[R] Error pvclust package: Error in hclust(distance, method = method.hclust)

[Peter Langfelder]

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 <jovanisouza5 using 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*****
>
>
>
>
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> 14/12/20
> 19:37:37
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