Help with Cluster Tutorial Error

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Help with Cluster Tutorial Error

Bill Poling
sessionInfo()
#R version 3.5.2 (2018-12-20)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows >= 8 x64 (build 9200)

Hello I am working through this tutorial https://www.r-bloggers.com/10-tips-for-choosing-the-optimal-number-of-clusters/
And I run into an error almost immediately at the point below like this:

 mammals <- raw_mammals %>% select(-name) # set rownames
#Error in select(., -name) : object 'p_links' not found

I have googled the error " R object 'p_links' not found"
https://stats.stackexchange.com/questions/113907/error-object-descr-not-found
However, the links I have found seem to be specific to an object that has been declared by the Op, and in my case I do not know where this object is supposed to be coming from?

I think this stems from the use of the dplyr Pkg?

https://dplyr.tidyverse.org/reference/select.html

Here is what I have so far:

#Data Set
# I will be using a lesser known data set from the cluster package: all.mammals.milk.1956, one which I haven't looked at before.
#
# This small dataset contains a list of 25 mammals and the constituents of their milk (water, protein, fat, lactose, ash percentages) from John Hartigan, Clustering Algorithms, Wiley, 1975.
#
# First let's load the required packages. Some of these are already in my library, those that are not were installed

library(tidyverse)
library(magrittr)
library(cluster)
install.packages("cluster.datasets")
install.packages("NbClust")
install.packages("clValid")
install.packages("ggfortify")
install.packages("clustree")
install.packages("ggiraphExtra")
library(cowplot)
library(cluster.datasets)
library(NbClust)
library(clValid)
library(ggfortify)
library(clustree)
library(ggiraphExtra)
library(dendextend)
library(factoextra)
library(FactoMineR)
library(corrplot)
library(GGally)
library(knitr)
library(kableExtra)


data("all.mammals.milk.1956")
raw_mammals <- all.mammals.milk.1956
str(raw_mammals)  #----------------------KNOW THY DATA

# 'data.frame':25 obs. of  6 variables:
# $ name   : chr  "Horse" "Orangutan" "Monkey" "Donkey" ...
# $ water  : num  90.1 88.5 88.4 90.3 90.4 87.7 86.9 82.1 81.9 81.6 ...
# $ protein: num  2.6 1.4 2.2 1.7 0.6 3.5 4.8 5.9 7.4 10.1 ...
# $ fat    : num  1 3.5 2.7 1.4 4.5 3.4 1.7 7.9 7.2 6.3 ...
# $ lactose: num  6.9 6 6.4 6.2 4.4 4.8 5.7 4.7 2.7 4.4 ...
# $ ash    : num  0.35 0.24 0.18 0.4 0.1 0.71 0.9 0.78 0.85 0.75 ...

#raw_mammals <- fread("Animal Milk Constituent Percentages.csv",header=TRUE, stringsAsFactors=TRUE)

# subset dataset
mammals <- raw_mammals %>% select(-name) # set rownames
#Error in select(., -name) : object 'p_links' not found  <--The Error

I hope this is enough information to help answer my question.

Thank you

WHP




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Re: Help with Cluster Tutorial Error

David Carlson
I'm not getting any error on that line in Windows 10. I did not try running anything past that line.

Have you tried restarting R and clearing your environment?

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352

-----Original Message-----
From: R-help <[hidden email]> On Behalf Of Bill Poling
Sent: Friday, February 15, 2019 7:37 AM
To: r-help ([hidden email]) <[hidden email]>
Subject: [R] Help with Cluster Tutorial Error

sessionInfo()
#R version 3.5.2 (2018-12-20)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows >= 8 x64 (build 9200)

Hello I am working through this tutorial https://www.r-bloggers.com/10-tips-for-choosing-the-optimal-number-of-clusters/
And I run into an error almost immediately at the point below like this:

 mammals <- raw_mammals %>% select(-name) # set rownames
#Error in select(., -name) : object 'p_links' not found

I have googled the error " R object 'p_links' not found"
https://stats.stackexchange.com/questions/113907/error-object-descr-not-found
However, the links I have found seem to be specific to an object that has been declared by the Op, and in my case I do not know where this object is supposed to be coming from?

