Glossary

Short definitions of terms used across this wiki, with links to where you will learn more.

• .at, .scenario.id: required columns in a scenario table: the time step when the scenario's parameter changes take effect, and the scenario's name. See Programmatically Defining Scenarios.
• ARTnet: a national online study of sexual partnerships among men who have sex with men in the United States. The ARTnet R package turns it into network and epidemic parameters.
• ARTnetData: the private R package that holds the ARTnet limited-use data. Access requires a data use agreement with Sam (see Home).
• at: the current time step inside a module.
• attribute: a value stored for each node (person), such as age or status. Read with get_attr() and written with set_attr().
• calibration: adjusting uncertain parameters until model outputs match observed targets. See Calibrating a Model.
• checkpoint: a saved simulation state that lets netsim() resume after an interruption. See Running Network Models with Checkpoints.
• compute node: a cluster machine that runs your jobs. You reach one only through Slurm (srun or sbatch). See Running R Interactively with srun.
• control_msm(), param_msm(), init_msm(): EpiModelHIV functions that set the simulation controls (including which module functions run), the parameters, and the initial conditions.
• dat: the main list object that netsim() passes from module to module. It holds the attributes, parameters, networks, and epidemic trackers for one simulation.
• default branch: the branch GitHub shows first and new branches start from. For EpiModelHIV-p and EpiModelHIV-Template it is currently v3.3.x, not main; check the branch menu on the repository page.
• epi tracker: a time series recorded during a simulation with set_epi(), for example incidence. Available afterward with as.data.frame(sim).
• EpiModel: the R package for simulating epidemics over networks that all our work builds on.
• EpiModelCOVID: our extension package with COVID-19 modules.
• EpiModelHIV, EpiModelHIV-p: our extension package with HIV and STI modules. The repository is EpiModelHIV-p ("p" for private, kept private until the work is published); the R package is called EpiModelHIV.
• EpiModelHIV-Template: the GitHub template repository you copy to start a new HIV project.
• EpiModelHPC: helper functions for running EpiModel on a Slurm cluster, including the step_tmpl_* workflow steps and the merging of simulation output.
• ERGM, TERGM: exponential-family random graph models and their temporal version. They are the statistical models behind our networks, estimated with netest().
• job array: one sbatch submission that runs many copies of the same script, each with its own SLURM_ARRAY_TASK_ID. See Running R Batch Jobs with sbatch.
• login node: clogin01, the machine you reach with ssh. Use it only to move files, run git, and submit or check jobs. Never run R there (see HPC Rules, Storage, and Getting Help).
• module: a function with arguments (dat, at) that carries out one process (aging, infection, testing). The modules for a model are listed in the control settings as *.FUN arguments.
• netest(), netdx(), netsim(): estimate the network model, diagnose it by simulation, and simulate the epidemic.
• NetID: your Emory login ID, in lowercase. It is also your HPC username.
• parameter: a fixed model input, read in a module with get_param(). Default values live in EpiModelHIV's inst/model_parameters.csv, and a project sets its own values in data/input/model_parameters.csv. See EpiModelHIV ‐ New Parameters and Attributes.
• partition: a named group of compute nodes. The lab's own partition is epimodel.
• PAT (personal access token): a GitHub token saved as GITHUB_PAT in your .Renviron file so R can install packages from our private repositories.
• pkgload::load_all(): loads a package's source code from a local folder into your R session without installing it. We use it to test EpiModelHIV changes quickly.
• NIA, PIA: the number and proportion of infections averted by an intervention scenario, compared with a reference scenario. See Processing Intervention Results.
• poz: shorthand in some parameter and scenario names for people with diagnosed HIV.
• project repository: your applied project (scripts, inputs, results), created from the template. Compare software repository.
• pull request (PR): on EpiModelHIV-p, each project keeps one PR from its branch open (never merged) so the team can see how it differs from the default branch and so automated checks run.
• renv, renv.lock, renv.lock.hpc: renv records the exact package versions a project uses. renv.lock is the full list for your computer; renv.lock.hpc is a shorter list that cluster jobs restore before they run. See Using renv for Reproducible R Environments.
• restart point: the saved end state of a burn-in simulation, used as the starting state for later calibration and intervention runs. See Making a Restart Point.
• scenario: a named set of parameter changes applied at a given time step, turned into a list with EpiModel::create_scenario_list().
• Slurm: the job scheduler on the RSPH cluster. Common commands: srun, sbatch, squeue, scancel. See Monitoring and Managing Slurm Jobs.
• slurmworkflow: an R package that writes a chain of Slurm jobs (a workflow) into a folder that you copy to the cluster and start with start_workflow.sh. See Running Project Workflows on the HPC.
• software repository: the package that holds the model modules, EpiModelHIV-p or EpiModelCOVID. You work on your own branch of it.
• Spack: the package manager we use to provide R and other software on the cluster, as in spack load r@<version>. See Using R via Spack on the HPC.
• sph: the short name we give the HPC login node in ~/.ssh/config, so ssh sph connects to clogin01.sph.emory.edu. See Setting Up Your HPC Environment.
• swfcalib: an R package for automated calibration on a Slurm cluster, built on slurmworkflow.
• tergmLite: a faster mode for resimulating networks during netsim() (set in the control settings), used in our applied models.
• tibble: a tidyverse data frame. EpiModelHPC merges simulation output into one tibble per scenario.
• time step: one iteration of the model. In EpiModelHIV models a time step is one week.
• VPN: Emory's virtual private network. It must be connected before you can reach the HPC.
• workflow: in slurmworkflow, a folder of generated job scripts. Project scripts named workflow-*.R create them.
• z-context.R: a file in each template chapter that switches settings between a small local run and a full-scale HPC run.