+/*********************************************************************************************************************************/
+double LinearAlgebra::calcKendall(vector<double>& x, vector<double>& y, double& sig){
+ try {
+ if (x.size() != y.size()) { m->mothurOut("[ERROR]: vector size mismatch."); m->mothurOutEndLine(); return 0.0; }
+
+ //format data
+ vector<spearmanRank> xscores;
+ for (int i = 0; i < x.size(); i++) {
+ spearmanRank member(toString(i), x[i]);
+ xscores.push_back(member);
+ }
+
+ //sort xscores
+ sort(xscores.begin(), xscores.end(), compareSpearman);
+
+ //convert scores to ranks of x
+ vector<spearmanRank*> ties;
+ int rankTotal = 0;
+ for (int j = 0; j < xscores.size(); j++) {
+ rankTotal += (j+1);
+ ties.push_back(&(xscores[j]));
+
+ if (j != xscores.size()-1) { // you are not the last so you can look ahead
+ if (xscores[j].score != xscores[j+1].score) { // you are done with ties, rank them and continue
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ (*ties[k]).score = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ (*ties[k]).score = thisrank;
+ }
+ }
+ }
+
+
+ //format data
+ vector<spearmanRank> yscores;
+ for (int j = 0; j < y.size(); j++) {
+ spearmanRank member(toString(j), y[j]);
+ yscores.push_back(member);
+ }
+
+ //sort yscores
+ sort(yscores.begin(), yscores.end(), compareSpearman);
+
+ //convert to ranks
+ map<string, float> rank;
+ vector<spearmanRank> yties;
+ rankTotal = 0;
+ for (int j = 0; j < yscores.size(); j++) {
+ rankTotal += (j+1);
+ yties.push_back(yscores[j]);
+
+ if (j != yscores.size()-1) { // you are not the last so you can look ahead
+ if (yscores[j].score != yscores[j+1].score) { // you are done with ties, rank them and continue
+ for (int k = 0; k < yties.size(); k++) {
+ float thisrank = rankTotal / (float) yties.size();
+ rank[yties[k].name] = thisrank;
+ }
+ yties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+ for (int k = 0; k < yties.size(); k++) {
+ float thisrank = rankTotal / (float) yties.size();
+ rank[yties[k].name] = thisrank;
+ }
+ }
+ }
+
+
+ int numCoor = 0;
+ int numDisCoor = 0;
+
+ //associate x and y
+ vector<spearmanRank> otus;
+ for (int l = 0; l < xscores.size(); l++) {
+ spearmanRank member(xscores[l].name, rank[xscores[l].name]);
+ otus.push_back(member);
+ }
+
+ int count = 0;
+ for (int l = 0; l < xscores.size(); l++) {
+
+ int numWithHigherRank = 0;
+ int numWithLowerRank = 0;
+ float thisrank = otus[l].score;
+
+ for (int u = l+1; u < xscores.size(); u++) {
+ if (otus[u].score > thisrank) { numWithHigherRank++; }
+ else if (otus[u].score < thisrank) { numWithLowerRank++; }
+ count++;
+ }
+
+ numCoor += numWithHigherRank;
+ numDisCoor += numWithLowerRank;
+ }
+
+ double p = (numCoor - numDisCoor) / (float) count;
+
+ sig = calcKendallSig(x.size(), p);
+
+ return p;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcKendall");
+ exit(1);
+ }
+}
+double LinearAlgebra::ran0(int& idum)
+{
+ const int IA=16807,IM=2147483647,IQ=127773;
+ const int IR=2836,MASK=123459876;
+ const double AM=1.0/double(IM);
+ int k;
+ double ans;
