric != "combo") && (metric != "vratio")) {
+ m->mothurOut("[ERROR]: " + metric + " is not a valid metric option for the cooccurrence command. Choices are cscore, checker, combo, vratio."); m->mothurOutEndLine(); abort = true;
+ }
+
+ matrix = validParameter.validFile(parameters, "matrix", false); if (matrix == "not found") { matrix = "sim2"; }
+
+ if ((matrix != "sim1") && (matrix != "sim2") && (matrix != "sim3") && (matrix != "sim4") && (matrix != "sim5" ) && (matrix != "sim6" ) && (matrix != "sim7" ) && (matrix != "sim8" ) && (matrix != "sim9" )) {
+ m->mothurOut("[ERROR]: " + matrix + " is not a valid matrix option for the cooccurrence command. Choices are sim1, sim2, sim3, sim4, sim5, sim6, sim7, sim8, sim9."); m->mothurOutEndLine(); abort = true;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+ m->setGroups(Groups);
+
+ string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, runs);
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "CooccurrenceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CooccurrenceCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ ofstream out;
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary";
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ out << "metric\tlabel\tScore\tpValue\n";
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ getCooccurrence(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ getCooccurrence(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+
+ if (m->control_pressed) { outputTypes.clear(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) { delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ getCooccurrence(lookup, out);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ out.close();
+
+ //reset groups parameter
+ delete input;
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+ try {
+ int numOTUS = thisLookUp[0]->getNumBins();
+ vector< vector<int> > initmatrix (thisLookUp.size());
+ vector< vector<int> > co_matrix (thisLookUp[0]->getNumBins());
+ for (int i = 0; i < thisLookUp[0]->getNumBins(); i++) { co_matrix[i].resize((thisLookUp.size()), 0); }
+ for (int i = 0; i < thisLookUp.size(); i++) { initmatrix[i].resize((thisLookUp[i]->getNumBins()), 0); }
+ vector<int> columntotal(thisLookUp.size(), 0);
+ vector<int> rowtotal(numOTUS, 0);
+
+ int rowcount = 0;
+ for (int i = 0; i < thisLookUp.size(); i++) {
+ for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
+ if (m->control_pressed) { return 0; }
+ int abund = thisLookUp[i]->getAbundance(j);
+
+ if(abund > 0) {
+ initmatrix[i][j] = 1;
+ co_matrix[j][i] = 1;
+ rowcount++;
+ columntotal[j]++;
+ }
+ }
+ rowtotal[i] = rowcount;
+ rowcount = 0;
+ }
+
+ //nrows is ncols of inital matrix. All the functions need this value. They assume the transposition has already taken place and nrows and ncols refer to that matrix.
+ //comatrix and initmatrix are still vectors of vectors of ints as in the original script. The abundancevector is only what was read in ie not a co-occurrence matrix!
+ int ncols = numOTUS;//rows of inital matrix
+ int nrows = thisLookUp.size();//OTUs
+ double initscore = 0.0;
+ //transpose matrix
+ int newmatrows = ncols;
+ int newmatcols = nrows;
+
+ //swap for transposed matrix
+ nrows = newmatrows;//ncols;
+ ncols = newmatcols;//nrows;
+
+ vector<int> initcolumntotal(ncols, 0);
+ vector<int> initrowtotal(nrows, 0);
+ vector<double> stats;
+
+ TrialSwap2 trial;
+
+ initcolumntotal = rowtotal;
+ initrowtotal = columntotal;
+ trial.update_row_col_totals(co_matrix, rowtotal, columntotal);
+
+ if (metric == "cscore") { initscore = trial.calc_c_score(co_matrix, rowtotal); }
+ else if (metric == "checker") { initscore = trial.calc_checker(co_matrix, rowtotal); }
+ else if (metric == "vratio") { initscore = trial.calc_vratio(rowtotal, columntotal); }
+ else if (metric == "combo") { initscore = trial.calc_combo(co_matrix); }
+ else { m->mothurOut("[ERROR]: No metric selected!\n"); m->control_pressed = true; return 1; }
+
+ m->mothurOut("Initial c score: " + toString(initscore)); m->mothurOutEndLine();
+
+ //nullmatrix burn in
+ for(int i=0;i<10000;i++) {
+ if (m->control_pressed) { return 0; }
+ if (matrix == "sim1") {
+ trial.sim1(co_matrix);
+ }else if (matrix == "sim2") {
+ trial.sim2(co_matrix);
+ }else if (matrix == "sim3") {
+ trial.sim3(initmatrix);
+ co_matrix = initmatrix;
+ }else if (matrix == "sim4") {
+ trial.sim4(columntotal, rowtotal, co_matrix);
+ }else if (matrix == "sim5") {
+ trial.sim5(initcolumntotal, initrowtotal, initmatrix);
+ trial.transpose_matrix(initmatrix,co_matrix);
+ }else if (matrix == "sim6") {
+ trial.sim6(columntotal, co_matrix);
+ }else if (matrix == "sim7") {
+ trial.sim7(initcolumntotal, initmatrix);
+ co_matrix = initmatrix;
+ }else if (matrix == "sim8") {
+ trial.sim8(columntotal, rowtotal, co_matrix);
+ }else if (matrix == "sim9") {
+ trial.swap_checkerboards (co_matrix);
+ }else{
+ m->mothurOut("[ERROR]: No model selected! \n");
+ m->control_pressed = true;
+ }
+ }
+
+ //run
+ for(int i=0;i<runs;i++) {
+ if (m->control_pressed) { return 0; }
+ //calc metric of nullmatrix
+ if (matrix == "sim1") {
+ trial.sim1(co_matrix);
+ }else if (matrix == "sim2") {
+ trial.sim2(co_matrix);
+ }else if (matrix == "sim3") {
+ trial.sim3(initmatrix);
+ co_matrix = initmatrix;
+ }else if (matrix == "sim4") {
+ trial.sim4(columntotal, rowtotal, co_matrix);
