[R] Error nmf - Input matrix x contains at least one null or NA-filled row
Ragia .
ragia11 at hotmail.com
Sat Jun 11 00:42:44 CEST 2016
Dear group,
kindly I am trying to factorize document term matrix via NMF and got the following Error
show up
Error: NMF::nmf - 2/2 fit(s) threw an error.
# Error(s) thrown:
- run #1: NMF::nmf - Input matrix x contains at least one null or NA-filled row.
when I partition the matrix it works till I reached the last 10 rows ..they have a problem that I do not know
the fitting line is fit<-nmf((dtmm[90:100,]), 4, "lee", nrun=2)
And
the matrix is 100 row ..so the last 10 rows that make the problem are as follows:
dtm.sample <- dput(dtmm[90:100,])
structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), .Dim = c(11L, 475L), .Dimnames = structure(list(Docs = c("90",
"91", "92", "93", "94", "95", "96", "97", "98", "99", "100"),
Terms = c("âdawlahâ", "ââââââââââðÿâ" ,
"âââââââââðÿââ" , "abdullah",
"abo", "abu", "acc", "accept", "account", "actual", "administr",
"adnani", "advanc", "advic", "akh", "akhi", "alaykum", "aleppo",
"aljusiya", "allah", "allow", "almost", "alqaa", "alqaeda",
"alshabaab", "although", "ameen", "amisom", "amp", "anorsmte2sbtltsm8s8",
"anybodi", "apost", "aqap", "area", "armi", "aslm", "assad",
"asse", "attack", "attacksharvest", "audio", "avail", "â9th",
"baathist", "back", "baghdadi", "baiji", "bakeri", "barakallahu",
"battali", "battl", "bayah", "beat", "beehiv", "behalf",
"behind", "best", "biggest", "bless", "blood", "border",
"bought", "boy", "break", "brighten", "brother", "busi",
"bywith", "came", "cant", "capit", "carri", "chang", "channel",
"circl", "circumst", "citi", "citizen", "civilian", "claim",
"clarif", "clip", "collect", "comb", "come", "comment", "complet",
"confirm", "control", "countri", "countrysid", "crimin",
"cub", "currenc", "damascus", "dawah", "dawlah", "day", "death",
"declar", "definit", "dez1", "dialogu", "didnt", "disbeliev",
"dislik", "distribut", "divis", "doesnt", "doma", "downaqapth",
"download", "drastic", "ðÿ", "e58qi7sl7uu", "either", "els",
"encircl", "eng", "english", "enter", "etc", "ever", "everi",
"except", "face", "farrida", "fatih", "feekum", "fight",
"fighter", "finish", "first", "franc", "frontlin", "fsa",
"ù
ø", "general", "generat", "give", "god", "goe", "gold",
"great", "group", "half", "haqq", "harvest", "hasan", "hashd",
"hassan", "hazm", "hea", "headlock", "help", "hes", "hijrah",
"histori", "hiwar", "hold", "holi", "hom", "honey", "htt",
"ifnobodi", "imamah", "imarah", "impoant", "infight", "inshallah",
"integr", "intervenerad", "introduct", "iraq", "is2", "iseasi",
"islam", "islamicst", "isra", "jan13", "jannaal", "jannal",
"jawlani", "jazakallahu", "jihad", "job", "joedanianauthor",
"jordanian", "jurud", "just", "justic", "kid", "kill", "kilometr",
"knight", "know", "knw", "konkur", "kuffar", "kuwaiti", "lago",
"last", "leader", "leaflet", "leav", "lebanon", "lego", "let",
"libya", "like", "link", "live", "love", "made", "make",
"maqdisi", "march", "marea", "mari", "massiv", "may", "measur",
"meet", "messag", "militari", "militia", "missil", "mojahdin",
"mosqu", "mubahala", "muhajireen4", "muham", "mujahideen",
"murabit", "muslim", "nabi", "nam", "nasir", "nationalist",
"never", "new", "news", "nigeria", "nohaleppo", "noth", "noufaliy",
"now", "nusra", "occupi", "one", "ongo", "oni", "øøø", "øøøø",
"øøøøùøø", "øøøù", "øøøù", "øøøù" , "øøøùøù",
"øøù", "øøùøø", "øøùû" , "øøùøùù", "øøùùøø",
"øøùù
ø", "øøù
û", "øøùø", "øøùøù", "øøùûùøùû",
"øøùø", "øøùù", "øøùùøùùøøø", "øù", "øùø", "øùøùùøâââââââââââðÿââ" ,
"øùùøøùøùøùø" , "øùøøù", "øùø", "øùø", "øùøøøù