+
+ idum ^= MASK;
+ k=idum/IQ;
+ idum=IA*(idum-k*IQ)-IR*k;
+ if (idum < 0) idum += IM;
+ ans=AM*idum;
+ idum ^= MASK;
+ return ans;
+}
+
+double LinearAlgebra::ran1(int &idum)
+{
+ const int IA=16807,IM=2147483647,IQ=127773,IR=2836,NTAB=32;
+ const int NDIV=(1+(IM-1)/NTAB);
+ const double EPS=3.0e-16,AM=1.0/IM,RNMX=(1.0-EPS);
+ static int iy=0;
+ static vector<int> iv(NTAB);
+ int j,k;
+ double temp;
+
+ if (idum <= 0 || !iy) {
+ if (-idum < 1) idum=1;
+ else idum = -idum;
+ for (j=NTAB+7;j>=0;j--) {
+ k=idum/IQ;
+ idum=IA*(idum-k*IQ)-IR*k;
+ if (idum < 0) idum += IM;
+ if (j < NTAB) iv[j] = idum;
+ }
+ iy=iv[0];
+ }
+ k=idum/IQ;
+ idum=IA*(idum-k*IQ)-IR*k;
+ if (idum < 0) idum += IM;
+ j=iy/NDIV;
+ iy=iv[j];
+ iv[j] = idum;
+ if ((temp=AM*iy) > RNMX) return RNMX;
+ else return temp;
+}
+
+double LinearAlgebra::ran2(int &idum)
+{
+ const int IM1=2147483563,IM2=2147483399;
+ const int IA1=40014,IA2=40692,IQ1=53668,IQ2=52774;
+ const int IR1=12211,IR2=3791,NTAB=32,IMM1=IM1-1;
+ const int NDIV=1+IMM1/NTAB;
+ const double EPS=3.0e-16,RNMX=1.0-EPS,AM=1.0/double(IM1);
+ static int idum2=123456789,iy=0;
+ static vector<int> iv(NTAB);
+ int j,k;
+ double temp;
+
+ if (idum <= 0) {
+ idum=(idum==0 ? 1 : -idum);
+ idum2=idum;
+ for (j=NTAB+7;j>=0;j--) {
+ k=idum/IQ1;
+ idum=IA1*(idum-k*IQ1)-k*IR1;
+ if (idum < 0) idum += IM1;
+ if (j < NTAB) iv[j] = idum;
+ }
+ iy=iv[0];
+ }
+ k=idum/IQ1;
+ idum=IA1*(idum-k*IQ1)-k*IR1;
+ if (idum < 0) idum += IM1;
+ k=idum2/IQ2;
+ idum2=IA2*(idum2-k*IQ2)-k*IR2;
+ if (idum2 < 0) idum2 += IM2;
+ j=iy/NDIV;
+ iy=iv[j]-idum2;
+ iv[j] = idum;
+ if (iy < 1) iy += IMM1;
+ if ((temp=AM*iy) > RNMX) return RNMX;
+ else return temp;
+}
+
+double LinearAlgebra::ran3(int &idum)
+{
+ static int inext,inextp;
+ static int iff=0;
+ const int MBIG=1000000000,MSEED=161803398,MZ=0;
+ const double FAC=(1.0/MBIG);
+ static vector<int> ma(56);
+ int i,ii,k,mj,mk;
+
+ if (idum < 0 || iff == 0) {
+ iff=1;
+ mj=labs(MSEED-labs(idum));
+ mj %= MBIG;
+ ma[55]=mj;
+ mk=1;
+ for (i=1;i<=54;i++) {
+ ii=(21*i) % 55;
+ ma[ii]=mk;
+ mk=mj-mk;
+ if (mk < int(MZ)) mk += MBIG;
+ mj=ma[ii];
+ }
+ for (k=0;k<4;k++)
+ for (i=1;i<=55;i++) {
+ ma[i] -= ma[1+(i+30) % 55];
+ if (ma[i] < int(MZ)) ma[i] += MBIG;
+ }
+ inext=0;
+ inextp=31;
+ idum=1;
+ }
+ if (++inext == 56) inext=1;
+ if (++inextp == 56) inextp=1;
+ mj=ma[inext]-ma[inextp];
+ if (mj < int(MZ)) mj += MBIG;
+ ma[inext]=mj;
+ return mj*FAC;
+}
+
+double LinearAlgebra::ran4(int &idum)
+{
+#if defined(vax) || defined(_vax_) || defined(__vax__) || defined(VAX)
+ static const unsigned long jflone = 0x00004080;
+ static const unsigned long jflmsk = 0xffff007f;
+#else
+ static const unsigned long jflone = 0x3f800000;
+ static const unsigned long jflmsk = 0x007fffff;
+#endif
+ unsigned long irword,itemp,lword;
+ static int idums = 0;
+
+ if (idum < 0) {
+ idums = -idum;
+ idum=1;
+ }
+ irword=idum;
+ lword=idums;
+ psdes(lword,irword);
+ itemp=jflone | (jflmsk & irword);
+ ++idum;
+ return (*(float *)&itemp)-1.0;
+}
+
+void LinearAlgebra::psdes(unsigned long &lword, unsigned long &irword)
