Code and metadata for the paper "Linking virus structures to modes of transmission". This document can be regenerated by running:
make clean
make
in this directory.
The code requires R and the R packages:
ggplot2knitrdplyrtidyrparallelapephylolmphytools
print(sessionInfo())## R version 3.4.4 (2018-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
##
## 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=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] phytools_0.6-60 maps_3.3.0 phylolm_2.6 ape_5.2
## [5] tidyr_0.8.1 dplyr_0.8.0.1 knitr_1.22 ggplot2_3.1.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.0 pillar_1.3.1
## [3] compiler_3.4.4 plyr_1.8.4
## [5] tools_3.4.4 digest_0.6.22
## [7] evaluate_0.13 tibble_2.0.1
## [9] gtable_0.2.0 nlme_3.1-137
## [11] lattice_0.20-38 pkgconfig_2.0.2
## [13] rlang_0.3.1 fastmatch_1.1-0
## [15] Matrix_1.2-14 igraph_1.2.2
## [17] expm_0.999-3 xfun_0.6
## [19] coda_0.19-2 withr_2.1.2
## [21] stringr_1.3.1 globals_0.12.4
## [23] combinat_0.0-8 scatterplot3d_0.3-41
## [25] grid_3.4.4 tidyselect_0.2.5
## [27] glue_1.3.0 listenv_0.7.0
## [29] R6_2.2.2 plotrix_3.7-4
## [31] future.apply_1.1.0 phangorn_2.4.0
## [33] animation_2.6 purrr_0.2.5
## [35] magrittr_1.5 MASS_7.3-50
## [37] scales_0.5.0 codetools_0.2-15
## [39] mnormt_1.5-5 assertthat_0.2.0
## [41] future_1.11.1.1 colorspace_1.3-2
## [43] numDeriv_2016.8-1 quadprog_1.5-5
## [45] stringi_1.2.4 lazyeval_0.2.1
## [47] munsell_0.5.0 clusterGeneration_1.3.4
## [49] crayon_1.3.4
