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.

R and Rstudio

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.

EpiModel and Statnet Packages

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