Nothing
##
## compare keyness() results against data from reference implementation (Evert 2022)
##
library(corpora)
## reference data (test code follows at bottom of script)
######################################################################
MRSAKeywords <-
structure(list(lemma = c("10-mal", "100-fach", "500-fach", "ABs",
"Abhusten", "Abstrich", "Abszess", "Abwehrtrick", "Achso", "Achterhoek",
"Acinetobacter", "Acinetobacter-Stamm", "Agrar-Lobby", "Ahlheit",
"Aktivierungslink", "Allergiehäufigkeit", "Allerweltskeim",
"Allgemeinstation", "Ambroxol", "Andere", "Anderen", "Ankündigungsfrist",
"Ansatzweise", "Ansteckung", "Ansteckungszahl", "Antbiotika",
"Antibiogramm", "Antibios", "Antibiotika", "Antibiotika-Einnahme",
"Antibiotika-Einsatz", "Antibiotika-Forschung", "Antibiotika-Gabe",
"Antibiotika-Gruppe", "Antibiotika-Hersteller", "Antibiotika-Klasse",
"Antibiotika-Kris", "Antibiotika-Monitoring", "Antibiotika-Resistenz",
"Antibiotika-Resistenz-Strategie", "Antibiotika-Resistenzstrategie",
"Antibiotika-Rezept", "Antibiotika-Therapie", "Antibiotika-Verordnung",
"Antibiotika-Verschreibung", "Antibiotika-resistent", "Antibiotikabehandlung",
"Antibiotikadose", "Antibiotikaeinnahme", "Antibiotikaeinsatz",
"Antibiotikaforschung", "Antibiotikagabe", "Antibiotikagruppe",
"Antibiotikaklasse", "Antibiotikamissbrauch", "Antibiotikaresistenz",
"Antibiotikas", "Antibiotikastrategie", "Antibiotikatherapie",
"Antibiotikaverbrauch", "Antibiotikaverordnung", "Antibiotikaverwendung",
"Antibiotikawirkstoff", "Antibiotikum", "Antibiotikum-Resistenz",
"Antiobiotika", "Apfalter", "Artengrenze", "Artgerechte", "Artikel",
"Arzt", "Arzteinkommen", "Atemsystem", "Atemwegsentzündung",
"Augusta-Klinik", "Ausbreitung", "Avatarbild", "Baby-Drama",
"Babystation", "Bagatellerkrankung", "Bakterie", "Bakterien-Stamm",
"Bakterienart", "Bakterienfamilie", "Bakteriengen", "Bakterienherd",
"Bakterieninfektion", "Bakterienkiller", "Bakterienkolonie",
"Bakterienresistenz", "Bakterienstamm", "Bakterienvariante",
"Bakterienwachstum", "Bakterienzahl", "Bakteriophage", "Bakteriophagen",
"Bakterium", "Basishygiene", "Bauern-Lobby", "Behandlung", "Behandlungsregime",
"Bekämpfungsmethode", "Berghäuser", "Bestimmtenantibiotikum",
"Beta-Laktamase", "BfR", "Billigpersonal", "Bindungsprotein",
"Biofilm", "Biotier", "Biotierhaltung", "Bittersalz", "Blaha",
"Blutdruckmesse", "Blutvergiftung", "Bodenbakterium", "Bowinkelmann",
"Brandverletzte", "Breitband-Antibiotikum", "Breitbandantibiotikum",