+{
+ const int NITER=4;
+ static const unsigned long c1[NITER]={
+ 0xbaa96887L, 0x1e17d32cL, 0x03bcdc3cL, 0x0f33d1b2L};
+ static const unsigned long c2[NITER]={
+ 0x4b0f3b58L, 0xe874f0c3L, 0x6955c5a6L, 0x55a7ca46L};
+ unsigned long i,ia,ib,iswap,itmph=0,itmpl=0;
+
+ for (i=0;i<NITER;i++) {
+ ia=(iswap=irword) ^ c1[i];
+ itmpl = ia & 0xffff;
+ itmph = ia >> 16;
+ ib=itmpl*itmpl+ ~(itmph*itmph);
+ irword=lword ^ (((ia = (ib >> 16) |
+ ((ib & 0xffff) << 16)) ^ c2[i])+itmpl*itmph);
+ lword=iswap;
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcKendallSig(double n, double r){
+ try {
+
+ double sig = 0.0;
+ double svar=(4.0*n+10.0)/(9.0*n*(n-1.0));
+ double z= r/sqrt(svar);
+ sig=erfcc(fabs(z)/1.4142136);
+
+ if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+
+ return sig;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcKendallSig");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcKruskalWallis(vector<spearmanRank>& values, double& pValue){
+ try {
+ double H;
+ set<string> treatments;
+
+ //rank values
+ sort(values.begin(), values.end(), compareSpearman);
+ vector<spearmanRank*> ties;
+ int rankTotal = 0;
+ vector<int> TIES;
+ for (int j = 0; j < values.size(); j++) {
+ treatments.insert(values[j].name);
+ rankTotal += (j+1);
+ ties.push_back(&(values[j]));
+
+ if (j != values.size()-1) { // you are not the last so you can look ahead
+ if (values[j].score != values[j+1].score) { // you are done with ties, rank them and continue
+ if (ties.size() > 1) { TIES.push_back(ties.size()); }
+ for (int k = 0; k < ties.size(); k++) {
+ double thisrank = rankTotal / (double) ties.size();
+ (*ties[k]).score = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+ if (ties.size() > 1) { TIES.push_back(ties.size()); }
+ for (int k = 0; k < ties.size(); k++) {
+ double thisrank = rankTotal / (double) ties.size();
+ (*ties[k]).score = thisrank;
+ }
+ }
+ }
+
+
+ // H = 12/(N*(N+1)) * (sum Ti^2/n) - 3(N+1)
+ map<string, double> sums;
+ map<string, double> counts;
+ for (set<string>::iterator it = treatments.begin(); it != treatments.end(); it++) { sums[*it] = 0.0; counts[*it] = 0; }
+
+ for (int j = 0; j < values.size(); j++) {
+ sums[values[j].name] += values[j].score;
+ counts[values[j].name]+= 1.0;
+ }
+
+ double middleTerm = 0.0;
+ for (set<string>::iterator it = treatments.begin(); it != treatments.end(); it++) {
+ middleTerm += ((sums[*it]*sums[*it])/counts[*it]);
+ }
+
+ double firstTerm = 12 / (double) (values.size()*(values.size()+1));
+ double lastTerm = 3 * (values.size()+1);
+
+ H = firstTerm * middleTerm - lastTerm;
+
+ //adjust for ties
+ if (TIES.size() != 0) {
+ double sum = 0.0;
+ for (int j = 0; j < TIES.size(); j++) { sum += ((TIES[j]*TIES[j]*TIES[j])-TIES[j]); }
+ double result = 1.0 - (sum / (double) ((values.size()*values.size()*values.size())-values.size()));
+ H /= result;
+ }
+
+ //Numerical Recipes pg221
+ pValue = 1.0 - (gammp(((treatments.size()-1)/(double)2.0), H/2.0));
+
+ return H;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcKruskalWallis");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+//thanks http://www.johndcook.com/cpp_phi.html
