Hierarchical clustering

with scaled cases

Author

Raphael Saldanha

Last modification

December 1, 2023 | 09:07:18 +01:00

This notebooks aims to explore hierarchical clustering of municipalities considering scaled dengue cases time series.

Packages

library(tidyverse)
library(lubridate)
library(arrow)
library(timetk)
library(dtwclust)
library(kableExtra)
library(tictoc)
source("../functions.R")

Load data

Load the bundled data (326 municipalities, pop \(\geq\) 100k inhab.) with standardized cases and keep only the municipality code, date and cases variables.

tdengue <- open_dataset(sources = data_dir("bundled_data/tdengue.parquet")) %>%
    select(mun, date, cases) %>%
    collect()

Prepare data

tdengue <- tdengue %>%
  mutate(mun = paste0("m_", mun)) %>%
  arrange(mun, date) %>%
  pivot_wider(names_from = mun, values_from = cases) %>%
  select(-date) %>%
  t() %>%
  tslist()

Clustering

tic()
clust <- tsclust(
  series = tdengue, 
  type = "hierarchical", 
  k = 5,
  distance = "dtw_basic",
  seed = 123,
  control = hierarchical_control(method = "average")
)
toc()
44.964 sec elapsed
ggdendro::ggdendrogram(clust, size = .3, labels = F)

Session info

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] tictoc_1.2       kableExtra_1.3.4 dtwclust_5.5.12  dtw_1.23-1      
 [5] proxy_0.4-27     timetk_2.9.0     arrow_13.0.0.1   lubridate_1.9.3 
 [9] forcats_1.0.0    stringr_1.5.0    dplyr_1.1.3      purrr_1.0.2     
[13] readr_2.1.4      tidyr_1.3.0      tibble_3.2.1     ggplot2_3.4.4   
[17] tidyverse_2.0.0 

loaded via a namespace (and not attached):
  [1] rlang_1.1.2         magrittr_2.0.3      clue_0.3-65        
  [4] furrr_0.3.1         flexclust_1.4-1     compiler_4.3.2     
  [7] systemfonts_1.0.5   vctrs_0.6.4         reshape2_1.4.4     
 [10] rvest_1.0.3         lhs_1.1.6           tune_1.1.2         
 [13] pkgconfig_2.0.3     fastmap_1.1.1       ellipsis_0.3.2     
 [16] labeling_0.4.3      utf8_1.2.4          promises_1.2.1     
 [19] rmarkdown_2.25      prodlim_2023.08.28  tzdb_0.4.0         
 [22] bit_4.0.5           xfun_0.41           modeltools_0.2-23  
 [25] jsonlite_1.8.7      recipes_1.0.8       later_1.3.1        
 [28] parallel_4.3.2      cluster_2.1.4       R6_2.5.1           
 [31] stringi_1.7.12      rsample_1.2.0       parallelly_1.36.0  
 [34] rpart_4.1.21        Rcpp_1.0.11         assertthat_0.2.1   
 [37] dials_1.2.0         iterators_1.0.14    knitr_1.45         
 [40] future.apply_1.11.0 zoo_1.8-12          httpuv_1.6.12      
 [43] Matrix_1.6-1.1      splines_4.3.2       nnet_7.3-19        
 [46] timechange_0.2.0    tidyselect_1.2.0    rstudioapi_0.15.0  
 [49] yaml_2.3.7          timeDate_4022.108   codetools_0.2-19   
 [52] listenv_0.9.0       lattice_0.22-5      plyr_1.8.9         
 [55] shiny_1.7.5.1       withr_2.5.2         evaluate_0.23      
 [58] future_1.33.0       survival_3.5-7      RcppParallel_5.1.7 
 [61] xml2_1.3.5          xts_0.13.1          pillar_1.9.0       
 [64] foreach_1.5.2       stats4_4.3.2        shinyjs_2.1.0      
 [67] generics_0.1.3      hms_1.1.3           munsell_0.5.0      
 [70] scales_1.2.1        xtable_1.8-4        globals_0.16.2     
 [73] class_7.3-22        glue_1.6.2          tools_4.3.2        
 [76] data.table_1.14.8   RSpectra_0.16-1     webshot_0.5.5      
 [79] gower_1.0.1         grid_4.3.2          yardstick_1.2.0    
 [82] ipred_0.9-14        colorspace_2.1-0    cli_3.6.1          
 [85] DiceDesign_1.9      workflows_1.1.3     parsnip_1.1.1      
 [88] fansi_1.0.5         viridisLite_0.4.2   ggdendro_0.1.23    
 [91] svglite_2.1.2       lava_1.7.3          gtable_0.3.4       
 [94] GPfit_1.0-8         digest_0.6.33       ggrepel_0.9.4      
 [97] farver_2.1.1        htmlwidgets_1.6.2   htmltools_0.5.7    
[100] lifecycle_1.0.4     httr_1.4.7          hardhat_1.3.0      
[103] mime_0.12           bit64_4.0.5         MASS_7.3-60
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