Paper on arXiv: https://arxiv.org/abs/2105.09223
This repo contains the code to generate the plots, tables for this paper, the paper pdf itself as well as the code to run the simulations. Since running the simulations needs quite a few resources the results of the simulations are also contained.
./arxiv
: Arxiv version of the paper../benchmark
: Contains the code that runs the benchmarks (batchtools_grid.R
) and creates the results given in./benchmark_results
.setwd('./benchmark')
to run the code../benchmark_results
: Results of the benchmark experiments../generator
: Code that creates the tables and figures from the files in./benchmark_results
.setwd('.')
(the directory of this README) to run the code../generated
: Figures and tables created by the code in./generator
.Makefile
:make plots
generates plots and tables.make pdf
generates themain.pdf
.make all
runs the two above.- Use
make tinytex
in case some tex packages are missing. Tinytex can deal with that and generate themain.pdf
as well. make benchmark
runs the expensive experiments. Only recommended if you have set upbatchtools
with access to a cluster.
To run the generators you have to install:
pkgs = c("data.table","ggplot2","scales","stringi","knitr","kableExtra","dplyr","mlr3misc","gridExtra","memoise","smoof","batchtools","FNN","tidyr","colorspace","scales","BBmisc")
install.packages(pkgs)
Also pdfcrop is needed:
sudo apt-get install texlive-extra-utils
pacman -S texlive-core
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.04
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] smoof_1.6.0.2 checkmate_2.0.0 ParamHelpers_1.14 memoise_2.0.1
[5] gridExtra_2.3 mlr3misc_0.10.0 dplyr_1.0.7 kableExtra_1.3.4
[9] knitr_1.37 stringi_1.7.6 scales_1.1.1 ggplot2_3.3.5
[13] data.table_1.14.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 svglite_2.0.0 FNN_1.1.3 tidyr_1.1.4
[5] prettyunits_1.1.1 digest_0.6.28 utf8_1.2.2 R6_2.5.1
[9] backports_1.3.0 evaluate_0.14 httr_1.4.2 pillar_1.6.4
[13] progress_1.2.2 rlang_0.4.12 lazyeval_0.2.2 misc3d_0.9-1
[17] rstudioapi_0.13 rmarkdown_2.10 labeling_0.4.2 mco_1.15.6
[21] webshot_0.5.2 stringr_1.4.0 htmlwidgets_1.5.3 munsell_0.5.0
[25] compiler_3.6.3 xfun_0.29 pkgconfig_2.0.3 systemfonts_1.0.2
[29] BBmisc_1.11 htmltools_0.5.1.1 tcltk_3.6.3 tidyselect_1.1.1
[33] tibble_3.1.6 batchtools_0.9.15 fansi_1.0.2 viridisLite_0.4.0
[37] crayon_1.4.2 withr_2.4.3 rappdirs_0.3.3 jsonlite_1.7.3
[41] gtable_0.3.0 lifecycle_1.0.1 magrittr_2.0.1 cachem_1.0.5
[45] farver_2.1.0 xml2_1.3.2 brew_1.0-6 ellipsis_0.3.2
[49] generics_0.1.0 vctrs_0.3.8 fastmatch_1.1-3 plot3D_1.4
[53] RColorBrewer_1.1-2 tools_3.6.3 RJSONIO_1.3-1.4 glue_1.6.0
[57] purrr_0.3.4 hms_1.1.1 parallel_3.6.3 fastmap_1.1.0
[61] colorspace_2.0-2 base64url_1.4 rvest_1.0.1 plotly_4.10.0