Man pages for kholsinger/Hickory
Analysis of within-population inbreeding and population differentiation
| analyze_codominant | Estimate f and theta from codominant marker data |
| analyze_codominant_t0 | Estimate f from codominant marker data assuming theta = 0,... |
| analyze_dominant | Estimate f and theta from dominant marker data |
| analyze_dominant_t0 | Estimate f from dominant marker data assuming theta = 0,... |
| analyze_f | Estimate inbreeding coefficients at each population/locus... |
| compare | Compare two models using already calculated estimates of... |
| count_genos | Count the genotypes at a single locus in a single population |
| diagnose_bulk_ess | Report bulk ESS for parameters exceeding a specified... |
| diagnose_tail_ess | Report tail ESS for parameters exceeding a specified... |
| energy_plot | Plot energy versus specified parameters for one chain |
| Hickory-package | The 'Hickory' package. |
| initialize_chains | Initialize pi, f, and theta based on priors Note: Depends on... |
| initialize_locus_pop | Initialize locus-specific thetas Note: Depends on... |
| inv_logit | Calculate the inverse logit of x |
| logit | Calculate the logit of p |
| logit_prior | Set mean and standard deviation on the logit scale given... |
| loo | Leave-one-out cross validation for Hickory models |
| read_marker_data | Read marker data from a CSV file |
| report | Summarize locus-, population-, or both specific estimates of... |
| report_ | Summarize estimates. Not intended for direct use. Use... |
| report_outliers | Report locus or population outliers |
| report_outliers_ | Report outliers. Not intended for direct use. Use... |
| set_alpha | Put alpha ("tightness" of locus-specific theta) in global... |
| set_priors | Put priors in global namespace so that they are available to... |
| summarize_f | Summarize the results of 'analyze_f()' |
