as.dendogram.hbscan not found
Closed this issue · 8 comments
gemcavoy commented
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 commented
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 ***@***.***> 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"
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub, or mute the thread.
gemcavoy commented
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 ***@***.***> 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 ***@***.***> 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"
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#47 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AFYpnLQUMSdLD4xBkZB0MUZ3gfw0n0Nrks5r10v-gaJpZM4NOTIU>
.
gemcavoy commented
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 ***@***.***> 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 ***@***.***> 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 ***@***.***> 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"
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub, or mute the thread.
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#47 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AFYpnLQUMSdLD4xBkZB0MUZ3gfw0n0Nrks5r10v-gaJpZM4NOTIU>
> .
>
elbamos commented
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 ***@***.***> 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 ***@***.***> 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 ***@***.***> 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"
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub, or mute the thread.
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#47 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AFYpnLQUMSdLD4xBkZB0MUZ3gfw0n0Nrks5r10v-gaJpZM4NOTIU>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or mute the thread.
gemcavoy commented
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 ***@***.***> wrote:
@gemcavoy <https://github.com/gemcavoy> Can you confirm you're able to
use it now?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#47 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AFYpnK0Y9_QwRSlQI-cr-TBNK6jwXIctks5r2QHngaJpZM4NOTIU>
.
elbamos commented
Yeah I totally failed to update the example. Sorry!
… On May 3, 2017, at 9:08 PM, gemcavoy ***@***.***> 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 ***@***.***> wrote:
> @gemcavoy <https://github.com/gemcavoy> Can you confirm you're able to
> use it now?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#47 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AFYpnK0Y9_QwRSlQI-cr-TBNK6jwXIctks5r2QHngaJpZM4NOTIU>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or mute the thread.
elbamos commented
fixed in 0.2.1 - please reopen if I'm mistaken, and thank you for the report!