"Bremen-Mitte", "Brustmuskulatur", "Böggemann", "Bülach", "C-reaktiv",
"CDU-Gesundheitsexperte", "CORRECT", "CVUA", "Campylobacter-Bakterie",
"Cannabis-Medikament", "Carbapenem", "Carbapenem-Antibiotikum",
"Carbapenem-Resistenz", "Carbapenem-resistent", "Carbapenemase",
"Carbapeneme", "Carbapenemen", "Cephalosporine", "Charité",
"Chefarzt", "Chinolone", "Chlamydia", "Chloramphenicol", "Clindamycin",
"Clostridium", "Colistin", "Colistin-Resistenz", "Curti", "DART",
"DDD", "DGHM", "DGKH", "Darm", "Darm-Keim", "Darmbakterie", "Darmbakterium",
"Darmbewohner", "Darmflora", "Darmkeim", "Dekolonisierungsmaßnahme",
"Demzufolge", "Deshalb", "Desinfektion", "Desinfektionsmittel",
"Desinfektor", "Desweiteren", "Dettenkofer", "Diakonie-Krankenhaus",
"Dosiergerät", "Dox", "Doxy", "Drei-Bett-Zimmer", "Durchfall",
"E-Coli-Bakterie", "ECDC", "EHEC", "ENDO-Klinik", "ESBL", "ESBL-Bakterie",
"ESBL-Bildner", "ESBL-Gene", "ESBL-Keim", "ESBL-Klebsiellen",
"ESBL-Resistenzgen", "ESBL-bildend", "ESBL-produzierend", "ESBLbilden",
"Egal", "Eigentlich", "Eingangsscreening", "Einmalkittel", "Einsatz",
"Einzelgabe", "Eisenspeicher", "Eitererreger", "Eiterherd", "Eiterung",
"Eiweißproduktion", "Ekblom", "Endokarditis", "Enterobakterien",
"Enterokokken", "Entzündung", "Enzym", "Erbgutabschnitt", "Erkrankung",
"Erkältung", "Erkältungshusten", "Erreger", "Escherichia",
"Experte", "Fall", "Falschdiagnose", "Fleisch", "Fluorchinolone",
"Folgeoperation", "Forenteilnehmer", "Forist", "Forscher", "Fosfomycin",
"Frieden", "Frühchen", "Frühchen-Station", "Frühchenstation",
"Frühgeborene", "Gasbrand", "Gastmeier", "Gefahr", "Gemäss",
"Gen", "Generika", "Gentransfer", "Gesundheit", "Gesundheitsamt",
"Gesundheitsstaatsrat", "Grossteil", "Grünen", "Handhygiene",
"Hans-Iko", "Harnweg", "Harnweginfektion", "Harnwegsentzündung",
"Harnwegsinfekt", "Harnwegsinfektion", "Hausarzt", "Haut", "Hautbakterie",
"Hautbarriere", "Hochleistungszucht", "Humanbereich", "Humanmedizin",
"Hygiene", "Hygiene-Experte", "Hygiene-Fachkraft", "Hygiene-Maßnahme",
"Hygiene-Standard", "Hygienebeauftragte", "Hygieneexperte", "Hygienefachkraft",
"Hygienefrage", "Hygienemanagement", "Hygienemangel", "Hygienemaßnahme",
"Hygienepersonal", "Hygieneregel", "Hygieneskandal", "Hygienestandard",
"Hygieneverordnung", "Hygienevorschrift", "Hygieniker", "Händedesinfektion",
"Händehygiene", "Händewaschen", "Images", "Immunsystem", "Infekt",
"Infektiologe", "Infektiologie", "Infektion", "Infektionserreger",