+ }else if (matrix == "sim5") {
+ trial.sim5(initcolumntotal, initrowtotal, initmatrix);
+ trial.transpose_matrix(initmatrix,co_matrix);
+ }else if (matrix == "sim6") {
+ trial.sim6(columntotal, co_matrix);
+ }else if (matrix == "sim7") {
+ trial.sim7(initcolumntotal, initmatrix);
+ co_matrix = initmatrix;
+ }else if (matrix == "sim8") {
+ trial.sim8(columntotal, rowtotal, co_matrix);
+ }else if (matrix == "sim9") {
+ trial.swap_checkerboards (co_matrix);
+ }else{
+ m->mothurOut("[ERROR]: No model selected! \n");
+ m->control_pressed = true;
+ }
+ //
+ //
+ trial.update_row_col_totals(co_matrix, rowtotal, columntotal);
+
+ if (metric == "cscore") {
+ stats.push_back(trial.calc_c_score(co_matrix, rowtotal));
+ }else if (metric == "checker") {
+ stats.push_back(trial.calc_checker(co_matrix, rowtotal));
+ }else if (metric == "vratio") {
+ stats.push_back(trial.calc_vratio(rowtotal, columntotal));
+ }else if (metric == "combo") {
+ stats.push_back(trial.calc_combo(co_matrix));
+ }else {
+ m->mothurOut("[ERROR]: No metric selected!\n");
+ m->control_pressed = true;
+ return 1;
+ }
+
+ }
+
+ double total = 0.0;
+ for (int i=0; i<stats.size();i++) { total+=stats[i]; }
+
+ double nullMean = double (total/(double)stats.size());
+
+ m->mothurOutEndLine(); m->mothurOut("average metric score: " + toString(nullMean)); m->mothurOutEndLine();
+
+ double pvalue = 0.0;
+ if (metric == "cscore" || metric == "checker") { pvalue = trial.calc_pvalue_greaterthan (stats, initscore); }
+ else{ pvalue = trial.calc_pvalue_lessthan (stats, initscore); }
+
+ m->mothurOut("pvalue: " + toString(pvalue)); m->mothurOutEndLine();
+ out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << pvalue << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "Cooccurrence");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
--- /dev/null
+#include "trialswap2.h"
+
+
+//The sum_of_squares, havel_hakimi and calc_c_score algorithms have been adapted from I. Miklos and J. Podani. 2004. Randomization of presence-absence matrices: comments and new algorithms. Ecology 85:86-92.
+
+
+/**************************************************************************************************/
+int TrialSwap2::intrand(int n){
+ try {
+ double z;
+
+ z = (double)random() * (double)n / (double)RAND_MAX;
+ if(z>=n)
+ z=n-1;
+ if(z<0)
+ z=0;
+ return((int)floor(z));
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "intrand");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/* completely random matrix, all column and row totals are variable, matrix size is the same
+ *
+ *
+ */
+/**************************************************************************************************/
+int TrialSwap2::sim1(vector<vector<int> > &co_matrix){
+ try {
+ vector<int> randRow;
+ vector<vector<int> > tmpmatrix;
+ int nrows = co_matrix.size();
+ int ncols = co_matrix[0].size();
+
+ //clear co_matrix
+ // for(i=0;i<nrows;i++)
+ // {
+ // co_matrix.clear();
+ // }
+
+ //cout << "building matrix" << endl;
+ for(int i=0;i<nrows;i++){
+ if (m->control_pressed) { break; }
+
+ for(int j=0;j<ncols;j++){
+ double randNum = rand() / double(RAND_MAX);
+ //cout << randNum << endl;
+
+ if(randNum > 0.5) {
+ randRow.push_back(1);
+ }else{
+ randRow.push_back(0);
+ }
+ }
+ tmpmatrix.push_back(randRow);
+ randRow.clear();
+ //cout << endl;
+ }
+ co_matrix = tmpmatrix;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim1");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ *row sums fixed, columns equiprobable
+ */
+void TrialSwap2::sim2(vector<vector<int> > &co_matrix)
+{
+ try {
+
+ for(int i=0;i<co_matrix.size();i++)
+ {
+ if (m->control_pressed) { break; }
+ random_shuffle( co_matrix[i].begin(), co_matrix[i].end() );
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim2");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::sim2plus(vector<int> rowtotal, vector<vector<int> > &co_matrix)
+{
+ try {
+ int nrows = co_matrix.size();
+ int ncols = co_matrix[0].size();
+ double cellprob = 1.0/ncols;
+ vector<double> cellprobvec;
+ vector<int> tmprow;
+ vector<vector<int> > tmpmatrix;
+ //double randNum;
+
+ double start = 0.0;
+
+ for(int i=0; i<ncols; i++)
+ {
+ if (m->control_pressed) { return 0; }
+ cellprobvec.push_back(start + cellprob);
+ start = cellprobvec[i];
+ }
+
+ for(int i=0; i<nrows; i++)
+ {
+ tmprow.assign(ncols, 0);
+
+ while( accumulate( tmprow.begin(), tmprow.end(), 0 ) < rowtotal[i])
+ {
+ if (m->control_pressed) { return 0; }
+ double randNum = rand() / double(RAND_MAX);
+ //cout << randNum << endl;
+ if(randNum <= cellprobvec[0])
+ {
+ tmprow[0] = 1;
+ continue;
+ }
+ for(int j=1;j<ncols;j++)
+ {
+ //cout << range[j] << endl;
+ if(randNum <= cellprobvec[j] && randNum > cellprobvec[j-1] && tmprow[j] != 1)
+ {
+ tmprow[j] = 1;
+ }
+ }
+ }
+ tmpmatrix.push_back(tmprow);
+ tmprow.clear();
+ }
+ co_matrix = tmpmatrix;
+ tmpmatrix.clear();
+ cellprobvec.clear();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim2plus");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ * same as sim2 but using initmatrix which is the initial co-occurrence matrix before transposition
+ * may have to be changed depending on what matrix 'seed' is used. One way to use is to transpose
+ * every null matrix before using an index and use the random matrix as a seed for the next null.