+double LinearAlgebra::pnorm(double x){
+ try {
+ // constants
+ double a1 = 0.254829592;
+ double a2 = -0.284496736;
+ double a3 = 1.421413741;
+ double a4 = -1.453152027;
+ double a5 = 1.061405429;
+ double p = 0.3275911;
+
+ // Save the sign of x
+ int sign = 1;
+ if (x < 0)
+ sign = -1;
+ x = fabs(x)/sqrt(2.0);
+
+ // A&S formula 7.1.26
+ double t = 1.0/(1.0 + p*x);
+ double y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*exp(-x*x);
+
+ return 0.5*(1.0 + sign*y);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "pnorm");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcWilcoxon(vector<double>& x, vector<double>& y, double& sig){
+ try {
+ double W = 0.0;
+ sig = 0.0;
+
+ vector<spearmanRank> ranks;
+ for (int i = 0; i < x.size(); i++) {
+ if (m->control_pressed) { return W; }
+ spearmanRank member("x", x[i]);
+ ranks.push_back(member);
+ }
+
+ for (int i = 0; i < y.size(); i++) {
+ if (m->control_pressed) { return W; }
+ spearmanRank member("y", y[i]);
+ ranks.push_back(member);
+ }
+
+ //sort values
+ sort(ranks.begin(), ranks.end(), compareSpearman);
+
+ //convert scores to ranks of x
+ vector<spearmanRank*> ties;
+ int rankTotal = 0;
+ vector<int> TIES;
+ for (int j = 0; j < ranks.size(); j++) {
+ if (m->control_pressed) { return W; }
+ rankTotal += (j+1);
+ ties.push_back(&(ranks[j]));
+
+ if (j != ranks.size()-1) { // you are not the last so you can look ahead
+ if (ranks[j].score != ranks[j+1].score) { // you are done with ties, rank them and continue
+ if (ties.size() > 1) { TIES.push_back(ties.size()); }
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ (*ties[k]).score = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+ if (ties.size() > 1) { TIES.push_back(ties.size()); }
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ (*ties[k]).score = thisrank;
+ }
+ }
+ }
+
+ //from R wilcox.test function
+ //STATISTIC <- sum(r[seq_along(x)]) - n.x * (n.x + 1)/2
+ double sumRanks = 0.0;
+ for (int i = 0; i < ranks.size(); i++) {
+ if (m->control_pressed) { return W; }
+ if (ranks[i].name == "x") { sumRanks += ranks[i].score; }
+ }
+
+ W = sumRanks - x.size() * ((double)(x.size() + 1)) / 2.0;
+
+ //exact <- (n.x < 50) && (n.y < 50)
+ bool findExact = false;
+ if ((x.size() < 50) && (y.size() < 50)) { findExact = true; }
+
+
+ if (findExact && (TIES.size() == 0)) { //find exact and no ties
+ //PVAL <- switch(alternative, two.sided = {
+ //p <- if (STATISTIC > (n.x * n.y/2))
+ PWilcox wilcox;
+ double pval = 0.0;
+ if (W > ((double)x.size()*y.size()/2.0)) {
+ //pwilcox(STATISTIC-1, n.x, n.y, lower.tail = FALSE)
+ pval = wilcox.pwilcox(W-1, x.size(), y.size(), false);
+ }else {
+ //pwilcox(STATISTIC,n.x, n.y)
+ pval = wilcox.pwilcox(W, x.size(), y.size(), true);
+ }
+ sig = 2.0 * pval;
+ if (1.0 < sig) { sig = 1.0; }
+ }else {
+ //z <- STATISTIC - n.x * n.y/2
+ double z = W - (double)(x.size() * y.size()/2.0);
+ //NTIES <- table(r)
+ double sum = 0.0;
+ for (int j = 0; j < TIES.size(); j++) { sum += ((TIES[j]*TIES[j]*TIES[j])-TIES[j]); }
+
