Man pages for TheoPannetier/hamr
Utility package for comrad
| batch_id_to_job_ids | Get job IDs from a batch ID |
| cat_ml_log_hpc | Fetch and print dd ML log from Peregrine |
| cat_sim_hpc | Fetch and print simulation log from Peregrine |
| compare_comrad_versions | Compare installed comrad versions between HPC and local... |
| compare_comsie_versions | Compare installed comsie versions between HPC and local... |
| complete_logbook_entries | Complete logbook entries after job completion |
| comrad_params_grid | Shortcut for grid of sigma_alpha, sigma_k values |
| comsie_params_grid | Shortcut for grid of sigma_alpha, gamma values |
| copy_sim_csv_to_hd | Copy comrad files to hard drive |
| copy_sim_log_to_hd | Copy comrad files to hard drive |
| create_comrad_params | Create a list of standard comrad parameters |
| create_comsie_params | Create a list of standard comsie parameters |
| default_params_doc | Documentation for main 'comrad' arguments. |
| download_data_with_fossil_hpc | Download DD ML result files from Peregrine |
| download_data_without_fossil_hpc | Download DD ML result files from Peregrine |
| download_logbook_hpc | Download the logbook from Peregrine to local |
| download_sim_hpc | Download simulation files from Peregrine |
| extract_ggplot_data | Extract data from a ggplot |
| filter_aic_best | Filter best ML results and compute AIC-based selection scores |
| filter_aic_best2 | Filter best ML results and compute AIC-based selection scores... |
| get_ml_rates | Get maximum likelihood estimates of DD rates |
| has_job_completed | Has a job completed? |
| install_comrad_hpc | Install comrad on the Peregrine HPC |
| install_comsie_hpc | Install 'comsie' on the Peregrine HPC |
| install_DAISIE_hpc | Install 'DAISIE' on the Peregrine HPC |
| install_DDD_hpc | Install 'DDD' on the Peregrine HPC |
| is_dd_ml_on_hd | Check if a dd_ml result file is present on my external hard... |
| is_dd_ml_on_local | Check if a dd_ml result file is present on the local PC |
| is_on_peregrine | Is code being run on peregrine? |
| is_sim_on_drive | Check if a simulation file is present on Google Drive |
| is_sim_on_hd | Check if a simulation file is present on my external hard... |
| is_sim_on_hpc | Fetch and print simulation log from Peregrine |
| is_sim_on_local | Check if a simulation file is present on the local PC |
| job_ids_from_string | Extract job IDs from a string |
| job_id_to_batch_id | Get batch ID from a job ID |
| job_info | Call 'jobinfo' on Peregrine |
| job_runtime | Get job runtime on Peregrine |
| job_status | Get job status on Peregrine |
| path_to_fabrika_hpc | Path to 'fabrika' on the Peregrine HPC |
| path_to_fabrika_local | Path to 'fabrika' on a local computer |
| path_to_hd | Path to my external hard drive, 'morozilka' |
| path_to_log_hd | Path to a simulation log file on external hard drive |
| path_to_log_hpc | Path to a simulation log file on Peregrine |
| path_to_log_local | Path to a simulation log file on local computer |
| path_to_sim_hd | Path to a simulation data file on external hard drive |
| path_to_sim_hpc | Path to a simulation data file on Peregrine |
| path_to_sim_local | Path to a simulation data file on local computer |
| pipe | Pipe operator |
| plot_aicw | Plot DD models AIC weights as a barplot |
| plot_ml_rates | Plot maximum likelihood estimates of DD rates |
| queue | Check the queue on Peregrine |
| read_logbook | Read logbook |
| read_ml_with_fossil | Read and combine 'dd_ML' results |
| read_ml_without_fossil | Read and combine 'dd_ML' results |
| reduce_sampling_hpc | Reduce the sampling of a simulated community |
| run_comrad_sim_hpc | Run comrad simulations on the Peregrine HPC |
| run_comsie_sim_hpc | Run comrad simulations on the Peregrine HPC |
| runtime_to_hms | Convert Peregrine time format to HMS |
| summary_last_gen_hpc | Summary of the last generation on the HPC |
| update_logbook_drive | Update the logbook on Google Drive |
| upload_bash_hpc | Upload 'run_dd_ml.bash' to Peregrine |
| upload_rscript_hpc | Upload a fabrika R script to Peregrine |
| upload_sim_bash_hpc | Upload 'run_comrad_sim.bash' to Peregrine |
| upload_sim_drive | Upload simulation files to Google Drive |
| write_path_to_fabrika_local | Overwrite 'path_to_fabrika_local' |
