sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
relabundfile = validParameter.validFile(parameters, "relabund", true);
if (relabundfile == "not open") { relabundfile = ""; abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
relabundfile = validParameter.validFile(parameters, "relabund", true);
if (relabundfile == "not open") { relabundfile = ""; abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
//fill matrix with shared relative abundances, re-center
for (int i = 0; i < lookupFloat.size(); i++) {
matrix[i].resize(numOTUs, 0);
//fill matrix with shared relative abundances, re-center
for (int i = 0; i < lookupFloat.size(); i++) {
matrix[i].resize(numOTUs, 0);
pcaData << name_list[i] << '\t';
for(int j=0;j<numEigenValues;j++){
pcaData << G[i][j] << '\t';
pcaData << name_list[i] << '\t';
for(int j=0;j<numEigenValues;j++){
pcaData << G[i][j] << '\t';