"Infektionsforschung", "Infektionsgefahr", "Infektionshygiene",
"Infektionskrankheit", "Infektionsprävention", "Infektionsrate",
"Infektionsrisiko", "Infektionsschutzgesetz", "Infektionsspezialist",
"Infektionszahl", "Institute", "Intensivpatient", "Intensivstation",
"Interreg", "Isolationsmaßnahme", "KEYSTONE", "KISS", "KPC",
"KPC-Keim", "KRINKO", "Kaase", "Katheter", "Keim", "Keim-Alarm",
"Keim-Ausbruch", "Keim-Kris", "Keim-Skandal", "Keimausbruch",
"Keimbefall", "Keimbekämpfung", "Keimbelastung", "Keimflora",
"Keiminfektion", "Keimkris", "Keimproblem", "Keimskandal", "Keimträger",
"Killer-Keim", "Killerbakterie", "Killerkeim", "Klebsiella",
"Klebsiella-Bakterie", "Klebsiellen", "Klinik", "Klinik-Keim",
"Klinik-Mitarbeiter", "Klinikhygiene", "Klinikhygieniker", "Klinikinfektion",
"Klinikkeim", "Klinikpersonal", "Klinikum", "Koch-Institut",
"Koch-Instituts", "Kranke", "Krankenhaus", "Krankenhaus-Aufenthalt",
"Krankenhaus-Hygiene", "Krankenhaus-Hygieniker", "Krankenhaus-Infektion",
"Krankenhaus-Keim", "Krankenhaus-MRSA", "Krankenhausbakterie",
"Krankenhauserreger", "Krankenhaushygiene", "Krankenhaushygieniker",
"Krankenhausinfektion", "Krankenhauskeim", "Krankenhausmediziner",
"Krankenhauspatient", "Krankenhausskandal", "Krankheit", "Krankheitserreger",
"Krankheitskeim", "Kurbelradio", "Körper", "Labor", "Leser-Kommentar",
"Linezolid", "Linktext", "Lungenentzündung", "Lutschtablett",
"MRE", "MRGN", "MRGN-Erreger", "MRGN-Keim", "MRSA", "MRSA-Bakterie",
"MRSA-Bakterium", "MRSA-Erkrankung", "MRSA-Erreger", "MRSA-Fall",
"MRSA-Infektion", "MRSA-Keim", "MRSA-Patient", "MRSA-Problem",
"MRSA-Stamm", "MRSA-Test", "MRSA-Träger", "MRSA-frei", "Massenbehandlung",
"Massentierhaltung", "Mastanlage", "Mastbeschleuniger", "Mastbetrieb",
"Mastfutter", "Maßnahme", "Medikament", "Medizin", "Mediziner",
"Mensch", "Menscheit", "Methicillin", "Methicillin-resistent",
"Methicillin-resistente", "Methicillin-resistenten", "Methicillin-resistenter",
"Methillicin-resistent", "Mikroaufnahme", "Mikrobe", "Mikrobiologe",
"Mikrobiologie", "Mikroorganism", "Mittel", "Multiresistent",
"Multiresistente", "Multiresistenz", "Mutation", "NZZ-Konto",
"Nasenhöhle", "Nasenvorhof", "National", "Nebenwirkung", "Neu-Delhi-Metallo-Beta-Laktamase",
"Nosokomiale", "Not-Operation", "Notfall-Antibiotikum", "Notfallantibiotikum",
"ONLINE", "OP", "OP-Wunde", "ORSA", "Omnivoren", "Operation",
"PDF-Ratgeber", "PETA", "Patient", "Patientenkontakt", "Paul-Ehrlich-Gesellschaft",
"Penicillin", "Penicillium", "Penizillin", "Penizilline", "Personal",
