Man pages for statdivlab/happi
a hierarchical approach to pangenomics inference
| calculate_p | Calculating p function |
| doBoot | Function to run a bootstrap iteration |
| doPerm | Function to run a permutation iteration |
| expit | expit: inverse of logit |
| genInits | Function for generating initial starts for estimated beta |
| genInits_f | Function for generating initial starts for estimated f |
| happi | Main function for happi, p=q=1; this script contains the... |
| happi_multi_cov | Main function for happi, p=q=1; this script contains the... |
| incomplete_loglik | Function for calculating incomplete log likelihood |
| logit | logit: function for logit calculation |
| logit_data | Dataset of subsampling sims of logit_DRR102664 Arimizu E.... |
| npLRT | Non parametric LRT aka permutation test |
| pbLRT | parametric boostrap LRT implementation |
| pipe | Pipe operator |
| run_em | General E-M Algorithm |
| run_wasserman | # Wasserman split test function |
| simulate_b | Internal simulate function for parametric bootstrap |
| TM7_data | Dataset of Saccharibacteria MAGs from Shaiber et al. 2020. |
| update_beta | Function for updating betas |
| update_f | Function for updating f |
| warningcheck_update_f | Function for checking update_f |
