Last updated: 2019-05-24

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Introduction

This markdown file will contain the code used to perform the self-organising map (SOM) analysis on the prepared variable data as seen in the Variable preparation vignette.

# Packages used in this vignette
library(tidyverse) # Base suite of functions
library(ncdf4) # For opening and working with NetCDF files
library(lubridate) # For convenient date manipulation

# Set number of cores
doMC::registerDoMC(cores = 50)

# Disable scientific notation for numeric values
  # I just find it annoying
options(scipen = 999)

Session information

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.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       

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

other attached packages:
 [1] lubridate_1.7.4 ncdf4_1.16      forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.7.6     purrr_0.2.5     readr_1.1.1     tidyr_0.8.1    
 [9] tibble_1.4.2    ggplot2_3.0.0   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4  haven_1.1.2       lattice_0.20-35  
 [4] colorspace_1.3-2  htmltools_0.3.6   yaml_2.2.0       
 [7] rlang_0.2.2       R.oo_1.22.0       pillar_1.3.0     
[10] glue_1.3.0        withr_2.1.2       R.utils_2.7.0    
[13] doMC_1.3.5        modelr_0.1.2      readxl_1.1.0     
[16] bindrcpp_0.2.2    foreach_1.4.4     bindr_0.1.1      
[19] plyr_1.8.4        munsell_0.5.0     gtable_0.2.0     
[22] workflowr_1.1.1   cellranger_1.1.0  rvest_0.3.2      
[25] R.methodsS3_1.7.1 codetools_0.2-15  evaluate_0.11    
[28] knitr_1.20        parallel_3.6.0    broom_0.5.0      
[31] Rcpp_0.12.18      scales_1.0.0      backports_1.1.2  
[34] jsonlite_1.5      hms_0.4.2         digest_0.6.16    
[37] stringi_1.2.4     grid_3.6.0        rprojroot_1.3-2  
[40] cli_1.0.0         tools_3.6.0       magrittr_1.5     
[43] lazyeval_0.2.1    crayon_1.3.4      whisker_0.3-2    
[46] pkgconfig_2.0.2   xml2_1.2.0        iterators_1.0.10 
[49] assertthat_0.2.0  rmarkdown_1.10    httr_1.3.1       
[52] rstudioapi_0.7    R6_2.2.2          nlme_3.1-137     
[55] git2r_0.23.0      compiler_3.6.0

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