"Pflegeheimen", "Pflegepersonal", "Pfleger", "Pflegeschlüssel",
"Phage", "Phagen", "Phagentherapie", "Pharma-Lobby", "Pharmaindustrie",
"Pierard", "Plasmide", "Popp", "Posted", "Problem", "Problemkeim",
"Pseudomonas", "Quell", "RKI", "Redaktionsempfehlung", "Referenzzentrum",
"Reserve-Antibiotikum", "Reserveantibiotikum", "Reservemedikament",
"Reservemittel", "Resistent", "Resistente", "Resistenz", "Resistenz-Gen",
"Resistenzbildung", "Resistenzentwicklung", "Resistenzgen", "Resistenzmechanismus",
"Resistenzproblem", "Resistenzproblematik", "Resistenzrat", "Resistenzrate",
"Resistenzrisiko", "Resistenztest", "Risikopatient", "Robert-Koch-Institut",
"Robert-Koch-Instituts", "Routine-Eingriff", "Routine-OP", "SPIEGEL",
"SPIEGEL-Verlag", "Schlachtbedingung", "Schleimhaut", "Schwein",
"Schätzungsweise", "Screening", "Selektionsdruck", "Sendedatum",
"Sendungshinweis", "Sepsis", "Spital", "Spitalhygiene", "Spitalhygieniker",
"Spitalinfektion", "Spitalkeim", "Spitalskeim", "Stall", "Stamm",
"Standardhygiene", "Staphylococcus", "Staphylokokken", "Staphylokokken-Infektion",
"Staphylokokkus", "Station", "Stattdessen", "Sterillium", "Stoffklasse",
"Streptokokken", "Studie", "Substanz", "Super-Bakterium", "Super-Erreger",
"Super-Keim", "Superbakterie", "Superbakterium", "Superbug",
"Supererreger", "Superinfektion", "Superkeim", "Swissnoso", "Symptom",
"Teixobactin", "Tetracycline", "The", "Therapie", "Tier", "Tierarzt",
"Tierhaltung", "Tiermast", "Tierzucht", "Tigecyclin", "Tigezyklin",
"Todesfall", "Toilettenhygiene", "UKL", "UKSH", "US-Forscher",
"US-Gesundheitsbehörde", "USA", "Umweltmedizin", "Uniklinik",
"Uniklinikum", "Universitätsklinikum", "Untersuchung", "Ursache",
"VRE", "VRE-Keim", "Vancomycin", "Vancomycin-resistent", "Verbreitung",
"Verordnungspraxis", "Verschreibung", "Virus", "Virus-Grippe",
"Vor-Antibiotika-Zeit", "WHO", "Wann", "Weltgesundheitsorganisation",
"Wie", "Wirkstoff", "Wissenschaftler", "Wundabstrich", "Wunddrainage",
"Wunde", "Wundermedizin", "Wundinfektion", "Wundkeim", "Zastrow",
"Zellwand", "abtöten", "abwehrgeschwächt", "aeruginosa", "ander",
"anstecken", "antibakteriell", "antibiotika-resistent", "antibiotikaresistent",
"antibiotisch", "antimikrobiell", "asymptomatischen", "aureus",
"ausbreiten", "auslösen", "ausser", "bakteriell", "baumanii",
"baumannii", "befallen", "behandelbar", "behandeln", "bekannt",
"bekämpfen", "bereits", "besiedeln", "bis", "bräuchten", "cassandros",
