These are instructions for installing all of the the software you will need for the workshop, Network Modeling for Epidemics.
To allow us to quickly move through the material in Day 1, we ask
that you install the necessary software, R,
Rstudio, EpiModel and statnetWeb,
along with the dependent R packages from the Statnet project (that
happens automatically when you install EpiModel and
statnetWeb. Please plan ahead to have this installed before
the workshop starts on Monday using the instructions below. If you have
any questions about software installation, please contact the course
instructor, Sam Jenness
before the course.
EpiModel runs on the R statistical software
platform. The current version of R is 4.2.0; please install
this version on your computer. It is available on CRAN.
Note that if you are updating from a 3.X or earlier version of R to a 4.X version, you will need to reinstall all of your packages as well. An easy way to do that is shown here
The instructors will use Rstudio for the workshop. This
is a popular front-end IDE (integrated development environment) for
R, and is recommended if you are relatively new to
R. It is available on the Rstudio website. Please make sure you
have installed the most recent version of this app too.
After installing R, you will need to install the
EpiModel software package. With an open R
console window, install EpiModel and its main related
packages by typing the following.
install.packages("EpiModel", dependencies = TRUE)R may prompt you to select a mirror site. In addition to
EpiModel itself, this step will also install or update the
needed statnet software, including the
ergm, tergm, network, and
networkDynamic packages.
In addition, you will need to install the statnetWeb
software package, using similar commands:
install.packages("statnetWeb")Finally, if you have an older version of any of the packages installed, you should update your packages accordingly with:
update.packages()After installation, test that EpiModel and
statnetWeb load correctly:
library("EpiModel")
library("statnetWeb")Finally, check that the installed versions of EpiModel,
ergm, tergm, network,
networkDynamic, and statnetWeb all match those
listed below under “other attached packages”:
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] statnetWeb_0.5.6 latticeExtra_0.6-30 lattice_0.20-45
[4] shiny_1.7.1 EpiModel_2.3.0 statnet.common_4.6.0
[7] tergm_4.1.0 ergm_4.2.2 networkDynamic_0.11.2
[10] network_1.17.2 deSolve_1.32
loaded via a namespace (and not attached):
[1] sass_0.4.1 jsonlite_1.8.0 foreach_1.5.2
[4] bslib_0.3.1 assertthat_0.2.1 renv_0.15.5
[7] yaml_2.3.5 robustbase_0.95-0 pillar_1.7.0
[10] glue_1.6.2 digest_0.6.29 RColorBrewer_1.1-3
[13] promises_1.2.0.1 colorspace_2.0-3 htmltools_0.5.2
[16] httpuv_1.6.5 Matrix_1.4-1 pkgconfig_2.0.3
[19] purrr_0.3.4 xtable_1.8-4 scales_1.2.0
[22] sna_2.7 jpeg_0.1-9 later_1.3.0
[25] tibble_3.1.7 generics_0.1.3 ggplot2_3.3.6
[28] ellipsis_0.3.2 cachem_1.0.6 lazyeval_0.2.2
[31] cli_3.3.0 deldir_1.0-6 magrittr_2.0.3
[34] crayon_1.5.1 mime_0.12 memoise_2.0.1
[37] evaluate_0.15 fansi_1.0.3 doParallel_1.0.17
[40] nlme_3.1-158 MASS_7.3-57 tools_4.2.0
[43] lifecycle_1.0.1 stringr_1.4.0 interp_1.1-2
[46] trust_0.1-8 munsell_0.5.0 compiler_4.2.0
[49] jquerylib_0.1.4 rlang_1.0.3 grid_4.2.0
[52] iterators_1.0.14 rstudioapi_0.13 rmarkdown_2.14
[55] gtable_0.3.0 codetools_0.2-18 DBI_1.1.2
[58] R6_2.5.1 lpSolveAPI_5.5.2.0-17.7 rle_0.9.2
[61] knitr_1.39 dplyr_1.0.9 fastmap_1.1.0
[64] utf8_1.2.2 ape_5.6-2 stringi_1.7.6
[67] parallel_4.2.0 Rcpp_1.0.8.3 png_0.1-7
[70] vctrs_0.4.1 DEoptimR_1.0-11 tidyselect_1.1.2
[73] xfun_0.31 coda_0.19-4 Last updated: 2022-07-07