+ */
+/**************************************************************************************************/
+void TrialSwap2::sim3(vector<vector<int> > &initmatrix)
+{
+ try {
+ for(int i=0;i<initmatrix.size();i++)
+ {
+ if (m->control_pressed) { break; }
+ random_shuffle( initmatrix[i].begin(), initmatrix[i].end() );
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim3");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ *
+ *
+ *
+ */
+/**************************************************************************************************/
+int TrialSwap2::sim4(vector<int> columntotal, vector<int> rowtotal, vector<vector<int> > &co_matrix)
+{
+ try {
+ vector<double> colProb;
+ vector<int> tmprow;//(ncols, 7);
+ vector<vector<int> > tmpmatrix;
+ vector<double> range;
+ vector<double> randNums;
+ int ncols = columntotal.size();
+ int nrows = rowtotal.size();
+ tmprow.clear();
+
+ double colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
+ //cout << "col sum: " << colSum << endl;
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ colProb.push_back(columntotal[i]/colSum);
+ }
+
+ double start = 0.0;
+
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ range.push_back(start + colProb[i]);
+ start = range[i];
+ }
+
+ for(int i=0;i<nrows;i++)
+ {
+ tmprow.assign(ncols, 0);
+ if (m->control_pressed) { return 0; }
+
+ while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < rowtotal[i])
+ {
+ if (m->control_pressed) { return 0; }
+
+ double randNum = rand() / double(RAND_MAX);
+ if(randNum <= range[0])
+ {
+ tmprow[0] = 1;
+ continue;
+ }
+ for(int j=1;j<ncols;j++)
+ {
+ if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
+ {
+ tmprow[j] = 1;
+ }
+
+ }
+ }
+ tmpmatrix.push_back(tmprow);
+ tmprow.clear();
+ }
+
+ co_matrix = tmpmatrix;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim4");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ * inverse of sim4, MUST BE TRANSPOSED BEFORE CO-OCCURRENCE ANALYSIS
+ *
+ *
+ */
+/**************************************************************************************************/
+int TrialSwap2::sim5(vector<int> initcolumntotal,vector<int> initrowtotal, vector<vector<int> > &initmatrix)
+{
+ try {
+ vector<double> colProb;
+ vector<int> tmprow;//(ncols, 7);
+ vector<vector<int> > tmpmatrix;
+ vector<double> range;
+ vector<double> randNums;
+ int ncols = initcolumntotal.size();
+ int nrows = initrowtotal.size();
+
+ tmprow.clear();
+
+ double colSum = accumulate( initcolumntotal.begin(), initcolumntotal.end(), 0 );
+ //cout << "col sum: " << colSum << endl;
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ colProb.push_back(initcolumntotal[i]/colSum);
+ }
+
+ double start = 0.0;
+
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ range.push_back(start + colProb[i]);
+ start = range[i];
+ }
+
+ for(int i=0;i<nrows;i++)
+ {
+ tmprow.assign(ncols, 0);
+ if (m->control_pressed) { return 0; }
+
+ while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < initrowtotal[i])
+ {
+ if (m->control_pressed) { return 0; }
+
+ double randNum = rand() / double(RAND_MAX);
+ if(randNum <= range[0])
+ {
+ tmprow[0] = 1;
+ continue;
+ }
+ for(int j=1;j<ncols;j++)
+ {
+ if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
+ {
+ tmprow[j] = 1;
+ }
+
+ }
+ }
+ tmpmatrix.push_back(tmprow);
+ tmprow.clear();
+ }
+
+ initmatrix = tmpmatrix;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim5");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ *
+ *
+ *
+ */
+/**************************************************************************************************/
+int TrialSwap2::sim6(vector<int> columntotal, vector<vector<int> > &co_matrix)
+{
+ try {
+ vector<vector<int> > tmpmatrix;
+ vector<double> colProb;
+ vector<int> tmprow;
+ vector<double> range;
+ int ncols = columntotal.size();
+ int nrows = co_matrix.size();
+
+ int colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
+
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ colProb.push_back(columntotal[i]/double (colSum));
+ }
+
+ double start = 0.0;
+
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ range.push_back(start + colProb[i]);
+ start = range[i];
+ }
+
+ for(int i=0;i<nrows;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ tmprow.assign(ncols, 0);
+ int tmprowtotal;
+ tmprowtotal = (rand() / double (RAND_MAX)) * 10;
+ while ( tmprowtotal > ncols) {
+ if (m->control_pressed) { return 0; }
+ tmprowtotal = (rand() / double (RAND_MAX)) * 10;
+ }
+ //cout << tmprowtotal << endl;
+ //cout << accumulate( tmprow.begin(), tmprow.end(), 0 ) << endl;
+
+ while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < tmprowtotal)
+ {
+ if (m->control_pressed) { return 0; }
+ double randNum = rand() / double(RAND_MAX);
+ //cout << randNum << endl;
+ if(randNum <= range[0])
+ {
+ tmprow[0] = 1;
+ continue;
+ }
+ for(int j=1;j<ncols;j++)
+ {
+ //cout << range[j] << endl;
+ if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
+ {
+ tmprow[j] = 1;
+ }
+
+ }
+
+
+ }
+
+ tmpmatrix.push_back(tmprow);
+ tmprow.clear();
+ }
+
+ co_matrix = tmpmatrix;