+ //SIGMA <- sqrt((n.x * n.y/12) * ((n.x + n.y + 1) -
+ //sum(NTIES^3 - NTIES)/((n.x + n.y) * (n.x + n.y -
+ //1))))
+ double sigma = 0.0;
+ double firstTerm = (double)(x.size() * y.size()/12.0);
+ double secondTerm = (double)(x.size() + y.size() + 1) - sum / (double)((x.size() + y.size()) * (x.size() + y.size() - 1));
+ sigma = sqrt(firstTerm * secondTerm);
+
+ //CORRECTION <- switch(alternative, two.sided = sign(z) * 0.5, greater = 0.5, less = -0.5)
+ double CORRECTION = 0.0;
+ if (z < 0) { CORRECTION = -1.0; }
+ else if (z > 0) { CORRECTION = 1.0; }
+ CORRECTION *= 0.5;
+
+ z = (z - CORRECTION)/sigma;
+
+ //PVAL <- switch(alternative, two.sided = 2 * min(pnorm(z), pnorm(z, lower.tail = FALSE)))
+ sig = pnorm(z);
+ if ((1.0-sig) < sig) { sig = 1.0 - sig; }
+ sig *= 2;
+ }
+
+ return W;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcWilcoxon");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+double LinearAlgebra::choose(double n, double k){
+ try {
+ n = floor(n + 0.5);
+ k = floor(k + 0.5);
+
+ double lchoose = gammln(n + 1.0) - gammln(k + 1.0) - gammln(n - k + 1.0);
+
+ return (floor(exp(lchoose) + 0.5));
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "choose");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcSpearman(vector<double>& x, vector<double>& y, double& sig){
+ try {
+ if (x.size() != y.size()) { m->mothurOut("[ERROR]: vector size mismatch."); m->mothurOutEndLine(); return 0.0; }
+
+ //format data
+ double sf = 0.0; //f^3 - f where f is the number of ties in x;
+ double sg = 0.0; //f^3 - f where f is the number of ties in y;
+ map<float, int> tableX;
+ map<float, int>::iterator itTable;
+ vector<spearmanRank> xscores;
+
+ for (int i = 0; i < x.size(); i++) {
+ spearmanRank member(toString(i), x[i]);
+ xscores.push_back(member);
+
+ //count number of repeats
+ itTable = tableX.find(x[i]);
+ if (itTable == tableX.end()) {
+ tableX[x[i]] = 1;
+ }else {
+ tableX[x[i]]++;
+ }
+ }
+
+
+ //calc LX
+ double Lx = 0.0;
+ for (itTable = tableX.begin(); itTable != tableX.end(); itTable++) {
+ double tx = (double) itTable->second;
+ Lx += ((pow(tx, 3.0) - tx) / 12.0);
+ }
+
+
+ //sort x
+ sort(xscores.begin(), xscores.end(), compareSpearman);
+
+ //convert scores to ranks of x
+ //convert to ranks
+ map<string, float> rankx;
+ vector<spearmanRank> xties;
+ int rankTotal = 0;
+ for (int j = 0; j < xscores.size(); j++) {
+ rankTotal += (j+1);
+ xties.push_back(xscores[j]);
+
+ if (j != xscores.size()-1) { // you are not the last so you can look ahead
+ if (xscores[j].score != xscores[j+1].score) { // you are done with ties, rank them and continue
+ for (int k = 0; k < xties.size(); k++) {
+ float thisrank = rankTotal / (float) xties.size();
+ rankx[xties[k].name] = thisrank;
+ }
+ int t = xties.size();
+ sf += (t*t*t-t);
+ xties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+ for (int k = 0; k < xties.size(); k++) {
+ float thisrank = rankTotal / (float) xties.size();
+ rankx[xties[k].name] = thisrank;
+ }
+ }
+ }
+
+ //format x
+ vector<spearmanRank> yscores;
+ map<float, int> tableY;
+ for (int j = 0; j < y.size(); j++) {
