[R] 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Another possible issue could be some outdated packages...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 <dcarlson using tamu.edu> 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 <r-help-bounces using r-project.org> On Behalf Of Bill Poling
>Sent: Friday, February 15, 2019 7:37 AM
>To: r-help (r-help using r-project.org) <r-help using r-project.org>
>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
>
>
>
>
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-- 
Sent from my phone. Please excuse my brevity.