I think this stems from the use of the dplyr Pkg?

https://dplyr.tidyverse.org/reference/select.html

Here is what I have so far:

#Data Set
# I will be using a lesser known data set from the cluster package: all.mammals.milk.1956, one which I haven't looked at before.
#
# This small dataset contains a list of 25 mammals and the constituents of their milk (water, protein, fat, lactose, ash percentages) from John Hartigan, Clustering Algorithms, Wiley, 1975.
#
# First let's load the required packages. Some of these are already in my library, those that are not were installed

library(tidyverse)
library(magrittr)
library(cluster)
install.packages("cluster.datasets")
install.packages("NbClust")
install.packages("clValid")
install.packages("ggfortify")
install.packages("clustree")
install.packages("ggiraphExtra")
library(cowplot)
library(cluster.datasets)
library(NbClust)
library(clValid)
library(ggfortify)
library(clustree)
library(ggiraphExtra)
library(dendextend)
library(factoextra)
library(FactoMineR)
library(corrplot)
library(GGally)
library(knitr)
library(kableExtra)


data("all.mammals.milk.1956")
raw_mammals <- all.mammals.milk.1956
str(raw_mammals)  #----------------------KNOW THY DATA

# 'data.frame':25 obs. of  6 variables:
# $ name   : chr  "Horse" "Orangutan" "Monkey" "Donkey" ...
# $ water  : num  90.1 88.5 88.4 90.3 90.4 87.7 86.9 82.1 81.9 81.6 ...
# $ protein: num  2.6 1.4 2.2 1.7 0.6 3.5 4.8 5.9 7.4 10.1 ...
# $ fat    : num  1 3.5 2.7 1.4 4.5 3.4 1.7 7.9 7.2 6.3 ...
# $ lactose: num  6.9 6 6.4 6.2 4.4 4.8 5.7 4.7 2.7 4.4 ...
# $ ash    : num  0.35 0.24 0.18 0.4 0.1 0.71 0.9 0.78 0.85 0.75 ...

#raw_mammals <- fread("Animal Milk Constituent Percentages.csv",header=TRUE, stringsAsFactors=TRUE)

# subset dataset
mammals <- raw_mammals %>% select(-name) # set rownames
#Error in select(., -name) : object 'p_links' not found  <--The Error

I hope this is enough information to help answer my question.

Thank you

WHP




Confidentiality Notice This message is sent from Zelis. ...{{dropped:9}}

______________________________________________
[hidden email] 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.
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Re: Help with Cluster Tutorial Error

Jeff Newmiller
Another possible issue could be some outdated packages... be sure to update all packages.

On February 15, 2019 7:05:44 AM PST, David L Carlson <[hidden email]> wrote:

