Ansley, I think you may have an old version of clustsig: the current one should not give an error of missing undef.zero. Please check if you need to update.
cheers, j.o. > On 7 Oct 2016, at 19:21 pm, Sarah Goslee <sarah.gos...@gmail.com> wrote: > > I can't duplicate your error. Assuming the attached document describes > your data, it works fine. I changed the code to use braycurtis instead > of euclidean, as you wanted, and it does return a warning, just as the > help file documents. > > So you'll need to provide more information. > > > data<- structure(list(necsur = c(1L, 4L, 0L, 8L, 0L, 1L), necame = c(4L, > 5L, 9L, 9L, 4L, 7L), niccar = c(1L, 1L, 1L, 2L, 1L, 4L), nicorb = c(2L, > 20L, 23L, 26L, 3L, 12L), nicpus = c(0L, 0L, 1L, 0L, 0L, 0L), > nictor = c(0L, 2L, 1L, 3L, 2L, 1L), delgib = c(10L, 31L, > 47L, 48L, 15L, 55L), cancha = c(5L, 6L, 4L, 4L, 1L, 6L), > melbis = c(3L, 0L, 1L, 3L, 0L, 1L), atelec = c(4L, 6L, 28L, > 22L, 8L, 52L), copmin = c(0L, 0L, 1L, 1L, 0L, 1L), ontcon = c(3L, > 3L, 11L, 7L, 1L, 2L), ontdep = c(2L, 0L, 0L, 0L, 0L, 0L), > onthec = c(17L, 15L, 9L, 6L, 6L, 2L), ontstr = c(0L, 0L, > 0L, 1L, 1L, 0L), onttau = c(20L, 13L, 6L, 2L, 0L, 2L), ontpen = c(2L, > 3L, 5L, 3L, 2L, 4L), onttub = c(2L, 3L, 4L, 1L, 1L, 0L), > phavin = c(1L, 0L, 0L, 0L, 0L, 1L), Phyili = c(0L, 0L, 0L, > 0L, 0L, 1L), canvir = c(0L, 1L, 0L, 0L, 0L, 0L), hybill = c(1L, > 0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L, 0L, 1L, 1L), > galjan = c(0L, 0L, 1L, 1L, 0L, 0L), cyclosig = c(0L, 0L, > 0L, 0L, 1L, 0L), omomon = c(1L, 2L, 4L, 10L, 1L, 6L), trofov = c(1L, > 2L, 3L, 1L, 0L, 1L), trouni = c(1L, 0L, 0L, 1L, 0L, 0L), > troter = c(0L, 1L, 1L, 0L, 0L, 0L), eusass = c(9L, 8L, 23L, > 14L, 11L, 28L), hiscoe = c(2L, 1L, 10L, 4L, 2L, 4L), hisabb = c(0L, > 0L, 0L, 0L, 2L, 0L), cremax = c(4L, 7L, 1L, 2L, 2L, 5L), > plamac = c(1L, 0L, 3L, 2L, 2L, 2L), plafem = c(0L, 0L, 0L, > 0L, 0L, 0L), plafos = c(1L, 1L, 3L, 2L, 1L, 2L), placom = c(6L, > 3L, 3L, 10L, 13L, 7L), tacfim = c(0L, 0L, 1L, 0L, 0L, 0L)), .Names > = c("necsur", > "necame", "niccar", "nicorb", "nicpus", "nictor", "delgib", "cancha", > "melbis", "atelec", "copmin", "ontcon", "ontdep", "onthec", "ontstr", > "onttau", "ontpen", "onttub", "phavin", "Phyili", "canvir", "hybill", > "cyclev", "galjan", "cyclosig", "omomon", "trofov", "trouni", > "troter", "eusass", "hiscoe", "hisabb", "cremax", "plamac", "plafem", > "plafos", "placom", "tacfim"), row.names = c("AP-0", "AP-100", > "AP-200", "AP-300", "ST-0", "ST-100"), class = "data.frame") > > >> simprof(data, num.expected=1000, num.simulated=999, > + method.cluster="average", method.distance="braycurtis", > + method.transform="identity", alpha=0.05, > + sample.orientation="row", const=0, > + silent=TRUE, increment=100, > + undef.zero=TRUE, warn.braycurtis=TRUE) > $numgroups > [1] 2 > > $pval > [,1] [,2] [,3] > [1,] -3 -4 NA > [2,] -6 1 0.461461461 > [3,] -1 -2 NA > [4,] -5 3 0.905905906 > [5,] 2 4 0.003003003 > > $hclust > > Call: > hclust(d = rawdata.dist, method = method.cluster) > > Cluster method : average > Number of objects: 6 > > > $significantclusters > $significantclusters[[1]] > [1] "ST-100" "AP-200" "AP-300" > > $significantclusters[[2]] > [1] "ST-0" "AP-0" "AP-100" > > > Warning messages: > 1: This version of the Bray-Curtis index does not use standardization. > 2: To use the standardized version, use "actual-braycurtis". > 3: See the help documentation for more information. > > > On Thu, Oct 6, 2016 at 8:43 PM, Ansley Silva <daily.p...@gmail.com> wrote: >> Hello all, >> >> I'm using R version 3.3.1, clustsig package. >> >> I have a community dataset and I originally used hclust in the vegan >> package to get dendrograms, however I need significance on the groups that >> were formed. I'd really like to use SIMPROF to look for significance among >> the groups, but I am running into errors. >> >> >> These are the errors I get: >> >>> simprof(apst, num.expected=1000, num.simulated=999, >> method.cluster="average", method.distance="braycurtis", alpha=0.05, >> sample.orientation = "column", const = 0, silent = TRUE,increment=100) >> >> Error: argument "undef.zero" is missing, with no default >> In addition: Warning messages: >> 1: This version of the Bray-Curtis index does not use standardization. >> 2: To use the standardized version, use "actual-braycurtis". >> 3: See the help documentation for more information. >> >>> simprof(apst, num.expected=1000, num.simulated=999, >> method.cluster="average", method.distance="actual-braycurtis", alpha=0.05, >> sample.orientation = "column", const = 0, silent = TRUE,increment=100) >> >> Error in if (denom != 0) { : missing value where TRUE/FALSE needed >> >>> simprof(apst, num.expected=1000, num.simulated=999, >> method.cluster="average", method.distance="braycurtis", alpha=0.05, >> sample.orientation = "column", const = 0, silent = TRUE,increment=100) >> >> Error: argument "undef.zero" is missing, with no default >> In addition: Warning messages: >> 1: This version of the Bray-Curtis index does not use standardization. >> 2: To use the standardized version, use "actual-braycurtis". >> 3: See the help documentation for more information. >> >>> simprof(apst, num.expected=1000, num.simulated=999, >> method.cluster="average", >> method.transform="log",method.distance="braycurtis", alpha=0.05, >> sample.orientation = "column", const = 0, silent = TRUE,increment=100) >> >> Error in if (pval > alpha) { : missing value where TRUE/FALSE needed >> In addition: Warning messages: >> 1: This version of the Bray-Curtis index does not use standardization. >> 2: To use the standardized version, use "actual-braycurtis". >> 3: See the help documentation for more information. >> >> >> >> I have some samples were the columns added up to zero, so I tried removing >> them since I was using method.transform="log". But that didn't seem to >> change anything. >> I also tried transposing the data, but no luck there. >> I am using braycurtis, but have tried actual-braycurtis and that did not >> help. >> I have also tried tweeking undef.zero. >> >> >> If anyone could help provide some solutions, that would be greatly >> appreciated. >> Please and thank you, >> >> -- >> Ansley Silva >> > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology