Help with Kmeans output and using broom to tidy etc..
Please use dput()
On Tue, May 12, 2020 at 7:11 PM Poling, William <PolingW at aetna.com> wrote:
Hello Eric, thank you so much for your consideration.
Here are snippets of data that I hope will be helpful
WHP
geo1a <- geo1[, c(2:5)] <-- eliminating ID which is not useful for my
purposes anyway
#This is for R-Help use
geo1a <- geo1a %>% top_n(25)
state city latitude longitude
1 ME FAIRFIELD 44.64485 -69.65948
2 ME JONESPORT 44.57935 -67.56743
3 ME CASWELL 46.97529 -67.83023
4 ME ELLSWORTH 44.52916 -68.38717
5 ME VASSALBORO 44.45095 -69.60629
6 ME UNION 44.20059 -69.26123
7 ME PALERMO 44.45142 -69.41115
8 ME ORONO 44.87426 -68.68327
9 ME SANGERVILLE 45.10138 -69.33580
10 ME ISLESBORO 44.29015 -68.90812
11 ME TOPSHAM 43.93600 -69.96565
12 ME FREEPORT 43.84089 -70.11160
13 ME SKOWHEGAN 44.76687 -69.71644
14 ME MILLINOCKET 45.65501 -68.70261
15 ME ORRINGTON 44.72417 -68.74026
16 ME ST. GEORGE 43.96726 -69.20827
17 ME FORT FAIRFIELD 46.80911 -67.88079
18 ME MARS HILL 46.56580 -67.89006
19 ME FREEPORT 43.85302 -70.03726
20 ME EASTON 46.64143 -67.91203
21 ME WATERVILLE 44.53621 -69.65913
22 ME BRUNSWICK 43.87771 -69.96297
23 ME BRUNSWICK 43.91719 -69.89905
24 ME BUCKSPORT 44.60665 -68.81892
25 ME FAYETTE 44.46380 -70.12047
trnd1_tbla <- trnd1_tbl %>% top_n(25)
print(trnd1_tbla)
head(trnd1_tbla,n=25)
A tibble: 25 x 5
city state Basecountsum Basecount2 prop_of_total
<fct> <fct> <dbl> <dbl> <dbl>
1 ATLANTA GA 2352 12 0.00510
2 BRADENTON FL 2352 8 0.00340
3 BROOKLYN NY 2352 30 0.0128
4 CHARLOTTE NC 2352 8 0.00340
5 CHICAGO IL 2352 17 0.00723
6 COLUMBUS OH 2352 11 0.00468
7 CUMMING GA 2352 8 0.00340
8 DALLAS TX 2352 8 0.00340
9 ERIE PA 2352 12 0.00510
10 HOUSTON TX 2352 12 0.00510
# ... with 15 more rows
WHP
From: Eric Berger <ericjberger at gmail.com>
Sent: Tuesday, May 12, 2020 8:39 AM
To: Poling, William <PolingW at aetna.com>
Cc: r-help at r-project.org
Subject: [EXTERNAL] Re: [R] Help with Kmeans output and using broom to
tidy etc..
**** External Email - Use Caution ****
Can you create a reproducible example?
Your question involves objects that are unknown to us. (geo1, trnd1_tbl)
On Tue, May 12, 2020 at 2:41 PM Poling, William via R-help <mailto:
r-help at r-project.org> wrote:
#RStudio Version Version 1.2.1335 need this one--> 1.2.5019
sessionInfo()
# R version 4.0.0 Patched (2020-05-03 r78349)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 10 x64 (build 17763)
Hello:
I have data that I am trying to manipulate for Kmeans clustering.
Original data looks like this
str(geo1)
# 'data.frame': 2352 obs. of 5 variables:
# $ ID: Factor w/ 2352 levels "101040199600",..: 590 908 976 509 1674 690
1336 86 726 1702 ...