"coli", "coli-Bakterie", "dahin", "danach", "daraufhin", "derStandard",
"desinfizieren", "desto", "difficile", "dpa", "durchseuchen",
"eine", "einschleppen", "einsetzen", "eitrig", "entwickeln",
"erkranken", "et", "faecalis", "ferner", "for", "gefährlich",
"gelangen", "geschwächt", "gescreent", "gesund", "glaub", "gramnegativ",
"harmlos", "helfen", "hierbei", "hierzu", "hochresistent", "hospitalisiert",
"hygienisch", "häufig", "höchst", "immungeschwächt", "infizieren",
"infiziert", "isolieren", "jährlich", "jüngst", "klinisch",
"krank", "krankenhaushygienisch", "krankmachend", "lebensbedrohlich",
"lieber", "marcescens", "medizinisch", "meiste", "meisten", "mikrobiologisch",
"mulitresistenten", "multi-resistent", "multiresistent", "nachweisen",
"nicht-resistent", "nosokomiale", "nosokomialen", "nosokomialer",
"of", "pneumoniae", "politicon", "post-antibiotisch", "postantibiotisch",
"potenziell", "resistent", "schliesslich", "schwer", "selbe",
"selben", "sogenannt", "solange", "sprich", "standard", "sterben",
"testen", "tödlich", "unempfindlich", "untersuchen", "unwirksam",
"usw", "verabreichen", "verbreiten", "vermehren", "vermeidbar",
"verordnen", "verschreiben", "verursachen", "vieleicht", "waschen",
"weltweit", "wg", "wirken", "wirksam", "wirkungslos", "zB", "zb",
"zu", "zwischen", "ß-Lactam-Antibiotikum", "ärztlich", "über",
"überleben", "übertragen"), f1 = c(2L, 3L, 2L, 8L, 2L, 94L,
30L, 3L, 2L, 2L, 112L, 2L, 2L, 2L, 13L, 2L, 2L, 2L, 2L, 8L, 8L,
2L, 2L, 73L, 2L, 8L, 20L, 21L, 13L, 11L, 71L, 21L, 28L, 9L, 2L,
18L, 8L, 2L, 117L, 7L, 17L, 7L, 31L, 17L, 8L, 55L, 21L, 2L, 8L,
76L, 22L, 33L, 25L, 27L, 8L, 180L, 7L, 7L, 53L, 29L, 11L, 2L,
2L, 944L, 2L, 19L, 3L, 2L, 2L, 194L, 567L, 2L, 2L, 3L, 2L, 161L,
19L, 2L, 2L, 2L, 748L, 7L, 70L, 7L, 2L, 2L, 23L, 20L, 3L, 9L,
143L, 3L, 3L, 3L, 33L, 3L, 342L, 13L, 2L, 360L, 2L, 2L, 7L, 7L,
7L, 32L, 2L, 2L, 27L, 2L, 3L, 2L, 2L, 3L, 197L, 2L, 3L, 2L, 31L,
52L, 62L, 2L, 2L, 2L, 2L, 2L, 8L, 2L, 2L, 2L, 12L, 8L, 8L, 13L,
9L, 89L, 8L, 53L, 110L, 91L, 7L, 2L, 2L, 3L, 35L, 86L, 11L, 3L,
13L, 2L, 3L, 38L, 174L, 2L, 106L, 41L, 19L, 73L, 112L, 2L, 3L,
15L, 102L, 108L, 2L, 8L, 8L, 2L, 3L, 2L, 2L, 2L, 75L, 3L, 30L,
25L, 2L, 118L, 8L, 18L, 3L, 62L, 13L, 7L, 33L, 14L, 7L, 9L, 8L,
17L, 2L, 399L, 2L, 3L, 14L, 3L, 2L, 2L, 2L, 3L, 42L, 54L, 108L,
134L, 3L, 211L, 87L, 2L, 665L, 88L, 300L, 533L, 3L, 146L, 24L,
3L, 3L, 3L, 276L, 7L, 10L, 118L, 26L, 54L, 85L, 3L, 39L, 389L,
8L, 140L, 9L, 25L, 239L, 137L, 7L, 7L, 34L, 23L, 15L, 25L, 10L,