+ tmpmatrix.clear();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim6");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ * MUST BE TRANSPOSED BEFORE CO-OCCURRENCE ANALYSIS
+ *
+ *
+ */
+/**************************************************************************************************/
+int TrialSwap2::sim7(vector<int> initrowtotal, vector<vector<int> > &co_matrix)
+{
+ try {
+ vector<vector<double> > probmatrix;
+ vector<vector<int> > tmpmatrix;
+ vector<double> colProb;
+ vector<double> probrow;
+ vector<int> tmprow;
+ vector<double> range;
+ double nc;
+ int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
+
+ tmpmatrix.assign(nrows, vector<int>(ncols, 0.));
+
+ int rowsum = accumulate( initrowtotal.begin(), initrowtotal.end(), 0 );
+
+ nc = rowsum * ncols;
+ //cout << nc << endl;
+
+ //assign null matrix based on probabilities
+
+ double start = 0.0; // don't reset start -- probs should be from 0-1 thoughout the entire matrix
+
+ for(int i=0;i<nrows;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ //cout << initrowtotal[i]/double(nc) << endl;
+ double cellprob = initrowtotal[i]/double(nc);
+ //cout << cellprob << endl;
+ for(int j=0;j<ncols;j++)
+ {
+
+ probrow.push_back(start + cellprob);
+ //cout << probrow[j] << endl;
+ //cout << start << endl;
+ start = start + cellprob;
+ }
+ probmatrix.push_back(probrow);
+ probrow.clear();
+ }
+
+
+ //while(tmprowsum < rowsum)
+ //for(int k=0;k<rowsum;k++)
+ int k = 0;
+ while(k < rowsum)
+ {
+ if (m->control_pressed) { return 0; }
+ done:
+ //cout << k << endl;
+ //tmprowsum = accumulate( tmprowtotal.begin(), tmprowtotal.end(), 0 );
+ double randNum = rand() / double(RAND_MAX);
+ //cout << randNum << "+" << endl;
+ //special case for the first entry
+ if(randNum <= probmatrix[0][0] && tmpmatrix[0][0] != 1)
+ {
+ tmpmatrix[0][0] = 1;
+ k++;
+ //cout << k << endl;
+ continue;
+ }
+
+
+ for(int i=0;i<nrows;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ for(int j=0;j<ncols;j++)
+ {
+ //cout << probmatrix[i][j] << endl;
+ if(randNum <= probmatrix[i][j] && randNum > probmatrix[i][j-1] && tmpmatrix[i][j] != 1)
+ {
+ tmpmatrix[i][j] = 1;
+ k++;
+ //cout << k << endl;
+ goto done;
+ }
+ //else
+ //k = k-1;
+ }
+
+ }
+
+ }
+
+ co_matrix = tmpmatrix;
+ return 0;
+ //build probibility matrix
+ /* for(int i=0;i<nrows;i++)
+ {
+ for(int j=0;j<ncols;j++)
+ {
+ probrow.push_back(rowtotal[i]/nc);
+ }
+ probmatrix.pushback(probrow);
+ probrow.clear;
+ }
+ */
+
+ /* int colSum = accumulate( initcolumntotal.begin(), initcolumntotal.end(), 0 );
+
+ for(int i=0;i<ncols;i++)
+ {
+ colProb.push_back(initcolumntotal[i]/double (colSum));
+ }
+
+ double start = 0.0;
+
+ for(int i=0;i<ncols;i++)
+ {
+ range.push_back(start + colProb[i]);
+ start = range[i];
+ }
+
+ for(int i=0;i<nrows;i++)
+ {
+ tmprow.assign(ncols, 0);
+ int tmprowtotal;
+ tmprowtotal = (rand() / double (RAND_MAX)) * 10;
+ while ( tmprowtotal > ncols)
+ tmprowtotal = (rand() / double (RAND_MAX)) * 10;
+ //cout << tmprowtotal << endl;
+ //cout << accumulate( tmprow.begin(), tmprow.end(), 0 ) << endl;
+
+ while ( accumulate( tmprow.begin(), tmprow.end(), 0 ) < tmprowtotal)
+ {
+ double randNum = rand() / double(RAND_MAX);
+ //cout << randNum << endl;
+ if(randNum <= range[0])
+ {
+ tmprow[0] = 1;
+ continue;
+ }
+ for(int j=1;j<ncols;j++)
+ {
+ //cout << range[j] << endl;
+ if(randNum <= range[j] && randNum > range[j-1] && tmprow[j] != 1)
+ {
+ tmprow[j] = 1;
+ }
+ }
+ }
+
+ tmpmatrix.push_back(tmprow);
+ tmprow.clear();
+ }
+
+ initmatrix = tmpmatrix;
+ */
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim7");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*
+ *
+ *
+ *
+ */
+/**************************************************************************************************/
+int TrialSwap2::sim8(vector<int> columntotal, vector<int> rowtotal, vector<vector<int> > &co_matrix)
+{
+ try {
+ double prob;
+ double start = 0.0;
+ int ncols = columntotal.size(); int nrows = rowtotal.size();
+ double probarray[nrows * ncols];
+ double randnum;
+ int grandtotal;
+ int total = 0;
+
+ //double colSum = accumulate( columntotal.begin(), columntotal.end(), 0 );
+ double rowSum = accumulate( rowtotal.begin(), rowtotal.end(), 0 );
+
+ if (m->control_pressed) { return 0; }
+
+ //cout << "rowsum: " << rowSum << endl;
+
+ grandtotal = rowSum;
+
+ //create probability matrix with each site being between 0 and 1
+ for (int i=0;i<nrows;i++) {
+ if (m->control_pressed) { return 0; }
+ for (int j=0;j<ncols;j++) {
+ prob = (rowtotal[i] * columntotal[j])/(rowSum*rowSum);
+ if (prob == 0.0)
+ probarray[ncols * i + j] = -1;
+ else
+ probarray[ncols * i + j] = start + prob;
+ //probmatrixrow.pushback(start + prob);
+ start += prob;
+ }
+ }
+ //cout << "prbarray" << endl;
+ //for(int i=0;i<(nrows*ncols);i++)
+ //cout << probarray[i] << " ";
+ //cout << endl;
+
+ //generate random muber between 0 and 1 and interate through probarray until found
+ while (total < grandtotal) {
+ if (m->control_pressed) { return 0; }
+ randnum = rand() / double(RAND_MAX);
+ //cout << "rand num: " << randnum << endl;
+ if((randnum <= probarray[0]) && (probarray[0] != 2) ) {
