kulczynski vs skulczynski for collect.shared, summary,shared

collectsharedcommand.cpp and summarysharedcommand.cpp have CommandParameter pcalc with an option of skulczynski instead of kulczynski

I’m afraid I don’t follow - using calc=kulczynski in summary.shared and collect.shared seems to be working fine… What you’re looking at are the variable names in the source code, not what you actually need to enter to run the command.

Hope this helps,
Pat

If one chooses kulczynski in collect.shared there is no output file for that estimator:

mothur > collect.shared(shared=patient70.fn.shared,label=0.01-0.10,calc=kulczynski-jest-sorest)

0.01
0.10

Output File Names:
patient70.fn.jest
patient70.fn.sorest


mothur > collect.shared(shared=patient70.fn.shared,label=0.01-0.10,calc=skulczynski-jest-sorest)

skulczynski is not a valid estimator for the collect.shared command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker,
0.01
0.10

Output File Names:
patient70.fn.jest
patient70.fn.sorest

I presume that may result from an inconsistency in the name used for the kulczynski estimator.

$ grep -n ‘kulczynski[-"]’ collectsharedcommand.cpp
60: CommandParameter pcalc(“calc”, “Multiple”, “sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-skulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson”, “sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan”, “”, “”, “”,true,false); parameters.push_back(pcalc);
122: outputTypes[“skulczynski”] = tempOutNames;
136: outputTypes[“structkulczynski”] = tempOutNames;
193: outputTypes[“skulczynski”] = tempOutNames;
207: outputTypes[“structkulczynski”] = tempOutNames;
332: }else if (Estimators == “skulczynski”) {
333: cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+“kulczynski”)));
334: outputNames.push_back(fileNameRoot+“kulczynski”); outputTypes[“kulczynski”].push_back(fileNameRoot+“kulczynski”);
374: }else if (Estimators == “structkulczynski”) {
375: cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+“structkulczynski”)));
376: outputNames.push_back(fileNameRoot+“structkulczynski”); outputTypes[“structkulczynski”].push_back(fileNameRoot+“structkulczynski”);

Thanks for bringing this to our attention. It will be fixed in the next release of mothur.