let count = 0;

let for_table = []

for (const key in mod_results_json ) {

let absrel_u_branches = _.filter(_.map(mod_results_json[key]['aBSREL_UNFILTERED']['branch attributes'], d=> d['Corrected P-value']), d => d != null && d < pval)

let absrel_f_branches = _.filter(_.map(mod_results_json[key]['aBSREL_FILTERED']['branch attributes'], d=> d['Corrected P-value']), d => d != null && d < pval)

// Avery LRT calc

let avery_lrt_val = -2 * (mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Log Likelihood'] - mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Log Likelihood'])

let avery_e_p_val = chisqrprob(2, avery_lrt_val) / 2

// Filter based on the pvals

let avery_filt = avery_e_p_val < pval ? ['filtered', 'BUSTED-E'] : ['unfiltered', 'BUSTED']

// end lrt calc

// AGL LRT calc

// Based on https://sites.warnercnr.colostate.edu/gwhite/wp-content/uploads/sites/73/2017/04/LikelihoodRatioTests.pdf

// Get Log likelihoods of the models

let simple_model_ll = mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Log Likelihood'];

let alternative_model_ll = mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Log Likelihood'];

// you should always see LR ≥ 0

let lrt_val = -2 * simple_model_ll + 2 * alternative_model_ll;

console.log("Simple model LL: " + simple_model_ll + " Complex model LL " + alternative_model_ll);

console.log("Avery LRT: " + avery_lrt_val);

console.log("AGL LRT: " + lrt_val);

let e_p_val = chisqrprob(2, lrt_val)/2

// Filter based on the pvals

let filt = e_p_val < pval ? ['filtered', 'BUSTED-E'] : ['unfiltered', 'BUSTED']

// end lrt calc

if (lrt_val < 0) {

count += 1;

console.log ("Potential convergence issue! Avery! " + key);

}

const obj = {}

//overall

obj["ID"] = key

obj["Total sites"] = mod_results_json[key]['BUSTED_E']['input']['number of sites']

obj["Total sequences"] = mod_results_json[key]['BUSTED_E']['input']['number of sequences']

//BUSTED-E

obj["BUSTED-E filtered sites"] = _.reduce(mod_results_json[key]['FILTER']['filter'], (count, filter) => count + _.keys(filter).length, 0)

obj["Fraction of sites filtered"] = obj["BUSTED-E filtered sites"]/(obj["Total sites"] * obj["Total sequences"])

obj["Error p-val"] = e_p_val

obj["Filtered?"] = filt[0]

//aBSREL

obj["aBSREL selected branches"] = filt[0] === 'filtered' ? absrel_f_branches.length : absrel_u_branches.length

//BUSTED

obj["BUSTED selection p-val"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['test results']['p-value'] : mod_results_json[key]['BUSTED']['test results']['p-value']

obj["BUSTED(E?) ⍵1"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Rate Distributions']['Test'][1]['omega'] : mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['omega']

obj["BUSTED(E?) ⍵2"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Rate Distributions']['Test'][2]['omega'] : mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Rate Distributions']['Test'][1]['omega']

obj["BUSTED(E?) ⍵3"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Rate Distributions']['Test'][3]['omega'] : mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Rate Distributions']['Test'][2]['omega']

obj["BUSTED(E?) p1"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Rate Distributions']['Test'][1]['proportion'] : mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['proportion']

obj["BUSTED(E?) p2"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Rate Distributions']['Test'][2]['proportion'] : mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Rate Distributions']['Test'][1]['proportion']

obj["BUSTED(E?) p3"] = filt[0] === 'filtered' ? mod_results_json[key]['BUSTED_E']['fits']['Unconstrained model']['Rate Distributions']['Test'][3]['proportion'] : mod_results_json[key]['BUSTED']['fits']['Unconstrained model']['Rate Distributions']['Test'][2]['proportion']

for_table.push(obj)

}

console.log("Issues in " + count + " files");

return for_table

}