Re: [R-sig-eco] Errors with Simprof for cluster significance
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 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,] -61 0.461461461 > [3,] -1 -2 NA > [4,] -53 0.905905906 > [5,]24 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 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) >>
Re: [R-sig-eco] Errors with Simprof for cluster significance
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,] -61 0.461461461 [3,] -1 -2 NA [4,] -53 0.905905906 [5,]24 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 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
[R-sig-eco] Errors with Simprof for cluster significance
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 *"The clearest way into the Universe is through a forest wilderness." John Muir* *Graduate Research Assistant* *University of Georgia* *D.B. Warnell School of Forestry and Natural Resources* *180 East Green Street* *Athens, GA 30602* packages: vegan, clustsig 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(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