>I'm not getting any error on that line in Windows 10. I did not try
>running anything past that line.
>
>Have you tried restarting R and clearing your environment?
>
>----------------------------------------
>David L Carlson
>Department of Anthropology
>Texas A&M University
>College Station, TX 77843-4352
>
>-----Original Message-----
>From: R-help <[hidden email]> On Behalf Of Bill Poling
>Sent: Friday, February 15, 2019 7:37 AM
>To: r-help ([hidden email]) <[hidden email]>
>Subject: [R] Help with Cluster Tutorial Error
>
>sessionInfo()
>#R version 3.5.2 (2018-12-20)
>#Platform: x86_64-w64-mingw32/x64 (64-bit)
>#Running under: Windows >= 8 x64 (build 9200)
>
>Hello I am working through this tutorial
>https://www.r-bloggers.com/10-tips-for-choosing-the-optimal-number-of-clusters/
>And I run into an error almost immediately at the point below like
>this:
>
> mammals <- raw_mammals %>% select(-name) # set rownames
>#Error in select(., -name) : object 'p_links' not found
>
>I have googled the error " R object 'p_links' not found"
>https://stats.stackexchange.com/questions/113907/error-object-descr-not-found
>However, the links I have found seem to be specific to an object that
>has been declared by the Op, and in my case I do not know where this
>object is supposed to be coming from?
>
>I think this stems from the use of the dplyr Pkg?
>
>https://dplyr.tidyverse.org/reference/select.html
>
>Here is what I have so far:
>
>#Data Set
># I will be using a lesser known data set from the cluster package:
>all.mammals.milk.1956, one which I haven't looked at before.
>#
># This small dataset contains a list of 25 mammals and the constituents
>of their milk (water, protein, fat, lactose, ash percentages) from John
>Hartigan, Clustering Algorithms, Wiley, 1975.
>#
># First let's load the required packages. Some of these are already in
>my library, those that are not were installed
>
>library(tidyverse)
>library(magrittr)
>library(cluster)
>install.packages("cluster.datasets")
>install.packages("NbClust")
>install.packages("clValid")
>install.packages("ggfortify")
>install.packages("clustree")
>install.packages("ggiraphExtra")
>library(cowplot)
>library(cluster.datasets)
>library(NbClust)
>library(clValid)
>library(ggfortify)
>library(clustree)
>library(ggiraphExtra)
>library(dendextend)
>library(factoextra)
>library(FactoMineR)
>library(corrplot)
>library(GGally)
>library(knitr)
>library(kableExtra)
>
>
>data("all.mammals.milk.1956")
>raw_mammals <- all.mammals.milk.1956
>str(raw_mammals)  #----------------------KNOW THY DATA
>
># 'data.frame':25 obs. of  6 variables:
># $ name   : chr  "Horse" "Orangutan" "Monkey" "Donkey" ...
># $ water  : num  90.1 88.5 88.4 90.3 90.4 87.7 86.9 82.1 81.9 81.6 ...
># $ protein: num  2.6 1.4 2.2 1.7 0.6 3.5 4.8 5.9 7.4 10.1 ...
># $ fat    : num  1 3.5 2.7 1.4 4.5 3.4 1.7 7.9 7.2 6.3 ...
># $ lactose: num  6.9 6 6.4 6.2 4.4 4.8 5.7 4.7 2.7 4.4 ...
># $ ash    : num  0.35 0.24 0.18 0.4 0.1 0.71 0.9 0.78 0.85 0.75 ...
>
>#raw_mammals <- fread("Animal Milk Constituent
>Percentages.csv",header=TRUE, stringsAsFactors=TRUE)
>
># subset dataset
>mammals <- raw_mammals %>% select(-name) # set rownames
>#Error in select(., -name) : object 'p_links' not found  <--The Error
>
>I hope this is enough information to help answer my question.
>
>Thank you
>
>WHP
>
>
>
>
>Confidentiality Notice This message is sent from Zelis.
>...{{dropped:9}}
>
>______________________________________________
>[hidden email] 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.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] 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.
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Help with Cluster Tutorial Error

Bill Poling
In reply to this post by Bill Poling
Hi Jeff and David.

Yes, updating all my Pkgs has done the trick.

I will remember to try that first next time.

As always I appreciate your help.

Thank you.

WHP



From: Jeff Newmiller <[hidden email]>
Sent: Friday, February 15, 2019 10:48 AM
To: [hidden email]; David L Carlson <[hidden email]>; Bill Poling <[hidden email]>; r-help ([hidden email]) <[hidden email]>
Subject: Re: [R] Help with Cluster Tutorial Error

Another possible issue could be some outdated packages... be sure to update all packages.

On February 15, 2019 7:05:44 AM PST, David L Carlson <mailto:[hidden email]> wrote:

>I'm not getting any error on that line in Windows 10. I did not try
>running anything past that line.
>
>Have you tried restarting R and clearing your environment?
>
>----------------------------------------
>David L Carlson
>Department of Anthropology
>Texas A&M University
>College Station, TX 77843-4352
>
>-----Original Message-----
>From: R-help <mailto:[hidden email]> On Behalf Of Bill Poling
>Sent: Friday, February 15, 2019 7:37 AM
>To: r-help (mailto:[hidden email]) <mailto:[hidden email]>
>Subject: [R] Help with Cluster Tutorial Error
>
>sessionInfo()
>#R version 3.5.2 (2018-12-20)
>#Platform: x86_64-w64-mingw32/x64 (64-bit)
>#Running under: Windows >= 8 x64 (build 9200)
>
>Hello I am working through this tutorial
>https://www.r-bloggers.com/10-tips-for-choosing-the-optimal-number-of-clusters/
>And I run into an error almost immediately at the point below like
>this:
>
> mammals <- raw_mammals %>% select(-name) # set rownames
>#Error in select(., -name) : object 'p_links' not found
>
>I have googled the error " R object 'p_links' not found"
>https://stats.stackexchange.com/questions/113907/error-object-descr-not-found
>However, the links I have found seem to be specific to an object that
>has been declared by the Op, and in my case I do not know where this
>object is supposed to be coming from?
>
>I think this stems from the use of the dplyr Pkg?
>
>https://dplyr.tidyverse.org/reference/select.html
>
>Here is what I have so far:
>
>#Data Set
># I will be using a lesser known data set from the cluster package:
>all.mammals.milk.1956, one which I haven't looked at before.
>#
># This small dataset contains a list of 25 mammals and the constituents
>of their milk (water, protein, fat, lactose, ash percentages) from John
>Hartigan, Clustering Algorithms, Wiley, 1975.
>#
># First let's load the required packages. Some of these are already in
>my library, those that are not were installed
>
>library(tidyverse)
>library(magrittr)
>library(cluster)
>install.packages("cluster.datasets")
>install.packages("NbClust")
>install.packages("clValid")
>install.packages("ggfortify")
>install.packages("clustree")
>install.packages("ggiraphExtra")
>library(cowplot)
>library(cluster.datasets)
>library(NbClust)
>library(clValid)
>library(ggfortify)
>library(clustree)
>library(ggiraphExtra)
>library(dendextend)
>library(factoextra)
>library(FactoMineR)
>library(corrplot)
>library(GGally)
>library(knitr)
>library(kableExtra)
>
>
>data("all.mammals.milk.1956")
>raw_mammals <- all.mammals.milk.1956
>str(raw_mammals) #----------------------KNOW THY DATA
>
># 'data.frame':25 obs. of 6 variables:
># $ name : chr "Horse" "Orangutan" "Monkey" "Donkey" ...
># $ water : num 90.1 88.5 88.4 90.3 90.4 87.7 86.9 82.1 81.9 81.6 ...
># $ protein: num 2.6 1.4 2.2 1.7 0.6 3.5 4.8 5.9 7.4 10.1 ...
># $ fat : num 1 3.5 2.7 1.4 4.5 3.4 1.7 7.9 7.2 6.3 ...
># $ lactose: num 6.9 6 6.4 6.2 4.4 4.8 5.7 4.7 2.7 4.4 ...
># $ ash : num 0.35 0.24 0.18 0.4 0.1 0.71 0.9 0.78 0.85 0.75 ...
>
>#raw_mammals <- fread("Animal Milk Constituent
>Percentages.csv",header=TRUE, stringsAsFactors=TRUE)
>
># subset dataset
>mammals <- raw_mammals %>% select(-name) # set rownames
>#Error in select(., -name) : object 'p_links' not found <--The Error
>
>I hope this is enough information to help answer my question.
>
>Thank you
>
>WHP
>
>
>
>
>Confidentiality Notice This message is sent from Zelis.
>...{{dropped:9}}
>
>______________________________________________
>mailto:[hidden email] 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.

--
Sent from my phone. Please excuse my brevity.

Confidentiality Notice This message is sent from Zelis. This transmission may contain information which is privileged and confidential and is intended for the personal and confidential use of the named recipient only. Such information may be protected by applicable State and Federal laws from this disclosure or unauthorized use. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any disclosure, review, discussion, copying, or taking any action in reliance on the contents of this transmission is strictly prohibited. If you have received this transmission in error, please contact the sender immediately. Zelis, 2018.
______________________________________________
[hidden email] 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.