+ spearmanRank member(toString(j), y[j]);
+ yscores.push_back(member);
+
+ itTable = tableY.find(member.score);
+ if (itTable == tableY.end()) {
+ tableY[member.score] = 1;
+ }else {
+ tableY[member.score]++;
+ }
+
+ }
+
+ //calc Ly
+ double Ly = 0.0;
+ for (itTable = tableY.begin(); itTable != tableY.end(); itTable++) {
+ double ty = (double) itTable->second;
+ Ly += ((pow(ty, 3.0) - ty) / 12.0);
+ }
+
+ sort(yscores.begin(), yscores.end(), compareSpearman);
+
+ //convert to ranks
+ map<string, float> rank;
+ vector<spearmanRank> yties;
+ rankTotal = 0;
+ for (int j = 0; j < yscores.size(); j++) {
+ rankTotal += (j+1);
+ yties.push_back(yscores[j]);
+
+ if (j != yscores.size()-1) { // you are not the last so you can look ahead
+ if (yscores[j].score != yscores[j+1].score) { // you are done with ties, rank them and continue
+ for (int k = 0; k < yties.size(); k++) {
+ float thisrank = rankTotal / (float) yties.size();
+ rank[yties[k].name] = thisrank;
+ }
+ int t = yties.size();
+ sg += (t*t*t-t);
+ yties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+ for (int k = 0; k < yties.size(); k++) {
+ float thisrank = rankTotal / (float) yties.size();
+ rank[yties[k].name] = thisrank;
+ }
+ }
+ }
+
+ double di = 0.0;
+ for (int k = 0; k < x.size(); k++) {
+
+ float xi = rankx[toString(k)];
+ float yi = rank[toString(k)];
+
+ di += ((xi - yi) * (xi - yi));
+ }
+
+ double p = 0.0;
+
+ double n = (double) x.size();
+ double SX2 = ((pow(n, 3.0) - n) / 12.0) - Lx;
+ double SY2 = ((pow(n, 3.0) - n) / 12.0) - Ly;
+
+ p = (SX2 + SY2 - di) / (2.0 * sqrt((SX2*SY2)));
+
+ //Numerical Recipes 646
+ sig = calcSpearmanSig(n, sf, sg, di);
+
+ return p;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcSpearman");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcSpearmanSig(double n, double sf, double sg, double d){
+ try {
+
+ double sig = 0.0;
+ double probrs = 0.0;
+ double en=n;
+ double en3n=en*en*en-en;
+ double aved=en3n/6.0-(sf+sg)/12.0;
+ double fac=(1.0-sf/en3n)*(1.0-sg/en3n);
+ double vard=((en-1.0)*en*en*SQR(en+1.0)/36.0)*fac;
+ double zd=(d-aved)/sqrt(vard);
+ double probd=erfcc(fabs(zd)/1.4142136);
+ double rs=(1.0-(6.0/en3n)*(d+(sf+sg)/12.0))/sqrt(fac);
+ fac=(rs+1.0)*(1.0-rs);
+ if (fac > 0.0) {
+ double t=rs*sqrt((en-2.0)/fac);
+ double df=en-2.0;
+ probrs=betai(0.5*df,0.5,df/(df+t*t));
+ }else {
+ probrs = 0.0;
+ }
+
+ //smaller of probd and probrs is sig
+ sig = probrs;
+ if (probd < probrs) { sig = probd; }
+
+ if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+
+ return sig;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcSpearmanSig");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcPearson(vector<double>& x, vector<double>& y, double& sig){
+ try {
+ if (x.size() != y.size()) { m->mothurOut("[ERROR]: vector size mismatch."); m->mothurOutEndLine(); return 0.0; }
+
+ //find average X
+ float averageX = 0.0;
+ for (int i = 0; i < x.size(); i++) { averageX += x[i]; }
+ averageX = averageX / (float) x.size();
+
+ //find average Y
+ float sumY = 0.0;
+ for (int j = 0; j < y.size(); j++) { sumY += y[j]; }
