[R] cluster analysis error - mclust package
I am following instructions online for cluster analysis using the mclust package, and keep getting errors. http://www.statmethods.net/advstats/cluster.html These are the instructions (there is no sample dataset unfortunately): # Model Based Clustering library(mclust) fit - Mclust(mydata) plot(fit, mydata) # plot results print(fit) # display the best model This is what I did and the error I get: library(mclust) fit - Mclust(mydat) plot(fit, mydat) #plot results Error in match.arg(what, c(BIC, classification, uncertainty, density), : 'arg' must be NULL or a character vector My data is arranged so I have each row representing one individual with 9 values for morphological data. I want to see if they will group into 2 clusters, representing gender. I have tried using the instructions from the cran-r website, but they didn't work either Any help would be great, thank you -- View this message in context: http://r.789695.n4.nabble.com/cluster-analysis-error-mclust-package-tp4650842.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] cluster analysis in R
These are the errors I've been having. I have been trying 3 different things 1- Mclust: This is the example I have been following: # Model Based Clustering library(mclust) fit - Mclust(mydata) plot(fit, mydata) # plot results print(fit) # display the best model What I have done: fit - Mclust(mydat) plot(fit, mydat) #plot results Error in match.arg(what, c(BIC, classification, uncertainty, density), : 'arg' must be NULL or a character vector 2- Mclust using different website (cran-r) instructions This is the example: mydatMclust - Mclust(mydat) summary(mydatMclust) summary(mydatMclust, parameters = TRUE) plot(mydatMclust) There are a couple other steps but the plot is the problem. I get two plots, there should be four. One should be plotting all my individuals but it's plotting my variables instead. It's also taking a very long time. R script at this point says: Waiting to confirm page change… 3. Mcclust Instructions from cran-r: data(cls.draw2) # sample of 500 clusterings from a Bayesian cluster model tru.class - rep(1:8,each=50) # the true grouping of the observations psm2 - comp.psm(cls.draw2) # posterior similarity matrix # optimize criteria based on PSM mbind2 - minbinder(psm2) mpear2 - maxpear(psm2) # Relabelling k - apply(cls.draw2,1, function(cl) length(table(cl))) max.k - as.numeric(names(table(k))[which.max(table(k))]) relab2 - relabel(cls.draw2[k==max.k,]) # compare clusterings found by different methods with true grouping arandi(mpear2$cl, tru.class) arandi(mbind2$cl, tru.class) arandi(relab2$cl, tru.class) I called my data: mydat so I changed that where appropriate. I cannot get past one early step, psm2 - comp.psm(cls.draw2).. the error reads: Error: could not find function comp.psm I think I have all appropriate packages installed. I don't know what more to do on these three errors. Any help would be great! Thank you -- View this message in context: http://r.789695.n4.nabble.com/cluster-analysis-in-R-tp4649635p4650466.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] Bayesian cluster analysis - R functions
I want to try Bayesian cluster analysis. Someone suggested using package mcclust. Is there a website that says how to install mcclust or another appropriate Bayesian package? Including the appropriate R functions that I can follow? I am trying to get probability of membership for each individual I am trying to cluster Thank you! -- View this message in context: http://r.789695.n4.nabble.com/Bayesian-cluster-analysis-R-functions-tp4650337.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] cluster analysis in R
Thank you for replying! I made a new post asking if there are any websites or files on how to download package mclust (or other Bayesian cluster analysis packages) and the appropriate R functions? Sorry I don't know how this forum works yet -- View this message in context: http://r.789695.n4.nabble.com/cluster-analysis-in-R-tp4649635p4650341.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] cluster analysis in R
Thanks, I have been trying that site and another one (http://www.statmethods.net/advstats/cluster.html) I don't know if I should be doing mclust or mcclust, but either way, the codes are not working. I am following the guidelines online at: mcclust - http://cran.r-project.org/web/packages/mcclust/mcclust.pdf mclust - http://cran.r-project.org/ I am relatively new to R, but so far I have been able to figure out dfa, manova, pca... I cannot get these codes to work, I keep getting various errors. Are there other resources that have details about what codes to use or what to do when errors result? I have not found anything else helpful Thank you -- View this message in context: http://r.789695.n4.nabble.com/cluster-analysis-in-R-tp4649635p4650397.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] cluster analysis in R
I have two issues. 1-I am trying to use morphology to identify gender. I have 9 variables, both continuous and categorical. I was using two-step cluster analysis in SPSS because two-step could deal with different types of variables. But the output tells me that an animal is in cluster 1 or 2, it does not give me a probability (ex. 0.70 cluster 2). I also did not want to specify that I want two clusters, I wanted to see if analysis would naturally give me two clusters. These were all advantages to using SPSS but now I'm having trouble. Does cluster analysis in R give probabilities? Which type of cluster analysis in R is best to use? I did not think hierarchical analysis was a great choice, but maybe I'm wrong. I don't want to create the average variable, I want the analysis to do it on its own. I'm also new to R so would have to figure out the right codes to enter, etc. 2-I was also told to analyze each variable on its own before including it in cluster analysis. I had first included them all then teased out which ones were not important, but now have been asked to do the reverse. I cannot do cluster analysis on one variable -for example, one variable is either present or absent on an individual so of course cluster analysis gives me two clusters, one representing present and one representing absent. I was told to use regression, but how can regression also not give the same result? I feel like it would give me a line connecting a bunch of 0s to 1s. I don't know what to use, or if I can analyze each variable like this before putting them into cluster analysis. I ultimately want to only use the smallest number of variables necessary to identify gender. I have tried reading manuals etc and talking to people at my school, but nothing has helped. If anyone has any insight, that would be much appreciated Thank you! -- View this message in context: http://r.789695.n4.nabble.com/cluster-analysis-in-R-tp4649635.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
