These are instructions for installing EpiModel for use in the workshop, Network Modeling for Epidemics.

To allow us to quickly move through the software material in Day 1, we ask that you install the necessary software, EpiModel, along with the dependent R packages from the Statnet project. Please have R, EpiModel, and its dependent packages installed before the workshop using the instructions below. If you have any questions about software installation, please contact the course instructor, Sam, at sjennes@emory.edu before the course.

R and Rstudio

EpiModel runs on the R statistical software platform. The current version of R is 3.5.1; this version should be installed on your computer. It is available on CRAN.

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.

EpiModel

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.

After installation, test that EpiModel can load correctly by typing:

library("EpiModel")

Finally, check that the installed versions of EpiModel, ergm, tergm, network, and networkDynamic all match those listed below under “other attached packages”:

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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 utils     datasets  methods   base     

other attached packages:
[1] EpiModel_1.6.5       tergm_3.4.1          ergm_3.8.0          
[4] statnet.common_4.1.4 networkDynamic_0.9.0 network_1.13.0.1    
[7] deSolve_1.21        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18       RColorBrewer_1.1-2 bindr_0.1.1       
 [4] DEoptimR_1.0-8     compiler_3.5.1     pillar_1.3.0      
 [7] plyr_1.8.4         iterators_1.0.10   tools_3.5.1       
[10] digest_0.6.15      evaluate_0.11      tibble_1.4.2      
[13] nlme_3.1-137       gtable_0.2.0       lattice_0.20-35   
[16] pkgconfig_2.0.2    rlang_0.2.1        foreach_1.4.4     
[19] Matrix_1.2-14      yaml_2.2.0         parallel_3.5.1    
[22] bindrcpp_0.2.2     coda_0.19-1        dplyr_0.7.6       
[25] stringr_1.3.1      knitr_1.20         tidyselect_0.2.4  
[28] trust_0.1-7        rprojroot_1.3-2    grid_3.5.1        
[31] glue_1.3.0         robustbase_0.93-2  R6_2.2.2          
[34] rmarkdown_1.10     purrr_0.2.5        ggplot2_3.0.0     
[37] magrittr_1.5       codetools_0.2-15   backports_1.1.2   
[40] scales_1.0.0       htmltools_0.3.6    MASS_7.3-50       
[43] assertthat_0.2.0   ape_5.1            lpSolve_5.6.13    
[46] colorspace_1.3-2   stringi_1.2.4      doParallel_1.0.11 
[49] lazyeval_0.2.1     munsell_0.5.0      crayon_1.3.4      

Help and Tutorials

After loading the software, feel free to browse the help file documentation in advance of the workshop.

help(package = "EpiModel")
?EpiModel


Last updated: 2018-08-16