+ float Ybar = sumY / (float) y.size();
+
+ double r = 0.0;
+ double numerator = 0.0;
+ double denomTerm1 = 0.0;
+ double denomTerm2 = 0.0;
+
+ for (int j = 0; j < x.size(); j++) {
+ float Yi = y[j];
+ float Xi = x[j];
+
+ numerator += ((Xi - averageX) * (Yi - Ybar));
+ denomTerm1 += ((Xi - averageX) * (Xi - averageX));
+ denomTerm2 += ((Yi - Ybar) * (Yi - Ybar));
+ }
+
+ double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
+
+ r = numerator / denom;
+
+ //Numerical Recipes pg.644
+ sig = calcPearsonSig(x.size(), r);
+
+ return r;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcPearson");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcPearsonSig(double n, double r){
+ try {
+
+ double sig = 0.0;
+ const double TINY = 1.0e-20;
+ double z = 0.5*log((1.0+r+TINY)/(1.0-r+TINY)); //Fisher's z transformation
+
+ //code below was giving an error in betacf with sop files
+ //int df = n-2;
+ //double t = r*sqrt(df/((1.0-r+TINY)*(1.0+r+TINY)));
+ //sig = betai(0.5+df, 0.5, df/(df+t*t));
+
+ //Numerical Recipes says code below gives approximately the same result
+ sig = erfcc(fabs(z*sqrt(n-1.0))/1.4142136);
+ if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+
+ return sig;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcPearsonSig");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+vector<vector<double> > LinearAlgebra::getObservedEuclideanDistance(vector<vector<double> >& relAbundData){
+ try {
+
+ int numSamples = relAbundData.size();
+ int numOTUs = relAbundData[0].size();
+
+ vector<vector<double> > dMatrix(numSamples);
+ for(int i=0;i<numSamples;i++){
+ dMatrix[i].resize(numSamples);
+ }
+
+ for(int i=0;i<numSamples;i++){
+ for(int j=0;j<numSamples;j++){
+
+ if (m->control_pressed) { return dMatrix; }
+
+ double d = 0;
+ for(int k=0;k<numOTUs;k++){
+ d += pow((relAbundData[i][k] - relAbundData[j][k]), 2.0000);
+ }
+ dMatrix[i][j] = pow(d, 0.50000);
+ dMatrix[j][i] = dMatrix[i][j];
+
+ }
+ }
+ return dMatrix;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "getObservedEuclideanDistance");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+vector<double> LinearAlgebra::solveEquations(vector<vector<double> > A, vector<double> b){
+ try {
+ int length = (int)b.size();
+ vector<double> x(length, 0);
+ vector<int> index(length);
+ for(int i=0;i<length;i++){ index[i] = i; }
+ double d;
+
+ ludcmp(A, index, d); if (m->control_pressed) { return b; }
+ lubksb(A, index, b);
+
+ return b;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "solveEquations");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+vector<float> LinearAlgebra::solveEquations(vector<vector<float> > A, vector<float> b){
+ try {
+ int length = (int)b.size();
+ vector<double> x(length, 0);
+ vector<int> index(length);
+ for(int i=0;i<length;i++){ index[i] = i; }
+ float d;
+
+ ludcmp(A, index, d); if (m->control_pressed) { return b; }
+ lubksb(A, index, b);
+
+ return b;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "solveEquations");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+
