+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
+ if (Estimators[i] == "sobs") {
+ rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
+ outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
+ }else if (Estimators[i] == "chao") {
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
+ outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
+ }else if (Estimators[i] == "ace") {
+ if(abund < 5)
+ abund = 10;
+ rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
+ outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
+ }else if (Estimators[i] == "jack") {
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
+ outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
+ }else if (Estimators[i] == "shannon") {
+ rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
+ outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
+ }else if (Estimators[i] == "shannoneven") {
+ rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
+ outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
+ }else if (Estimators[i] == "heip") {
+ rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
+ outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
+ }else if (Estimators[i] == "r_shannonrange") {
+ rDisplays.push_back(new RareDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("r_shannonrange", variables))));
+ outputNames.push_back(getOutputFileName("r_shannonrange", variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannonrange", variables));
+ }else if (Estimators[i] == "smithwilson") {
+ rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
+ outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
+ }else if (Estimators[i] == "npshannon") {
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
+ outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
+ }else if (Estimators[i] == "simpson") {
+ rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
+ outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
+ }else if (Estimators[i] == "simpsoneven") {
+ rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
+ outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
+ }else if (Estimators[i] == "invsimpson") {
+ rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
+ outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
+ }else if (Estimators[i] == "bootstrap") {
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
+ outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
+ }else if (Estimators[i] == "coverage") {
+ rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
+ outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
+ }else if (Estimators[i] == "nseqs") {
+ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
+ outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
+ }
+ if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
+ }