[R] Help with Kmeans output and using broom to tidy etc..
Eric Berger
er|cjberger @end|ng |rom gm@||@com
Tue May 12 21:07:10 CEST 2020
Please use dput()
On Tue, May 12, 2020 at 7:11 PM Poling, William <PolingW using 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 using gmail.com>
> Sent: Tuesday, May 12, 2020 8:39 AM
> To: Poling, William <PolingW using aetna.com>
> Cc: r-help using 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 using 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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