We are not going to be able to help much without the data. You say it is "more or less" the same as the example data so maybe it is "less" similar than you think.
Another possibility is that you keep using fix() for some reason that you have not explained. That function calls edit() which can strip attributes and that can create problems with some data.frames and matrices as the manual page warns: "Editing an R object may change it in ways other than are obvious: see the comment under edit. See edit.data.frame for changes that can occur when editing a data frame or matrix." If you just want to look at the data use, View() not fix(). ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Brenzo Sent: Wednesday, May 20, 2015 3:59 AM To: r-help@r-project.org Subject: [R] Error after performing anosim function with vegan Hello, so I'm relatively new in R, but normally i don't have big problems by using R. But today i struggle a lot with an error message that occurred the first time. Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic I'm using just a normal anosim function and 2 weeks ago it was working fine with the same files and the same script. So maybe some of you can help me. Here is the total script: > data <-read.csv("H:\\PhD\\Ergebnisse Versuch Norwegen\\T-RFLP\\nirK > Adonis2.csv") > fix (data) > data1 <- (data [,-1]) > fix (data1) > cca.env<- read.csv ("H:\\PhD\\Ergebnisse Versuch > Norwegen\\T-RFLP\\env2.csv", + header= TRUE, ) > fix(cca.env) > du<- vegdist(data) > fix(du) > attach(cca.env) > dune.ano <- anosim(du, Sample) > summary(dune.ano) Call: anosim(dat = du, grouping = Sample) Dissimilarity: bray ANOSIM statistic R: Significance: 0.001 Permutation: free Number of permutations: 999 Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic it is more or less exactly the same matrix than in the example from R: > data(dune) > fix(dune) > data(dune.env) > fix(dune.env) > dune.dist <- vegdist(dune) > attach(dune.env) > dune.ano <- anosim(dune.dist, Management) > summary(dune.ano) Call: anosim(dat = dune.dist, grouping = Management) Dissimilarity: bray ANOSIM statistic R: 0.2579 Significance: 0.008 Permutation: free Number of permutations: 999 Upper quantiles of permutations (null model): 90% 95% 97.5% 99% 0.115 0.151 0.192 0.250 Dissimilarity ranks between and within classes: 0% 25% 50% 75% 100% N Between 4 58.50 104.00 145.500 188.0 147 BF 5 15.25 25.50 41.250 57.0 3 HF 1 7.25 46.25 68.125 89.5 10 NM 6 64.75 124.50 156.250 181.0 15 SF 3 32.75 53.50 99.250 184.0 15 Greetings Kristof -- View this message in context: http://r.789695.n4.nabble.com/Error-after-performing-anosim-function-with-vegan-tp4707444.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
