as.dendogram.hbscan not found

[gemcavoy]

When running this example and others, R can't find the as. dendogram.hdbscan

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as_dendrogram_hdbscan(hdbscanobj))

Error in plot(as_dendrogram_hdbscan(hdbscanobj)) : could not find function "as_dendrogram_hdbscan"

[elbamos]

Thanks for reporting - its an error in the example. It's as.dendrogram.hdbscan instead of as_dendrogram_hdbscan.

On May 2, 2017, at 11:27 AM, gemcavoy notifications@github.com wrote:

When running this example and others, R can't find the as. dendogram.hdbscan

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as_dendrogram_hdbscan(hdbscanobj))

Error in plot(as_dendrogram_hdbscan(hdbscanobj)) : could not find function "as_dendrogram_hdbscan"

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[gemcavoy]

Thanks very much for your reply.

I actually tried it that way as well before I raised the issue and got the same error. Tried it again just to confirm and still got the error.

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as.dendrogram.hdbscan(hdbscanobj))

On Tue, May 2, 2017 at 11:30 AM, elbamos notifications@github.com wrote:

Thanks for reporting - its an error in the example. It's as.dendrogram.hdbscan instead of as_dendrogram_hdbscan.

On May 2, 2017, at 11:27 AM, gemcavoy notifications@github.com wrote:

When running this example and others, R can't find the as. dendogram.hdbscan

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as_dendrogram_hdbscan(hdbscanobj))

Error in plot(as_dendrogram_hdbscan(hdbscanobj)) : could not find function "as_dendrogram_hdbscan"

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[gemcavoy]

Here's the session info if that's of use:

R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] RCurl_1.95-4.8 bitops_1.0-6 largeVis_0.2 Matrix_1.2-9 Rcpp_0.12.10 [6] rstan_2.15.1 StanHeaders_2.15.0-1 ggplot2_2.2.1

loaded via a namespace (and not attached): [1] lattice_0.20-35 codetools_0.2-15 grid_3.4.0 plyr_1.8.4 gtable_0.2.0 stats4_3.4.0 [7] scales_0.4.1 lazyeval_0.2.0 tools_3.4.0 munsell_0.4.3 parallel_3.4.0 compiler_3.4.0 [13] inline_0.3.14 colorspace_1.3-2 gridExtra_2.2.1 tibble_1.3.0

On Tue, May 2, 2017 at 12:24 PM, Greg McAvoy greg.mcavoy@gmail.com wrote:

Thanks very much for your reply.

I actually tried it that way as well before I raised the issue and got the same error. Tried it again just to confirm and still got the error.

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as.dendrogram.hdbscan(hdbscanobj))

On Tue, May 2, 2017 at 11:30 AM, elbamos notifications@github.com wrote:

Thanks for reporting - its an error in the example. It's as.dendrogram.hdbscan instead of as_dendrogram_hdbscan.

On May 2, 2017, at 11:27 AM, gemcavoy notifications@github.com wrote:

When running this example and others, R can't find the as. dendogram.hdbscan

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as_dendrogram_hdbscan(hdbscanobj))

Error in plot(as_dendrogram_hdbscan(hdbscanobj)) : could not find function "as_dendrogram_hdbscan"

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[elbamos]

Because you should only have to call as.dendrogram -- it's an s3 function. That's why I changed it.

On May 2, 2017, at 12:24 PM, gemcavoy notifications@github.com wrote:

Thanks very much for your reply.

I actually tried it that way as well before I raised the issue and got the same error. Tried it again just to confirm and still got the error.

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as.dendrogram.hdbscan(hdbscanobj))

On Tue, May 2, 2017 at 11:30 AM, elbamos notifications@github.com wrote:

Thanks for reporting - its an error in the example. It's as.dendrogram.hdbscan instead of as_dendrogram_hdbscan.

On May 2, 2017, at 11:27 AM, gemcavoy notifications@github.com wrote:

When running this example and others, R can't find the as. dendogram.hdbscan

data(iris) vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1) hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) plot(as_dendrogram_hdbscan(hdbscanobj))

Error in plot(as_dendrogram_hdbscan(hdbscanobj)) : could not find function "as_dendrogram_hdbscan"

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[elbamos]

@gemcavoy Can you confirm you're able to use it now?

[gemcavoy]

I was able to use it like this: plot(as.dendrogram(hdbscanobj))

Also, just FYI. I had to modify the example below (from the manual) to transpose "dat" in order to get it to work (as your instructions suggest), but the example in the manual doesn't use transpose. Runs great with that change.

library(largeVis)

The aggregation dataset can be downloaded from

https://github.com/elbamos/clusteringdatasets data(Aggregation) dat <- as.matrix(Aggregation[, 1:2]) aggregateVis <- largeVis(t(dat), K = 10, tree_threshold = 100, max_iter = 5, sgd_batches = 1) clusters <- hdbscan(aggregateVis, verbose = FALSE) gplot(clusters, dat)

On Wed, May 3, 2017 at 6:38 PM, elbamos notifications@github.com wrote:

@gemcavoy https://github.com/gemcavoy Can you confirm you're able to use it now?

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[elbamos]

Yeah I totally failed to update the example. Sorry!

On May 3, 2017, at 9:08 PM, gemcavoy notifications@github.com wrote:

I was able to use it like this: plot(as.dendrogram(hdbscanobj))

Also, just FYI. I had to modify the example below (from the manual) to transpose "dat" in order to get it to work (as your instructions suggest), but the example in the manual doesn't use transpose. Runs great with that change.

library(largeVis)

The aggregation dataset can be downloaded from

https://github.com/elbamos/clusteringdatasets data(Aggregation) dat <- as.matrix(Aggregation[, 1:2]) aggregateVis <- largeVis(t(dat), K = 10, tree_threshold = 100, max_iter = 5, sgd_batches = 1) clusters <- hdbscan(aggregateVis, verbose = FALSE) gplot(clusters, dat)

On Wed, May 3, 2017 at 6:38 PM, elbamos notifications@github.com wrote:

@gemcavoy https://github.com/gemcavoy Can you confirm you're able to use it now?

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[elbamos]

fixed in 0.2.1 - please reopen if I'm mistaken, and thank you for the report!