# $ state : Factor w/ 41 levels "AL","AR","AZ",..: 32 10 25 11 9
32 13 31 12 12 ...
# $ city : Factor w/ 1337 levels "ABBOTTSTOWN",..: 932 156 230
698 965 1330 515 727 1127 1304 ...
# $ latitude : num 40.4 31.2 40.8 42.1 26.8 ...
# $ longitude : num -79.9 -81.5 -74 -91.6 -82.1 ...
I created a subset adding column prop_of_total
str(trnd1_tbl)
tibble [1,457 x 5] (S3: tbl_df/tbl/data.frame)
$ city : Factor w/ 1337 levels "ABBOTTSTOWN",..: 1 2 3 4 5 6 7 8
9 10 ...
$ state : Factor w/ 41 levels "AL","AR","AZ",..: 32 36 10 28 12 36
10 11 26 38 ...
$ Basecountsum : num [1:1457] 2352 2352 2352 2352 2352 ...
$ Basecount2 : num [1:1457] 1 1 1 1 1 2 1 1 2 1 ...
$ prop_of_total: num [1:1457] 0.000425 0.000425 0.000425 0.000425
0.000425 ...
Then I spread it
trnd2_tbl <- trnd1_tbl %>%
dplyr::select(city, state, prop_of_total) %>%
spread(key = city, value = prop_of_total, fill = 0) #remove the NA's
with fill
str(trnd2_tbl)#tibble [41 x 1,338] (S3: tbl_df/tbl/data.frame)
Then I run a Kmeans
kmeans_obj1 <- trnd2_tbl %>%
dplyr::select(- state) %>%
kmeans(centers = 20, nstart = 100)
str(kmeans_obj1)
List of 9
$ cluster : int [1:41] 11 11 9 11 11 4 11 11 16 2 ...
$ centers : num [1:20, 1:1337] 0 0 0 0 0 0 0 0 0 0 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:20] "1" "2" "3" "4" ...
.. ..$ : chr [1:1337] "ABBOTTSTOWN" "ABILENE" "ACWORTH" "ADAMS" ...
$ totss : num 0.00158
$ withinss : num [1:20] 0 0 0 0 0 0 0 0 0 0 ...
$ tot.withinss: num 0.0000848
$ betweenss : num 0.0015
$ size : int [1:20] 1 1 1 1 1 1 1 1 1 1 ...
$ iter : int 3
$ ifault : int 0
- attr(*, "class")= chr "kmeans"
Then I go and try to tidy:
#Tidy, glance, augment
#Just makes it easier to use or view the obj's in the obj list
broom::tidy(kmeans_obj1) %>% glimpse()
broom::glance(kmeans_obj1)
##A tibble: 1 x 4
# totss tot.withinss betweenss iter
# <dbl> <dbl> <dbl> <int>
# 1 0.00158 0.0000848 0.00150 3
However, when I run this piece I get an error:
broom::augment(kmeans_obj1, trnd2_tbl) %>%
dplyr::select(city, .cluster)
#Error: Must subset columns with a valid subscript vector.
# The subscript has the wrong type `data.frame<
# u: double
# x: double
`.
i It must be numeric or character.
Here is the back trace:
rlang::last_error()
# Backtrace:
# 1. broom::augment(kmeans_obj1, trnd2_tbl)
# 9. dplyr::select(., city, .cluster)
# 11. tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
# 12. tidyselect:::eval_select_impl(...)
# 20. tidyselect:::vars_select_eval(...)
# 21. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
# 22. tidyselect:::eval_c(expr, data_mask, context_mask)
# 23. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
# 24. tidyselect:::walk_data_tree(new, data_mask, context_mask)
# 25. tidyselect:::as_indices_sel_impl(...)
# 26. tidyselect:::as_indices_impl(x, vars, strict = strict)
# 27. vctrs::vec_as_subscript(x, logical = "error")
I am not sure what I am supposed to fix?
Maybe someone has had similar error and can advise me please?
Thank you.
WHP
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