û",
"øùøøøù", "øùøøùøù", "øùøøùøùøùø", "øùøøùøø",
"øùøøùùù1436919", "øùøøùøù", "øùøùùø", "øùøùøùø" ,
"øùøùøø", "øùøùùù" , "øùøûøøø", "øùøûù", "øùùù",
"øùù
øøùøùùùùùø", "øùù
øù", "øùùùøøø", "øù
øøø",
"øù
øù", "øù
øùùø", "øù", "øùøø", "øùùø", "øùøøøù",
"øùøøø" , "øûø", "øûúø", "øùøùø", "pa2condit",
"paicip", "palestinian", "pamphlet", "path", "peopl", "petraeus",
"photo", "pleas", "pls", "poor", "popular", "post", "power",
"previous", "promis", "provid", "punish", "qusayr", "raid",
"raqqa", "raqqah", "regard", "releas", "rememb", "repeat",
"repo", "respons", "returnofthegolddinar", "reveng", "rule",
"russia", "sacrific", "saddamistseven", "safavid", "sahawat",
"sake", "salamu", "salvat", "samra", "saudi", "save", "saw",
"say", "sayna", "scholar", "second", "secur", "see", "select",
"seri", "shami", "sharä", "share", "sheikh", "shiit", "side",
"sinai", "sister", "soldier", "somalia", "soon", "sooninshaallah",
"spill", "spread", "srf", "sta", "state", "statement", "still",
"sub", "subtitl", "sultan", "sunnisthey", "suppo", "suspend",
"syria", "syrian", "syriasheikh", "takbirrr", "take", "taken",
"takfir", "talk", "taoosi", "tear", "tell", "ten", "the3",
"today", "tomorrow", "took", "top", "toward", "town", "tptcosnakcqb7mrstftw",
"transcriptoh", "translat", "translationâ", "tripoli", "true",
"truth", "tweet", "ùøùù
ø", "ùùø", "ùùøùøøù
øù",
"ùùøùøøùùøø", "ùøøùù", "ùøùøù", "ù
øøøûù", "ù
øøùøùù",
"ù
øøùù" , "ù
øøúøø", "ù
ùøùøø", "ù
ûú", "ùøøøøùùùøùøù" ,
"ùù", "ûøøúùú" , "ùøù" , "ûùúøûø" ,
"ûùúûøû" , "ùù" , "ùùù" , "ukh", "ukhti",
"ulama", "umayyad", "ûùøø", "ûû" , "updf", "use",
"ustrain", "ùùùù", "úû", "úù", "úùøú", "ùùù", "úû",
"vanish", "victori", "video", "videoeng", "videorejoic",
"videoth", "villag", "viral", "watch", "way", "week", "west",
"wilayat", "wilayatalfallujah", "wilayatalfurat", "wilayataljazirah",
"wilayatbarqah", "wilayatsalahuddin", "wilayatsayna", "wilayet",
"will", "wlaya", "wont", "word", "wuhayshi", "yarmouk", "yearsdayniil",
"yurkud", "zone", "zubayr")), .Names = c("Docs", "Terms")))
kindly I do not know why it do not work for those rwos?
example of working rows is the same matrix head
dtm.sample2 <- dput(head( dtmm))
structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(6L,
475L), .Dimnames = structure(list(Docs = c("1", "2", "3", "4",
"5", "6"), Terms = c("âdawlahâ", "ââââââââââðÿâ" ,
"âââââââââðÿââ" , "abdullah",
"abo", "abu", "acc", "accept", "account", "actual", "administr",
"adnani", "advanc", "advic", "akh", "akhi", "alaykum", "aleppo",
"aljusiya", "allah", "allow", "almost", "alqaa", "alqaeda", "alshabaab",
"although", "ameen", "amisom", "amp", "anorsmte2sbtltsm8s8",
"anybodi", "apost", "aqap", "area", "armi", "aslm", "assad",
"asse", "attack", "attacksharvest", "audio", "avail", "â9th",
"baathist", "back", "baghdadi", "baiji", "bakeri", "barakallahu",
"battali", "battl", "bayah", "beat", "beehiv", "behalf", "behind",
"best", "biggest", "bless", "blood", "border", "bought", "boy",
"break", "brighten", "brother", "busi", "bywith", "came", "cant",
"capit", "carri", "chang", "channel", "circl", "circumst", "citi",
"citizen", "civilian", "claim", "clarif", "clip", "collect",
"comb", "come", "comment", "complet", "confirm", "control", "countri",
"countrysid", "crimin", "cub", "currenc", "damascus", "dawah",
"dawlah", "day", "death", "declar", "definit", "dez1", "dialogu",
"didnt", "disbeliev", "dislik", "distribut", "divis", "doesnt",
"doma", "downaqapth", "download", "drastic", "ðÿ", "e58qi7sl7uu",
"either", "els", "encircl", "eng", "english", "enter", "etc",