7L, 43L, 65L, 87L, 193L, 3L, 3L, 3L, 9L, 107L, 420L, 27L, 7L,
15L, 12L, 39L, 21L, 46L, 7L, 28L, 63L, 129L, 16L, 37L, 33L, 71L,
26L, 70L, 57L, 73L, 39L, 55L, 11L, 251L, 106L, 29L, 41L, 780L,
22L, 26L, 30L, 3L, 143L, 37L, 22L, 48L, 42L, 8L, 25L, 8L, 33L,
248L, 3L, 7L, 3L, 3L, 31L, 11L, 7L, 16L, 60L, 936L, 9L, 8L, 12L,
10L, 29L, 23L, 8L, 23L, 3L, 15L, 7L, 7L, 15L, 26L, 23L, 20L,
43L, 107L, 13L, 40L, 575L, 17L, 3L, 21L, 8L, 23L, 39L, 45L, 210L,
36L, 25L, 117L, 733L, 3L, 17L, 9L, 11L, 34L, 8L, 10L, 30L, 260L,
39L, 130L, 269L, 3L, 39L, 3L, 263L, 227L, 32L, 3L, 276L, 142L,
12L, 14L, 8L, 238L, 3L, 38L, 32L, 11L, 9L, 411L, 39L, 7L, 7L,
28L, 31L, 78L, 134L, 29L, 17L, 28L, 12L, 13L, 10L, 3L, 138L,
24L, 12L, 39L, 3L, 250L, 445L, 228L, 240L, 770L, 3L, 56L, 16L,
60L, 20L, 56L, 9L, 3L, 81L, 99L, 106L, 70L, 294L, 9L, 78L, 61L,
69L, 13L, 3L, 9L, 11L, 119L, 12L, 8L, 3L, 11L, 9L, 36L, 77L,
7L, 3L, 3L, 192L, 9L, 3L, 819L, 29L, 12L, 152L, 17L, 33L, 9L,
213L, 18L, 104L, 94L, 3L, 8L, 32L, 21L, 3L, 108L, 8L, 16L, 15L,
7L, 536L, 35L, 72L, 155L, 61L, 9L, 60L, 65L, 162L, 12L, 11L,
3L, 17L, 482L, 24L, 62L, 78L, 73L, 18L, 32L, 9L, 8L, 19L, 8L,
9L, 77L, 138L, 13L, 3L, 3L, 19L, 9L, 3L, 58L, 112L, 3L, 99L,
27L, 3L, 3L, 80L, 80L, 30L, 8L, 21L, 12L, 9L, 114L, 143L, 10L,
258L, 95L, 3L, 17L, 210L, 30L, 3L, 3L, 30L, 315L, 132L, 11L,
11L, 9L, 41L, 34L, 11L, 11L, 15L, 55L, 10L, 114L, 9L, 13L, 8L,
184L, 282L, 99L, 132L, 141L, 60L, 9L, 11L, 213L, 3L, 8L, 35L,
10L, 9L, 174L, 59L, 117L, 76L, 135L, 236L, 219L, 60L, 15L, 47L,
33L, 171L, 3L, 62L, 195L, 3L, 9L, 120L, 12L, 119L, 12L, 190L,
220L, 3L, 3L, 188L, 3L, 141L, 8L, 66L, 40L, 134L, 21L, 60L, 574L,
136L, 55L, 16L, 132L, 81L, 46L, 3L, 257L, 162L, 214L, 9L, 216L,
18L, 78L, 119L, 76L, 458L, 374L, 215L, 479L, 136L, 43L, 9L, 9L,
110L, 14L, 27L, 11L, 18L, 8L, 181L, 72L, 26L, 215L, 3L, 14L,
94L, 355L, 38L, 386L, 225L, 13L, 3L, 11L, 14L, 576L, 220L, 152L,
22L, 270L, 9L, 78L, 166L, 380L, 10L, 10L, 32L, 3L, 105L, 476L,
9L, 64L, 392L, 139L, 206L, 292L, 21L, 101L, 278L, 8L, 33L, 112L,
51L, 3L, 299L, 8L, 35L, 73L, 3L, 14L, 624L, 296L, 10L, 32L, 35L,
13L, 42L, 98L, 3L, 26L, 24L, 54L, 778L, 9L, 446L, 13L, 27L, 351L,
9L, 8L, 3L, 580L, 188L, 259L, 135L, 311L, 88L, 9L, 137L, 248L,
134L, 82L, 114L, 218L, 277L, 3L, 113L, 233L, 3L, 351L, 257L,
131L, 19L, 8L, 170L, 18L, 9L, 124L, 79L, 195L, 245L), f2 = c(1L,
1L, 1L, 0L, 1L, 749L, 21L, 1L, 1L, 1L, 6L, 1L, 1L, 1L, 0L, 1L,
1L, 1L, 1L, 0L, 0L, 1L, 1L, 273L, 1L, 0L, 0L, 2L, 0L, 0L, 10L,