+ probarray[0] = 2;
+ total++;
+ continue;
+ }
+ for(int i=1;i<(nrows*ncols);i++) {
+ if (m->control_pressed) { return 0; }
+ if((randnum <= probarray[i]) && (randnum > probarray[i-1]) && (probarray[i] != 2) ) {
+ probarray[i] = 2;
+ total++;
+ break;
+ }
+ else
+ continue;
+ }
+ }
+ //cout << "prbarray" << endl;
+ //for(int i=0;i<(nrows*ncols);i++)
+ //cout << probarray[i] << " ";
+ //cout << endl;
+ for(int i=0;i<nrows;i++) {
+ if (m->control_pressed) { return 0; }
+ for(int j=0;j<ncols;j++) {
+ if(probarray[ncols * i + j] == 2)
+ co_matrix[i][j] = 1;
+ else
+ co_matrix[i][j] = 0;
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sim8");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::havel_hakimi(vector<int> rowtotal,vector<int> columntotal,vector<vector<int> > &co_matrix)
+{
+ try {
+ int nrows = co_matrix.size();
+ int ncols = co_matrix[0].size();
+ int i,j,k;
+ vector<int> r1; r1.resize(nrows,0);
+ vector<int> c; c.resize(ncols,0);
+ vector<int> c1; c1.resize(ncols,0);
+
+
+ for(i=0;i<nrows;i++) {
+ for(j=0;j<ncols;j++) {
+ co_matrix[i][j]=0;
+ }
+ }
+ for(i=0;i<nrows;i++) {
+ r1[i]=1;
+ }
+
+ for(i=0;i<ncols;i++)
+ {
+ c[i]=columntotal[i];
+ c1[i]=i;
+ }
+
+ for(k=0;k<nrows;k++)
+ {
+ if (m->control_pressed) { return 0; }
+ i=intrand(nrows);
+ while(r1[i]==0) {
+ if (m->control_pressed) { return 0; }
+ i=intrand(nrows);
+ }
+ r1[i]=0;
+ sho(c,c1,ncols);
+ for(j=0;j<rowtotal[i];j++)
+ {
+ if (m->control_pressed) { return 0; }
+ co_matrix[i][c1[j]]=1;
+ c[j]--;
+ if(c[j]<0)
+ m->mothurOut("Uhh! " + toString(c1[j]) + "\n");
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "havel_hakimi");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::sho(vector<int> c, vector<int> c1, int k)
+{
+ try {
+ int i,j,temp;
+
+ for(j=k-1;j>0;j--)
+ {
+ if (m->control_pressed) { return 0; }
+ for(i=0;i<j;i++)
+ {
+ if(c[i]<c[i+1])
+ {
+ temp=c[i];
+ c[i]=c[i+1];
+ c[i+1]=temp;
+ temp=c1[i];
+ c1[i]=c1[i+1];
+ c1[i+1]=temp;
+ }
+ }
+ }
+ for(j=1;j<1000;j++)
+ {
+ if (m->control_pressed) { return 0; }
+ i=intrand(k-1);
+ if(c[i]==c[i+1])
+ {
+ temp=c[i];
+ c[i]=c[i+1];
+ c[i+1]=temp;
+ temp=c1[i];
+ c1[i]=c1[i+1];
+ c1[i+1]=temp;
+ }
+ }
+ return(0);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "sho");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix,vector<int> rowtotal)
+{
+ try {
+ double cscore = 0.0;
+ double maxD;
+ double D;
+ double normcscore = 0.0;
+ int nonzeros = 0;
+ int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
+ vector<vector<double> > s(nrows, vector<double>(nrows,0.0)); //only fill half the matrix
+
+ for(int i=0;i<nrows-1;i++)
+ {
+
+ for(int j=i+1;j<nrows;j++)
+ {
+ if (m->control_pressed) { return 0; }
+ for(int k=0;k<ncols;k++)
+ {
+ if((co_matrix[i][k]==1)&&(co_matrix[j][k]==1)) //if both are 1s ie co-occurrence
+ s[i][j]++; //s counts co-occurrences
+ }
+
+ //rowtotal[i] = A, rowtotal[j] = B, ncols = P, s[i][j] = J
+ cscore += (rowtotal[i]-s[i][j])*(rowtotal[j]-s[i][j]);///(nrows*(nrows-1)/2);
+ D = (rowtotal[i]-s[i][j])*(rowtotal[j]-s[i][j]);
+
+ if(ncols < (rowtotal[i] + rowtotal[j]))
+ {
+ maxD = (ncols-rowtotal[i])*(ncols-rowtotal[j]);
+ }
+ else
+ {
+ maxD = rowtotal[i] * rowtotal[j];
+ }
+
+ if(maxD != 0)
+ {
+ normcscore += D/maxD;
+ nonzeros++;
+ }
+ }
+ }
+
+ cscore = cscore/(double)(nrows*(nrows-1)/2);
+ //cout << "normalized c score: " << normcscore/nonzeros << endl;
+
+ return cscore;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "calc_c_score");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int> rowtotal)
+{
+ try {
+ int cunits=0;
+ //int s[nrows][ncols];
+ int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
+ vector<vector<int> > s(nrows, vector<int>(nrows,0)); //only fill half the matrix
+
+ for(int i=0;i<nrows-1;i++)
+ {
+ for(int j=i+1;j<nrows;j++)
+ {
+ if (m->control_pressed) { return 0; }
+ //s[i][j]=0;
+ for(int k=0;k<ncols;k++)
+ {
+ //cout << s[i][j] << endl;
+ //iterates through the row and counts co-occurrences. The total number of co-occurrences for each row pair is kept in matrix s at location s[i][j].
+ if((co_matrix[i][k]==1)&&(co_matrix[j][k]==1)) //if both are 1s ie co-occurrence
+ s[i][j]++; //s counts co-occurrences
+
+ }
+ //cout << "rowtotal: " << rowtotal[i] << endl;
+ //cout << "co-occurrences: " << s[i][j] << endl;
+ //cunits+=(rowtotal[i]-s[i][j])*(rowtotal[j]-s[i][j]);
+ if (s[i][j] == 0)
+ {
+ cunits+=1;
+ }
+ //cunits+=s[i][j];
+ }
+ }
+
+ return cunits;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "calc_checker");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+double TrialSwap2::calc_vratio (vector<int> rowtotal, vector<int> columntotal)
+{
+ try {
+ int nrows = rowtotal.size();
+ int ncols = columntotal.size();
+ int sumCol = accumulate(columntotal.begin(), columntotal.end(), 0 );
+ // int sumRow = accumulate(rowtotal.begin(), rowtotal.end(), 0 );
+
+ double colAvg = (double) sumCol / (double) ncols;
+ // double rowAvg = (double) sumRow / (double) nrows;
+
+ double p = 0.0;
+
+ // double totalRowVar = 0.0;
+ double rowVar = 0.0;
+ double colVar = 0.0;
+
