Every text went through Shiberu's Japanese analyzer (fugashi with UniDic, the same tagger and dictionary-form rule the Reader uses), so each entry is a word as a learner looks it up: 言っ → 言う, 分かっ → 分かる.
Each source gives a rate per million words for every word, and a word's score is the median of its three rates. One source cannot push its own oddities up (names in example sentences, years in Wikipedia, archaic words in old novels): a second source has to agree. A word must appear in at least two sources.
Particles and auxiliaries stay in the list, because a reader meets them in every sentence. Left out: person names, numerals, symbols, words written only in Latin letters and over-long fragments.
Only counts are published: the files contain no text from any source.