I don't use pvclust but from a cursory reading and from the error indicating bootstrap I am guessing that pvclust carries out some sort of a sampling of the features on which you cluster. Since you only retain two features (coordinates), the sampling necessarily results in just one feature being retained, leading to an error. Just my guess though; understanding what pvclust does would help you diagnose the problem.
Peter On Mon, Dec 14, 2020 at 2:48 PM Jovani T. de Souza <jovanisou...@gmail.com> wrote: > This question was also made in > > https://stackoverflow.com/questions/65290436/error-pvclust-package-error-in-hclustdistance-method-method-hclust-must > > Question: > > Could you help me resolve the following error: > > Error in hclust(distance, method = method.hclust) : > must have n >= 2 objects to cluster > > I'm trying to use the `pvclust` package, but I'm not able to generate the > dendogram. If I use all data from the df database, I can generate it, but > as I am restricting only to the coordinates (Latitude and Longitude), it is > not working, it gives the error that I mentioned. Below, I entered an > executable code. > > Thank you so much! > > > ###USING PVCLUST > > library(rdist) > library(pvclust) > library(geosphere) > > df <- structure( > list(Industries = c(1,2,3,4,5,6,7), Latitude = c(-24.779225, > -24.789635, -24.763461, -24.794394, -24.747102,-24.781307,-24.761081), > Longitude = c(-49.934816, -49.922324, -49.911616, -49.906262, > -49.890796,-49.8875254,-49.8875254), > Waste = c(526, 350, 526, 469, 285, 433, 456)),class = > "data.frame", row.names = c(NA, -7L)) > > mat <- as.data.frame.matrix(df) > mat <- t(mat) > fit <- pvclust(mat, method.hclust="average", method.dist="euclidean") > fit > plot(fit) > pvrect(fit) > > > # RESTRICTING ONLY TO COORDINATES > coordinates<-subset(df,select=c("Latitude","Longitude")) > mat <- as.data.frame.matrix(coordinates) > mat <- t(mat) > fit <- pvclust(mat, method.hclust="average", method.dist="euclidean") > > fit <- pvclust(mat, method.hclust="average", method.dist="euclidean") > Bootstrap (r = 0.5)... Error in hclust(distance, method = > method.hclust) : > must have n >= 2 objects to cluster***** > > > > > [image: Mailtrack] > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&; > > > Remetente > notificado por > Mailtrack > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&; > > > 14/12/20 > 19:37:37 > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > [[alternative HTML version deleted]] ______________________________________________ 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.