1L, 1L, 0L, 1L, 1L, 0L, 1L, 8L, 0L, 0L, 0L, 5L, 0L, 0L, 0L, 5L,
1L, 0L, 28L, 4L, 6L, 1L, 0L, 0L, 15L, 0L, 0L, 6L, 2L, 0L, 1L,
1L, 367L, 1L, 1L, 1L, 1L, 1L, 5030L, 8468L, 1L, 1L, 1L, 1L, 555L,
0L, 1L, 1L, 1L, 528L, 0L, 23L, 0L, 1L, 1L, 7L, 1L, 1L, 0L, 14L,
1L, 1L, 1L, 4L, 1L, 117L, 0L, 1L, 4093L, 1L, 1L, 0L, 0L, 0L,
23L, 1L, 1L, 13L, 1L, 1L, 1L, 1L, 1L, 60L, 1L, 1L, 1L, 1L, 8L,
14L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,
2L, 0L, 6L, 328L, 649L, 0L, 1L, 1L, 1L, 16L, 0L, 0L, 1L, 0L,
1L, 1L, 0L, 252L, 1L, 35L, 23L, 3L, 41L, 76L, 1L, 1L, 0L, 35L,
91L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 186L, 1L, 4L, 9L, 1L, 4L,
0L, 1L, 1L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 17077L, 1L,
1L, 0L, 1L, 1L, 1L, 1L, 1L, 4L, 7L, 344L, 222L, 1L, 2190L, 292L,
1L, 473L, 33L, 6358L, 51849L, 1L, 2788L, 2L, 1L, 1L, 1L, 5684L,
0L, 0L, 75L, 5L, 8L, 67L, 1L, 5L, 14007L, 0L, 914L, 0L, 10L,
3926L, 406L, 0L, 0L, 0L, 4L, 1L, 8L, 0L, 0L, 9L, 9L, 480L, 2677L,
1L, 1L, 1L, 0L, 46L, 403L, 2L, 0L, 0L, 0L, 2L, 3L, 3L, 0L, 5L,
56L, 18L, 1L, 18L, 17L, 36L, 7L, 58L, 13L, 5L, 1L, 42L, 0L, 369L,
186L, 18L, 24L, 699L, 9L, 12L, 23L, 1L, 194L, 6L, 6L, 26L, 15L,
0L, 4L, 0L, 25L, 427L, 1L, 0L, 1L, 1L, 3L, 0L, 0L, 1L, 63L, 805L,
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), class = "data.frame", n1 = 1177, n2 = 341805, m = 20109L)
######################################################################
##
n1 <- attr(MRSAKeywords, "n1") # sample sizes
n2 <- attr(MRSAKeywords, "n2")
m <- attr(MRSAKeywords, "m") # family size (to correct for multiple testing)
compare.keyness <- function (measure, gold, name="", alpha=NULL, lambda=1) {
keyness.values <- keyness(MRSAKeywords$f1, n1, MRSAKeywords$f2, n2,
measure=measure, p.adjust=m, alpha=alpha, lambda=lambda)
reference.implementation <- MRSAKeywords[[gold]]
res <- all.equal(keyness.values, reference.implementation)
if (!isTRUE(res)) {
stop("keyness() doesn't match reference implementation for ", name, "\n", res)
}
cat(sprintf(" - keyness scores correct for %s\n", name))
}
compare.keyness("G2", "G2", name="log-likelihood (G2)")
compare.keyness("LogRatio", "LogRatio", name="LogRatio")
compare.keyness("LogRatio", "LogRatio.G2", name="LogRatio with G2 significance filter", alpha=.05)
compare.keyness("LRC", "LRC", name="LRC (conservative LogRatio)")
compare.keyness("PositiveLRC", "LRC.positive", name="Positive LRC")
compare.keyness("SimpleMaths", "SM", name="Simple Maths", lambda=100)
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