+void LinearAlgebra::ludcmp(vector<vector<double> >& A, vector<int>& index, double& d){
+ try {
+ double tiny = 1e-20;
+
+ int n = (int)A.size();
+ vector<double> vv(n, 0.0);
+ double temp;
+ int imax;
+
+ d = 1.0;
+
+ for(int i=0;i<n;i++){
+ double big = 0.0;
+ for(int j=0;j<n;j++){ if((temp=fabs(A[i][j])) > big ) big=temp; }
+ if(big==0.0){ m->mothurOut("Singular matrix in routine ludcmp\n"); }
+ vv[i] = 1.0/big;
+ }
+
+ for(int j=0;j<n;j++){
+ if (m->control_pressed) { break; }
+ for(int i=0;i<j;i++){
+ double sum = A[i][j];
+ for(int k=0;k<i;k++){ sum -= A[i][k] * A[k][j]; }
+ A[i][j] = sum;
+ }
+
+ double big = 0.0;
+ for(int i=j;i<n;i++){
+ double sum = A[i][j];
+ for(int k=0;k<j;k++){ sum -= A[i][k] * A[k][j]; }
+ A[i][j] = sum;
+ double dum;
+ if((dum = vv[i] * fabs(sum)) >= big){
+ big = dum;
+ imax = i;
+ }
+ }
+ if(j != imax){
+ for(int k=0;k<n;k++){
+ double dum = A[imax][k];
+ A[imax][k] = A[j][k];
+ A[j][k] = dum;
+ }
+ d = -d;
+ vv[imax] = vv[j];
+ }
+ index[j] = imax;
+
+ if(A[j][j] == 0.0){ A[j][j] = tiny; }
+
+ if(j != n-1){
+ double dum = 1.0/A[j][j];
+ for(int i=j+1;i<n;i++){ A[i][j] *= dum; }
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "ludcmp");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+
+void LinearAlgebra::lubksb(vector<vector<double> >& A, vector<int>& index, vector<double>& b){
+ try {
+ double total;
+ int n = (int)A.size();
+ int ii = 0;
+
+ for(int i=0;i<n;i++){
+ if (m->control_pressed) { break; }
+ int ip = index[i];
+ total = b[ip];
+ b[ip] = b[i];
+
+ if (ii != 0) {
+ for(int j=ii-1;j<i;j++){
+ total -= A[i][j] * b[j];
+ }
+ }
+ else if(total != 0){ ii = i+1; }
+ b[i] = total;
+ }
+ for(int i=n-1;i>=0;i--){
+ total = b[i];
+ for(int j=i+1;j<n;j++){ total -= A[i][j] * b[j]; }
+ b[i] = total / A[i][i];
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "lubksb");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+void LinearAlgebra::ludcmp(vector<vector<float> >& A, vector<int>& index, float& d){
+ try {
+ double tiny = 1e-20;
+
+ int n = (int)A.size();
+ vector<float> vv(n, 0.0);
+ double temp;
+ int imax;
+
+ d = 1.0;
+
+ for(int i=0;i<n;i++){
+ float big = 0.0;
+ for(int j=0;j<n;j++){ if((temp=fabs(A[i][j])) > big ) big=temp; }
+ if(big==0.0){ m->mothurOut("Singular matrix in routine ludcmp\n"); }
+ vv[i] = 1.0/big;
+ }
+
+ for(int j=0;j<n;j++){
+ if (m->control_pressed) { break; }
+ for(int i=0;i<j;i++){
+ float sum = A[i][j];
+ for(int k=0;k<i;k++){ sum -= A[i][k] * A[k][j]; }
+ A[i][j] = sum;
+ }
+
+ float big = 0.0;
+ for(int i=j;i<n;i++){
+ float sum = A[i][j];
+ for(int k=0;k<j;k++){ sum -= A[i][k] * A[k][j]; }
+ A[i][j] = sum;
+ float dum;
+ if((dum = vv[i] * fabs(sum)) >= big){
+ big = dum;
+ imax = i;
+ }
+ }
+ if(j != imax){
+ for(int k=0;k<n;k++){
+ float dum = A[imax][k];
+ A[imax][k] = A[j][k];
+ A[j][k] = dum;
+ }
+ d = -d;
+ vv[imax] = vv[j];
+ }
+ index[j] = imax;
+
+ if(A[j][j] == 0.0){ A[j][j] = tiny; }
+
+ if(j != n-1){
+ float dum = 1.0/A[j][j];
+ for(int i=j+1;i<n;i++){ A[i][j] *= dum; }
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "ludcmp");
+ exit(1);
+ }
+}
+