"ever", "everi", "except", "face", "farrida", "fatih", "feekum",
"fight", "fighter", "finish", "first", "franc", "frontlin", "fsa",
"ù
ø", "general", "generat", "give", "god", "goe", "gold", "great",
"group", "half", "haqq", "harvest", "hasan", "hashd", "hassan",
"hazm", "hea", "headlock", "help", "hes", "hijrah", "histori",
"hiwar", "hold", "holi", "hom", "honey", "htt", "ifnobodi", "imamah",
"imarah", "impoant", "infight", "inshallah", "integr", "intervenerad",
"introduct", "iraq", "is2", "iseasi", "islam", "islamicst", "isra",
"jan13", "jannaal", "jannal", "jawlani", "jazakallahu", "jihad",
"job", "joedanianauthor", "jordanian", "jurud", "just", "justic",
"kid", "kill", "kilometr", "knight", "know", "knw", "konkur",
"kuffar", "kuwaiti", "lago", "last", "leader", "leaflet", "leav",
"lebanon", "lego", "let", "libya", "like", "link", "live", "love",
"made", "make", "maqdisi", "march", "marea", "mari", "massiv",
"may", "measur", "meet", "messag", "militari", "militia", "missil",
"mojahdin", "mosqu", "mubahala", "muhajireen4", "muham", "mujahideen",
"murabit", "muslim", "nabi", "nam", "nasir", "nationalist", "never",
"new", "news", "nigeria", "nohaleppo", "noth", "noufaliy", "now",
"nusra", "occupi", "one", "ongo", "oni", "øøø", "øøøø", "øøøøùøø",
"øøøù", "øøøù", "øøøù" , "øøøùøù", "øøù", "øøùøø",
"øøùû" , "øøùøùù", "øøùùøø", "øøùù
ø", "øøù
û",
"øøùø", "øøùøù", "øøùûùøùû", "øøùø", "øøùù", "øøùùøùùøøø",
"øù", "øùø", "øùøùùøâââââââââââðÿââ" ,
"øùùøøùøùøùø" , "øùøøù", "øùø", "øùø", "øùøøøù
û",
"øùøøøù", "øùøøùøù", "øùøøùøùøùø", "øùøøùøø", "øùøøùùù1436919",
"øùøøùøù", "øùøùùø", "øùøùøùø" , "øùøùøø", "øùøùùù" ,
"øùøûøøø", "øùøûù", "øùùù", "øùù
øøùøùùùùùø",
"øùù
øù", "øùùùøøø", "øù
øøø", "øù
øù", "øù
øùùø", "øù",
"øùøø", "øùùø", "øùøøøù", "øùøøø" , "øûø", "øûúø",
"øùøùø", "pa2condit", "paicip", "palestinian", "pamphlet",
"path", "peopl", "petraeus", "photo", "pleas", "pls", "poor",
"popular", "post", "power", "previous", "promis", "provid", "punish",
"qusayr", "raid", "raqqa", "raqqah", "regard", "releas", "rememb",
"repeat", "repo", "respons", "returnofthegolddinar", "reveng",
"rule", "russia", "sacrific", "saddamistseven", "safavid", "sahawat",
"sake", "salamu", "salvat", "samra", "saudi", "save", "saw",
"say", "sayna", "scholar", "second", "secur", "see", "select",
"seri", "shami", "sharä", "share", "sheikh", "shiit", "side",
"sinai", "sister", "soldier", "somalia", "soon", "sooninshaallah",
"spill", "spread", "srf", "sta", "state", "statement", "still",
"sub", "subtitl", "sultan", "sunnisthey", "suppo", "suspend",
"syria", "syrian", "syriasheikh", "takbirrr", "take", "taken",
"takfir", "talk", "taoosi", "tear", "tell", "ten", "the3", "today",
"tomorrow", "took", "top", "toward", "town", "tptcosnakcqb7mrstftw",
"transcriptoh", "translat", "translationâ", "tripoli", "true",
"truth", "tweet", "ùøùù
ø", "ùùø", "ùùøùøøù
øù", "ùùøùøøùùøø",
"ùøøùù", "ùøùøù", "ù
øøøûù", "ù
øøùøùù", "ù
øøùù" ,
"ù
øøúøø", "ù
ùøùøø", "ù
ûú", "ùøøøøùùùøùøù" , "ùù",
"ûøøúùú" , "ùøù" , "ûùúøûø" , "ûùúûøû" ,
"ùù" , "ùùù" , "ukh", "ukhti", "ulama", "umayyad",
"ûùøø", "ûû" , "updf", "use", "ustrain", "ùùùù",
"úû", "úù", "úùøú", "ùùù", "úû", "vanish", "victori", "video",
"videoeng", "videorejoic", "videoth", "villag", "viral", "watch",
"way", "week", "west", "wilayat", "wilayatalfallujah", "wilayatalfurat",
"wilayataljazirah", "wilayatbarqah", "wilayatsalahuddin", "wilayatsayna",
"wilayet", "will", "wlaya", "wont", "word", "wuhayshi", "yarmouk",
"yearsdayniil", "yurkud", "zone", "zubayr")), .Names = c("Docs",
"Terms")))
thanks in advance
Ragia
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