Function reference • EpiModelHPC

All functions

EpiModelHPC-package EpiModelHPC: EpiModel Extensions for High-Performance Computing

check_cp(): Checks for Checkpointed Rdata Files

get_scenarios_batches_infos(): Helper function to access the file name elements of scenarios

get_scenarios_tibble_infos(): Helper function to access the infos on merged scenarios data.frame

initialize_cp(): Initializes Network Model after Checkpointing

make_calibrated_scenario(): Make an EpiModel scenario using the result of an swfcalib calibration

make_save_elements(): Create the save_elements vector for netsim_run_one_scenario

merge_netsim_scenarios(): Create a Single Sim File per Scenarios Using the Files From netsim_scenarios

merge_netsim_scenarios_tibble(): Create a Single Sim File per Scenarios Using the Files From netsim_scenarios

merge_simfiles(): Save Simulation Data from Stochastic Network Models

netsim_hpc(): Stochastic Network Models on High-Performance Computing Systems

netsim_run_one_scenario(): Run one netsim call with a scenario and saves the results deterministically

netsim_run_swfcalib_scenario(): Run one netsim call with the result of an swfcalib calibration

netsim_scenarios(): Function to run EpiModel network simulations with scenarios

netsim_scenarios_setup(): Helper function to create the parameters for netsim_run_one_scenario

netsim_swfcalib_output(): Function to run an EpiModel sim with the result of an swfcalib calibration

netsim_swfcalib_output_setup(): Helper function to create the parameters for netsim_run_swfcalib_scenario

process_simfiles(): Process sub-job simulation files saved as a series of Rdata files.

pull_env_vars(): Pull Standard Environmental Variables in Slurm Jobs

save_cpdata(): Saves for Network Simulation Rdata Files for Checkpointing

savesim(): Save Simulation Data from Stochastic Network Models

sbatch_master(): Create sbatch Bash Shell Script with Parameter Combination

step_tmpl_merge_netsim_scenarios(): Step Template to Create a Single Sim File per Scenarios Using the Files From netsim_scenarios

step_tmpl_merge_netsim_scenarios_tibble(): Step Template to Create a Single Sim File per Scenarios Using the Files From netsim_scenarios

step_tmpl_netsim_scenarios(): Step template to run EpiModel network simulations with scenarios

step_tmpl_netsim_swfcalib_output(): Step template to run sims with the result of an swfcalib calibration

step_tmpl_renv_restore(): Step template to update a project renv

swf_configs_hyak(): Preset of Configuration for the HYAK Cluster

swf_configs_rsph(): Preset of Configuration for the RSPH Cluster

swfcalib_proposal_to_scenario(): Convert an swfcalib Proposal into an EpiModel Scenario