#include "command.hpp"
#include "readtree.h"
-#include "treemap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
#include "sharedrabundvector.h"
#include "sharedrabundfloatvector.h"
#include "inputdata.h"
public:
IndicatorCommand(string);
IndicatorCommand();
- ~IndicatorCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~IndicatorCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "indicator"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
+ string getDescription() { return "calculate the indicator value for each OTU"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
ReadTree* read;
- TreeMap* treeMap;
- string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
+ CountTable* ct;
+ GroupMap* designMap;
+ string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
bool abort;
+ int iters, processors;
vector<string> outputNames, Groups;
- map<string, vector<string> > outputTypes;
vector<SharedRAbundVector*> lookup;
vector<SharedRAbundFloatVector*> lookupFloat;
int getShared();
int getSharedFloat();
int GetIndicatorSpecies(Tree*&);
+ int GetIndicatorSpecies();
set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
- vector<float> getValues(vector< vector<SharedRAbundVector*> >&);
- vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&);
+ vector<float> getValues(vector< vector<SharedRAbundVector*> >&, vector<string>&, map< vector<int>, vector<int> >);
+ vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&, vector<string>&, map< vector<int>, vector<int> >);
+
map<int, float> getDistToRoot(Tree*&);
+ map< vector<int>, vector<int> > randomizeGroupings(vector< vector<SharedRAbundVector*> >&, int);
+ map< vector<int>, vector<int> > randomizeGroupings(vector< vector<SharedRAbundFloatVector*> >&, int);
+
+ vector<float> driver(vector< vector<SharedRAbundFloatVector*> >&, int, vector<float>, int);
+ vector<float> driver(vector< vector<SharedRAbundVector*> >&, int, vector<float>, int);
+
+ vector<float> getPValues(vector< vector<SharedRAbundFloatVector*> >&, int, vector<float>);
+ vector<float> getPValues(vector< vector<SharedRAbundVector*> >&, int, vector<float>);
+
};
+/**************************************************************************************************/
+
+struct indicatorData {
+ vector< vector<SharedRAbundFloatVector*> > groupings;
+ MothurOut* m;
+ int iters, num;
+ vector<float> indicatorValues;
+ vector<float> pvalues;
+
+ indicatorData(){}
+ indicatorData(MothurOut* mout, int it, vector< vector<SharedRAbundFloatVector*> > ng, int n, vector<float> iv) {
+ m = mout;
+ iters = it;
+ groupings = ng;
+ indicatorValues = iv;
+ num = n;
+ }
+};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyIndicatorThreadFunction(LPVOID lpParam){
+ indicatorData* pDataArray;
+ pDataArray = (indicatorData*)lpParam;
+
+ try {
+
+ pDataArray->pvalues.resize(pDataArray->indicatorValues.size(), 0);
+
+ for(int i=0;i<pDataArray->iters;i++){
+ if (pDataArray->m->control_pressed) { break; }
+
+ //groupingsMap = randomizeGroupings(groupings, num);
+ ///////////////////////////////////////////////////////////////////////
+ map< vector<int>, vector<int> > randomGroupings;
+
+ for (int j = 0; j < pDataArray->num; j++) {
+
+ //get random groups to swap to switch with
+ //generate random int between 0 and groupings.size()-1
+ int z = pDataArray->m->getRandomIndex(pDataArray->groupings.size()-1);
+ int x = pDataArray->m->getRandomIndex(pDataArray->groupings.size()-1);
+ int a = pDataArray->m->getRandomIndex(pDataArray->groupings[z].size()-1);
+ int b = pDataArray->m->getRandomIndex(pDataArray->groupings[x].size()-1);
+ //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
+
+ vector<int> from;
+ vector<int> to;
+
+ from.push_back(z); from.push_back(a);
+ to.push_back(x); to.push_back(b);
+
+ randomGroupings[from] = to;
+ }
+ ///////////////////////////////////////////////////////////////////////
+
+ //vector<float> randomIndicatorValues = getValues(groupings, notUsedGroupings, randomGroupings);
+ ///////////////////////////////////////////////////////////////////////
+ vector<float> randomIndicatorValues;
+ map< vector<int>, vector<int> >::iterator it;
+
+ //for each otu
+ for (int i = 0; i < pDataArray->groupings[0][0]->getNumBins(); i++) {
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ vector<float> terms;
+ float AijDenominator = 0.0;
+ vector<float> Bij;
+
+ //get overall abundance of each grouping
+ for (int j = 0; j < pDataArray->groupings.size(); j++) {
+
+ float totalAbund = 0;
+ int numNotZero = 0;
+ for (int k = 0; k < pDataArray->groupings[j].size(); k++) {
+ vector<int> temp; temp.push_back(j); temp.push_back(k);
+ it = randomGroupings.find(temp);
+
+ if (it == randomGroupings.end()) { //this one didnt get moved
+ totalAbund += pDataArray->groupings[j][k]->getAbundance(i);
+ if (pDataArray->groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+ }else {
+ totalAbund += pDataArray->groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
+ if (pDataArray->groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
+ }
+
+ }
+
+ //mean abundance
+ float Aij = (totalAbund / (float) pDataArray->groupings[j].size());
+ terms.push_back(Aij);
+
+ //percentage of sites represented
+ Bij.push_back(numNotZero / (float) pDataArray->groupings[j].size());
+
+ AijDenominator += Aij;
+ }
+
+ float maxIndVal = 0.0;
+ for (int j = 0; j < terms.size(); j++) {
+ float thisAij = (terms[j] / AijDenominator); //relative abundance
+ float thisValue = thisAij * Bij[j] * 100.0;
+
+ //save largest
+ if (thisValue > maxIndVal) { maxIndVal = thisValue; }
+ }
+
+ randomIndicatorValues.push_back(maxIndVal);
+ }
+
+ ///////////////////////////////////////////////////////////////////////
+
+ for (int j = 0; j < pDataArray->indicatorValues.size(); j++) {
+ if (randomIndicatorValues[j] >= pDataArray->indicatorValues[j]) { pDataArray->pvalues[j]++; }
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "IndicatorCommand", "MyIndicatorThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
#endif
projects / mothur.git / blobdiff