+ for(int i=0;i<nrows;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ p = (double) rowtotal[i]/(double) ncols;
+ rowVar += p * (1.0-p);
+ }
+
+ for(int i=0;i<ncols;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ colVar += pow(((double) columntotal[i]-colAvg),2);
+ }
+
+ colVar = (1.0/(double)ncols) * colVar;
+
+ return colVar/rowVar;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "calc_vratio");
+ exit(1);
+ }
+
+}
+/**************************************************************************************************/
+int TrialSwap2::calc_combo (vector<vector<int> > &initmatrix)
+{
+ try {
+ int initrows = initmatrix.size();
+ int unique = 0;
+ int match = 0;
+ int matches = 0;
+ for(int i=0;i<initrows;i++)
+ {
+ match = 0;
+ for(int j=i+1;j<=initrows;j++)
+ {
+ if (m->control_pressed) { return 0; }
+ if( (initmatrix[i] == initmatrix[j]))
+ {
+ match++;
+ matches++;
+ break;
+ }
+ }
+
+ //on the last iteration of a previously matched row it will add itself because it doesn't match any following rows, so that combination is counted
+ if (match == 0)
+ unique++;
+ }
+ return unique;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "calc_combo");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix)
+{
+ try {
+ int ncols = co_matrix[0].size(); int nrows = co_matrix.size();
+ int i, j, k, l;
+ i=intrand(nrows);
+ while((j = intrand(nrows) ) == i ) {;if (m->control_pressed) { return 0; }}
+ k=intrand(ncols);
+ while((l = intrand(ncols) ) == k ) {;if (m->control_pressed) { return 0; }}
+ //cout << co_matrix[i][k] << " " << co_matrix[j][l] << endl;
+ //cout << co_matrix[i][l] << " " << co_matrix[j][k] << endl;
+ //cout << co_matrix[i][l] << " " << co_matrix[j][k] << endl;
+ //cout << co_matrix[i][l] << " " << co_matrix[j][k] << endl;
+ if((co_matrix[i][k]*co_matrix[j][l]==1 && co_matrix[i][l]+co_matrix[j][k]==0)||(co_matrix[i][k]+co_matrix[j][l]==0 && co_matrix[i][l]*co_matrix[j][k]==1)) //checking for checkerboard value and swap
+ {
+ co_matrix[i][k]=1-co_matrix[i][k];
+ co_matrix[i][l]=1-co_matrix[i][l];
+ co_matrix[j][k]=1-co_matrix[j][k];
+ co_matrix[j][l]=1-co_matrix[j][l];
+ //cout << "swapped!" << endl;
+ }
+ //cout << "i: " << i << " j: " << j << " k: " << " l: " << l << endl;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "swap_checkerboards");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+double TrialSwap2::calc_pvalue_greaterthan (vector<double> scorevec, double initialscore)
+{
+ try {
+ int runs = scorevec.size();
+ double p = 0.0;
+ for( int i=0;i<runs;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ if(scorevec[i]>=initialscore)
+ p++;
+ }
+ return p/(double)runs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "calc_pvalue_greaterthan");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+double TrialSwap2::calc_pvalue_lessthan (vector<double> scorevec, double initialscore)
+{
+ try {
+ int runs = scorevec.size();
+ double p = 0.0;
+ for( int i=0;i<runs;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ if(scorevec[i]<=initialscore)
+ p++;
+ }
+ return p/(double)runs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "calc_pvalue_lessthan");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vector<double> scorevec)
+{
+ try {
+ double t;
+ double sampleSD;
+ double sum = 0;
+
+ for(int i=0;i<runs;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ sum += pow((scorevec[i] - nullMean),2);
+ //cout << "scorevec[" << i << "]" << scorevec[i] << endl;
+ }
+
+ m->mothurOut("nullMean: " + toString(nullMean)); m->mothurOutEndLine();
+
+ m->mothurOut("sum: " + toString(sum)); m->mothurOutEndLine();
+
+ sampleSD = sqrt( (1/runs) * sum );
+
+ m->mothurOut("samplSD: " + toString(sampleSD)); m->mothurOutEndLine();
+
+ t = (nullMean - initialscore) / (sampleSD / sqrt(runs));
+
+ return t;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "t_test");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
+{
+ try {
+ m->mothurOut("matrix:"); m->mothurOutEndLine();
+
+ for (int i = 0; i < nrows; i++)
+ {
+ if (m->control_pressed) { return 0; }
+ for (int j = 0; j < ncols; j++)
+ {
+ m->mothurOut(toString(matrix[i][j]));
+ }
+ m->mothurOutEndLine();
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "print_matrix");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::transpose_matrix (vector<vector<int> > &initmatrix, vector<vector<int> > &co_matrix)//, int nrows, int nocols)
+{
+ try {
+ int ncols = initmatrix.size(); int nrows = initmatrix[0].size();
+ int tmpnrows = nrows;
+ //vector<vector<int> > tmpvec;
+ vector<int> tmprow;
+ if(!co_matrix.empty())
+ co_matrix.clear();
+ for (int i=0;i<nrows;i++)
+ {
+ if (m->control_pressed) { return 0; }
+ for (int j=0;j<ncols;j++)
+ {
+ tmprow.push_back(initmatrix[j][i]);
+ }
+ /*if (accumulate( tmprow.begin(), tmprow.end(), 0 ) == 0)
+ {
+ tmpnrows--;
+ }
+ else */
+ co_matrix.push_back(tmprow);
+ tmprow.clear();
+ }
+ nrows = tmpnrows;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "transpose_matrix");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrialSwap2::update_row_col_totals(vector<vector<int> > &co_matrix, vector<int> &rowtotal, vector<int> &columntotal)
