Context specific growth of the SARS-CoV-2 Delta variant

Code and data for all the statistical analysis done for estimating the context specific growth of the SARS-CoV-2 Delta variant across England.

The packages used in the R scripts are:

dplyr, lubridate, ggplot2, rstan, reshape2, loo, posterior, bayesplot, gridExtra, data.table, cowplot, boot

How to run the code:

1. Clone the repository to your local machine.
   
2. Open terminal/bash and change the directory to where the file is cloned, using cd. You should be able to see folders for data, outputs and src in this directory.
   
3. Type make and press enter.
   
4. You can now check the pdf files of the outputs in the outputs folder.

Note:

Due to data sharing agreements, the data on relative self mobility has not been made available, and instead a column with random numbers has been used. Hence the results will be different to those reported in the paper.

Reproducibility:

Should you be interested in reproducing the statistical results of the paper shown here please contact the correspnding author who will direct the request for aggregated mobility data used.

Session Info

R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] cowplot_1.1.1        loo_2.4.1            reshape2_1.4.4       boot_1.3-26         
 [5] posterior_1.1.0      rstan_2.21.2         StanHeaders_2.21.0-7 forcats_0.5.1       
 [9] stringr_1.4.0        purrr_0.3.4          readr_2.1.1          tidyr_1.1.4         
[13] tibble_3.1.6         ggplot2_3.3.5        tidyverse_1.3.1      lubridate_1.8.0     
[17] dplyr_1.0.7         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6           prettyunits_1.1.1    ps_1.6.0             assertthat_0.2.1    
 [5] utf8_1.2.2           V8_3.4.2             plyr_1.8.6           R6_2.5.1            
 [9] cellranger_1.1.0     backports_1.4.1      reprex_2.0.1         stats4_4.0.4        
[13] httr_1.4.2           pillar_1.6.4         rlang_0.4.12         curl_4.3.2          
[17] readxl_1.3.1         rstudioapi_0.13      callr_3.7.0          checkmate_2.0.0     
[21] munsell_0.5.0        tinytex_0.36         broom_0.7.11         compiler_4.0.4      
[25] modelr_0.1.8         xfun_0.29            pkgconfig_2.0.3      pkgbuild_1.2.0      
[29] tidyselect_1.1.1     tensorA_0.36.2       gridExtra_2.3        codetools_0.2-18    
[33] matrixStats_0.58.0   fansi_1.0.2          crayon_1.4.2         tzdb_0.2.0          
[37] dbplyr_2.1.1         withr_2.4.3          distributional_0.2.2 grid_4.0.4          
[41] jsonlite_1.7.3       gtable_0.3.0         lifecycle_1.0.1      DBI_1.1.2           
[45] magrittr_2.0.1       scales_1.1.1         RcppParallel_5.1.4   cli_3.1.0           
[49] stringi_1.7.6        farver_2.1.0         fs_1.5.2             xml2_1.3.3          
[53] ellipsis_0.3.2       generics_0.1.1       vctrs_0.3.8          tools_4.0.4         
[57] glue_1.6.0           hms_1.1.1            abind_1.4-5          parallel_4.0.4      
[61] processx_3.5.2       inline_0.3.18        colorspace_2.0-2     rvest_1.0.2         
[65] haven_2.4.3 ```