aquanet-mod

R scripts for AquaNet-Mod (The Aquaculture Disease Network Model).

Citation

If using these scripts, please cite the scripts, package and accompanying paper.

To cite the scripts:

Alewijnse, S., Millard, R., Ryder, D. and Guilder, J. R scripts for AquaNet-Mod (The Aquaculture Disease Network Model) github.com/CefasRepRes/aquanet-mod

To cite the package:

Millard, R., Alewijnse, S., Ryder, D. and Guilder, J. Functions to Execute AquaNet-Mod (The Aquaculture Disease Network Model) github.com/CefasRepRes/aquanet

To cite the paper:

Guilder, J., Ryder, D., Taylor, N. G. H., Alewijnse, S. R., Millard, R. S., Thrush, M. A., Peeler, E. J. & Tidbury, H. J. The aquaculture disease network model (AquaNet-Mod): a simulation model to evaluate disease spread and controls for the salmonid industry in England and Wales. In press.

Getting started

To get started you will need the following packages available from CRAN:

• igraph
• sf
• here
• Matrix
• doParallel
• doRNG
• data.table
• dplyr

You will also need to download the aquanet package, which is available at https://github.com/CefasRepRes/aquanet

Session info for reproducibility

R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8

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

other attached packages: [1] aquanet_2.0.0 dplyr_1.1.2 data.table_1.14.8 doRNG_1.8.6 rngtools_1.5.2 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2 yaml_2.3.7 Matrix_1.5-3 here_1.0.1 sf_1.0-12 igraph_1.4.2 beepr_1.3 remotes_2.4.2

loaded via a namespace (and not attached): [1] tidyselect_1.2.0 purrr_1.0.1 lattice_0.20-45 vctrs_0.6.3 generics_0.1.3 utf8_1.2.3 rlang_1.1.1 pkgbuild_1.4.0 e1071_1.7-13 pillar_1.9.0 glue_1.6.2 withr_2.5.0 DBI_1.1.3 bit64_4.0.5 plyr_1.8.8 audio_0.1-10 lifecycle_1.0.3 stringr_1.5.0 codetools_0.2-18 arrow_12.0.1 tzdb_0.4.0 callr_3.7.3 ps_1.7.2 curl_5.0.0 class_7.3-20 fansi_1.0.4 Rcpp_1.0.10 KernSmooth_2.23-20 classInt_0.4-9 desc_1.4.2 bit_4.0.5 digest_0.6.31 stringi_1.7.12 processx_3.8.0 grid_4.2.2 rprojroot_2.0.3 cli_3.6.1 tools_4.2.2 magrittr_2.0.3 proxy_0.4-27 tibble_3.2.1 crayon_1.5.2 pkgconfig_2.0.3 prettyunits_1.1.1 assertthat_0.2.1 rstudioapi_0.14 R6_2.5.1 units_0.8-1 compiler_4.2.2