+{
+ try {
+ //rowtotal.clear();
+ //columntotal.clear();
+ //generate (rowtotal.begin(), rowtotal.end(), 0);
+ //generate (columntotal.begin(), columntotal.end(), 0);
+ int nrows = co_matrix.size();
+ int ncols = co_matrix[0].size();
+ vector<int> tmpcolumntotal(ncols, 0);
+ vector<int> tmprowtotal(nrows, 0);
+
+ int rowcount = 0;
+
+ for (int i = 0; i < nrows; i++)
+ {
+ if (m->control_pressed) { return 0; }
+ for (int j = 0; j < ncols; j++)
+ {
+ if (co_matrix[i][j] == 1)
+ {
+ rowcount++;
+ tmpcolumntotal[j]++;
+ }
+ }
+ tmprowtotal[i] = rowcount;
+ rowcount = 0;
+ }
+ columntotal = tmpcolumntotal;
+ rowtotal = tmprowtotal;
+ /*cout << "rowtotal: ";
+ for(int i = 0; i<nrows; i++) { cout << rowtotal[i]; }
+ cout << " ";
+ cout << " coltotal: ";
+ for(int i = 0; i<ncols; i++) { cout << columntotal[i]; }
+ cout << endl;*/
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrialSwap2", "update_row_col_totals");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/*int main(int argc, char *argv[])
+{
+ srand (time(0));
+ char* input_filename = argv[1];
+ std::ifstream infile (input_filename);
+
+ //skip the first line of headers
+ getline(infile, line);
+ //get the first line of data
+ getline(infile, line);
+
+ nrows = 0;
+ ncols = 0;
+
+ //int numspaces = 0;
+ char nextChar;
+
+ for (int i=0; i<int(line.length()); i++)
+ {
+ nextChar = line.at(i); // gets a character
+ if (isspace(line[i]))
+ ncols++;
+ }
+
+ ncols = ncols-3;
+
+ cout << "number of OTUs: ";
+ cout << ncols << endl;
+
+ infile.close();
+
+ std::ifstream infile2 (input_filename);
+
+ //skip first line of headers
+ getline(infile2, line);
+
+ while (!infile2.eof())
+ {
+ getline(infile2, line);
+ if (!line.empty())
+ nrows++;
+ }
+
+ cout << "number of sites: ";
+ cout << nrows << endl;
+
+ infile2.close();
+
+ std::ifstream infile3 (input_filename);
+
+ //skip first line
+ getline(infile3, line);
+
+ //variables that depend on info from initial matrix
+ vector<vector<int> > co_matrix;//[nrows][ncols];
+ vector<vector<int> > initmatrix;
+ vector<int> tmprow;
+ vector<double> stats;
+ int tmpnrows = nrows;
+
+ for (int row1=0; row1<nrows; row1++) // first line was skipped when counting, so we can start from 0
+ {
+ //ignore first 3 cols in each row, data starts on the 3th col
+ for (int i = 0; i < 3; i++)
+ infile3 >> tmp;
+
+ for (int col=0; col<ncols; col++)
+ {
+ infile3 >> tmp;
+ //cout << tmp << endl;
+ if (atoi(tmp.c_str()) > 0)
+ tmprow.push_back(1);
+ else
+ tmprow.push_back(0);
+ }
+ if (accumulate( tmprow.begin(), tmprow.end(), 0 ) == 0)
+ {
+ tmpnrows--;
+ }
+ else
+ initmatrix.push_back(tmprow);
+ //add the row to the matrix
+ //initmatrix.push_back(tmprow);
+ tmprow.clear();
+ //cout << tmprow << endl;
+ }
+
+ infile3.close();
+ nrows = tmpnrows;
+
+ //print init matrix
+ /* cout << "original matrix:" << endl;
+
+ for (int i = 0; i < nrows; i++)
+ {
+ for (int j = 0; j < ncols; j++)
+ {
+ cout << initmatrix[i][j];
+ }
+ cout << endl;
+ } */
+
+ //for (i=0;i<ncols;i++)
+ //cout << "col "<< i<< ": " << columntotal[i] << endl;
+
+ //co_matrix is now initmatrix and newmatrix is now co_matrix
+
+ //remove cols where sum is 0
+
+ //transpose matrix
+ /* int newmatrows = ncols;
+ int newmatcols = nrows;
+ int initcols = ncols; //for the combo metric
+ int initrows = nrows; //for the combo metric
+ //swap for transposed matrix
+ nrows = newmatrows;//ncols;
+ ncols = newmatcols;//nrows;
+
+ vector<int> columntotal(ncols, 0);
+ vector<int> initcolumntotal(ncols, 0);
+ vector<int> initrowtotal(nrows, 0);
+ vector<int> rowtotal(nrows, 0);
+
+ transpose_matrix(initmatrix,co_matrix);
+ //remove degenerate rows and cols
+
+ //cout << "transposed matrix:" << endl;
+ int rowcount = 0;
+ for (int i = 0; i < nrows; i++)
+ {
+ for (int j = 0; j < ncols; j++)
+ {
+ if (co_matrix[i][j] == 1)
+ {
+ rowcount++;
+ columntotal[j]++;
+ }
+ //cout << co_matrix[i][j];
+ }
+ //cout << " row total: " << rowcount << endl;
+ //cout << endl;
+ rowtotal[i] = rowcount;
+ rowcount = 0;
+ }
+
+ initcolumntotal = rowtotal;
+ initrowtotal = columntotal;
+
+ cout << endl;
+
+ runs = atol(argv[2]);
+ int metric = atol(argv[3]);
+ int nullModel = atol(argv[4]);
+ double initscore;
+ update_row_col_totals(co_matrix, rowtotal, columntotal, ncols, nrows);
+ //do initial metric: checker, c score, v ratio or combo
+ switch(metric)
+ {
+ case 1:
+ //c score
+ initscore = calc_c_score(co_matrix, rowtotal);
+ cout << "initial c score: " << initscore << endl;
+ //print_matrix(co_matrix, nrows, ncols);
+ break;
+
+ case 2:
+ //checker
+ initscore = calc_checker(co_matrix, rowtotal);
+ cout << "initial checker score: " << initscore << endl;
+ break;
+
+ case 3:
+ //v ratio
+ initscore = calc_vratio(nrows, ncols, rowtotal, columntotal);
+ cout << "initial v ratio: " << initscore << endl;
+ break;
+
+ case 4:
+ //combo
+ initscore = calc_combo(initrows, initcols, initmatrix);
+ cout << "initial combo score: " << initscore << endl;
+ //set co_matrix equal to initmatrix because combo requires row comparisons
+ co_matrix = initmatrix;
+ break;
+
+ case 5:
+ //test!
