Executing the main script
simulation.R script will produce all the data, but beware, simulations will take some time - on a 16 core computer it takes about 8h. For this reason, the data is already provided in
utils.R specifies all the packages used in the simulation and for producing the figures. Note that it will attempt to install exact version of the packages with which this code was developed, so it might overwrite your version if you have installed some of these packages. It will also take a bit of time to install all of them.
Details on dependencies
The code has been tested on Linux machine:
Distributor ID: Ubuntu Description: Ubuntu 17.04 Release: 17.04 Codename: zesty Kernel: Linux 4.12.7
sessionInfo() output, with all necesary packages loaded:
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 17.04 Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.19.so locale:  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8  LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8  LC_PAPER=en_GB.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  doRNG_1.6.6 rngtools_1.2.4 pkgmaker_0.22 registry_0.3  doParallel_1.0.10 iterators_1.0.8 foreach_1.4.3 ggrepel_0.6.5  reshape2_1.4.2 dplyr_0.5.0 ggplot2_2.2.1 devtools_1.12.0 loaded via a namespace (and not attached):  Rcpp_0.12.10 magrittr_1.5 munsell_0.4.3 xtable_1.8-2  colorspace_1.3-2 R6_2.2.0 stringr_1.2.0 plyr_1.8.4  tools_3.4.0 grid_3.4.0 gtable_0.2.0 DBI_0.6-1  withr_1.0.2 lazyeval_0.2.0 assertthat_0.1 digest_0.6.12  tibble_1.3.0 codetools_0.2-15 memoise_1.0.0 stringi_1.1.5  compiler_3.4.0 scales_0.4.1