+
+ //print_matrix(co_matrix, nrows, ncols);
+ //sim1(nrows, ncols, co_matrix);
+ //sim2(nrows, ncols, co_matrix);
+ //sim3(initrows, initcols, initmatrix);
+ //sim4(columntotal, rowtotal, co_matrix);
+ //sim5(initcolumntotal, initmatrix);
+ //sim6(columntotal, co_matrix);
+ //sim7(initcolumntotal, initmatrix);
+ sim8(columntotal, rowtotal, co_matrix);
+ //print_matrix(initmatrix, initrows, initcols);
+ //print_matrix(co_matrix, nrows, ncols);
+
+ break;
+
+ default:
+ cout << "no metric selected!" << endl;
+ return 1;
+
+ }
+
+ //matrix initialization
+ //havel_hakimi(nrows, ncols, rowtotal, columntotal, co_matrix);
+ //sum_of_square(nrows, ncols, rowtotal, columntotal, co_matrix);
+ //co-matrix is now a random matrix with the same row and column totals as the initial matrix
+
+ //null matrix burn in
+ cout << "initializing null matrix...";
+ for(int l=0;l<10000;l++)
+ {
+ //swap_checkerboards (co_matrix);
+ //if(l%10 == 0)
+ switch(nullModel)
+ {
+ case 1:
+ //
+ sim1(nrows, ncols, co_matrix);
+ break;
+
+ case 2:
+ //sim2
+ sim2(nrows, ncols, co_matrix);
+ //sim2plus(nrows, ncols, initrowtotal, co_matrix);
+ break;
+
+ case 3:
+ //sim3
+ sim3(initrows, initcols, initmatrix);
+ //transpose_matrix(initmatrix,co_matrix);
+ co_matrix = initmatrix;
+ break;
+
+ case 4:
+ //sim4
+ sim4(columntotal, rowtotal, co_matrix);
+ break;
+
+ case 5:
+ //sim5
+ sim5(initcolumntotal, initrowtotal, initmatrix);
+ transpose_matrix(initmatrix,co_matrix);
+ //co_matrix = initmatrix;
+ break;
+
+ case 6:
+ sim6(columntotal, co_matrix);
+ break;
+
+ case 7:
+ //sim7(ncols, nrows, initrowtotal, co_matrix);
+ //transpose_matrix(initmatrix,co_matrix);
+ //co_matrix = initmatrix;
+ break;
+
+ case 8:
+ sim8(columntotal, rowtotal, co_matrix);
+ break;
+
+ case 9:
+ //swap_checkerboards
+ swap_checkerboards (co_matrix);
+ break;
+
+ default:
+ cout << "no null model selected!" << endl;
+ return 1;
+ }
+ }
+ cout << "done!" << endl;
+
+ //generate null matrices and calculate the metrics
+
+ cout << "run: " << endl;
+ for(int trial=0;trial<runs;trial++) //runs
+ {
+ printf("\b\b\b\b\b\b\b%7d",trial+1);
+ fflush(stdout);
+
+ switch(nullModel)
+ {
+ case 1:
+ //
+ sim1(nrows, ncols, co_matrix);
+ break;
+
+ case 2:
+ //sim2
+ sim2(nrows, ncols, co_matrix);
+ //for(int i=0;i<nrows;i++)
+ //cout << rowtotal[i] << " ";
+ //sim2plus(nrows, ncols, initrowtotal, co_matrix);
+ break;
+
+ case 3:
+ //sim3
+ for(int i=0;i<nrows;i++)
+ cout << " " << rowtotal[i];
+ sim3(initrows, initcols, initmatrix);
+ transpose_matrix(initmatrix,co_matrix);
+ break;
+
+ case 4:
+ //sim4
+ sim4(columntotal, rowtotal, co_matrix);
+ break;
+
+ case 5:
+ //sim5
+ sim5(initcolumntotal, initrowtotal, initmatrix);
+ transpose_matrix(initmatrix,co_matrix);
+ break;
+
+ case 6:
+ sim6(columntotal, co_matrix);
+ break;
+
+ case 7:
+ sim7(ncols, nrows, initrowtotal, co_matrix);
+ //print_matrix(co_matrix, nrows, ncols);
+ //transpose_matrix(initmatrix,co_matrix);
+ break;
+
+ case 8:
+ //sim8(initcolumntotal, initrowtotal, co_matrix);
+ //initrow and initcol are flipped because of transposition. this is super ugly!
+ sim8(initrowtotal, initcolumntotal, co_matrix);
+ break;
+
+ case 9:
+ //swap_checkerboards
+ swap_checkerboards (co_matrix);
+ break;
+
+ default:
+ cout << "no null model selected!" << endl;
+ return 1;
+ }
+
+ //cout << endl;
+ //print_matrix(co_matrix, nrows, ncols);
+ update_row_col_totals(co_matrix, rowtotal, columntotal, ncols, nrows);
+ //cout << columntotal[1]<<endl;
+ double tmp;
+ switch(metric)
+ {
+ case 1:
+ //c score
+ //swap_checkerboards(co_matrix);
+ //cout << "%" << tmp << " nrows " << nrows << " ncols " << ncols << " rowtotals ";
+ //for(int i = 0; i<nrows; i++) { cout << rowtotal[i]; }
+ //cout << endl;
+ tmp = calc_c_score(co_matrix, rowtotal);
+ //cout << "%" << tmp << " ";
+ stats.push_back(tmp);
+ //cout << "%" << tmp << " ";
+ //print_matrix(co_matrix, nrows, ncols);
+ break;
+
+ case 2:
+ //checker
+ //swap_checkerboards(co_matrix);
+ //cout << "%" << tmp << " nrows " << nrows << " ncols " << ncols << " rowtotals ";
+ //for(int i = 0; i<nrows; i++) { cout << rowtotal[i]; }
+ //cout << endl;
+ tmp = calc_checker(co_matrix, rowtotal);
+ stats.push_back(tmp);
+ //cout << "%" << tmp << endl;
+ break;
+
+ case 3:
+ //v ratio
+ stats.push_back(calc_vratio(nrows, ncols, rowtotal, columntotal));
+ break;
+
+ case 4:
+ //combo
+ stats.push_back(calc_combo(nrows, ncols, co_matrix));
+ break;
+
+ case 5:
+ //test!
+ break;
+
+ default:
+ cout << "no metric selected!" << endl;
+ return 1;
+
+ }
+
+ //print_matrix(co_matrix, nrows, ncols);
+ //print_matrix(initmatrix, initrows, initcols);
+
+ }
+
+ cout << endl;
+
+ double total = 0.0;
+ for (int i=0; i<stats.size();i++)
+ {
+ total+=stats[i];
+ }
+
+ double nullMean = double (total/stats.size());
+
+ cout << '\n' << "average metric score: " << nullMean << endl;
+
+ //cout << "t-test: " << t_test(initscore, runs, nullMean, stats) << endl;
+
+ if (metric == 1 || metric == 2)
+ cout << "pvalue: " << calc_pvalue_greaterthan (stats, initscore) << endl;
+ else
+ cout << "pvalue: " << calc_pvalue_lessthan (stats, initscore) << endl;
+
+ //print_matrix(co_matrix, nrows, ncols);
+
+ return 0;
+
+}*/
+/**************************************************************************************************/
+
+
projects / mothur.git / commitdiff