R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. > ### *
> ### > attach(NULL, name = "CheckExEnv") > assign(".CheckExEnv", as.environment(2), pos = length(search())) # base > ## add some hooks to label plot pages for base and grid graphics > setHook("plot.new", ".newplot.hook") > setHook("persp", ".newplot.hook") > setHook("grid.newpage", ".gridplot.hook") > > assign("cleanEx", + function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("default", "default") + set.seed(1) + options(warn = 1) + delayedAssign("T", stop("T used instead of TRUE"), + assign.env = .CheckExEnv) + delayedAssign("F", stop("F used instead of FALSE"), + assign.env = .CheckExEnv) + sch <- search() + newitems <- sch[! sch %in% .oldSearch] + for(item in rev(newitems)) + eval(substitute(detach(item), list(item=item))) + missitems <- .oldSearch[! .oldSearch %in% sch] + if(length(missitems)) + warning("items ", paste(missitems, collapse=", "), + " have been removed from the search path") + }, + env = .CheckExEnv) > assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now > assign("ptime", proc.time(), env = .CheckExEnv) > grDevices::postscript("cfa-Examples.ps") > assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv) > options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly")) > options(warn = 1) > library('cfa') > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "boot.cfa" > > ### * boot.cfa > > flush(stderr()); flush(stdout()) > > ### Name: boot.cfa > ### Title: Bootstrap-CFA > ### Aliases: boot.cfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > boot.cfa(configs,counts,runs=25) cnt.antitype cnt.type pct.types cnt.sig pct.cnt.sig B D E H 3 22 88 3 12 B D E G 25 0 0 0 0 B C F H 19 6 24 3 12 B C F G 25 0 0 0 0 B C E H 16 9 36 1 4 B C E G 0 25 100 0 0 A D F G 0 25 100 0 0 A D E H 25 0 0 1 4 A D E G 3 22 88 0 0 A C F H 14 11 44 1 4 A C F G 2 23 92 0 0 A C E H 11 14 56 1 4 A C E G 24 1 4 0 0 > > > > cleanEx(); ..nameEx <- "cfa" > > ### * cfa > > flush(stderr()); flush(stdout()) > > ### Name: cfa > ### Title: Analysis of configuration frequencies > ### Aliases: cfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > cfa(configs,counts) *** Analysis of configuration frequencies (CFA) *** label n expected Q chisq p.chisq sig.chisq 1 A C F H 50 27.745523 0.0208130786 17.85015097 2.390003e-05 TRUE 2 B C E G 182 151.626973 0.0321280867 6.08414666 1.364002e-02 FALSE 3 B C E H 14 22.545581 0.0079534145 3.23908086 7.190096e-02 FALSE 4 A D F G 35 27.074299 0.0074077112 2.32016088 1.277068e-01 FALSE 5 B D E H 6 3.271227 0.0024949263 2.27627104 1.313674e-01 FALSE 6 A C E H 54 63.931701 0.0096137894 1.54287598 2.141902e-01 FALSE 7 B C F G 57 65.804124 0.0085377809 1.17792931 2.777780e-01 FALSE 8 A C E G 411 429.963201 0.0284290175 0.83635759 3.604406e-01 FALSE 9 A D E G 69 62.385057 0.0063936276 0.70140942 4.023105e-01 FALSE 10 B D E G 19 22.000156 0.0027908431 0.40913052 5.224112e-01 FALSE 11 B C F H 8 9.784488 0.0016413375 0.32545353 5.683486e-01 FALSE 12 A C F G 182 186.598409 0.0050509674 0.11332017 7.363954e-01 FALSE 13 A D E H 10 9.276103 0.0006655156 0.05649217 8.121287e-01 FALSE z p.z sig.z 1 4.1832611 1.436785e-05 TRUE 2 2.6133207 4.483356e-03 FALSE 3 -1.9249306 9.728810e-01 FALSE 4 1.4450582 7.422078e-02 FALSE 5 1.2341243 1.085783e-01 FALSE 6 -1.3444226 9.105941e-01 FALSE 7 -1.1829917 8.815938e-01 FALSE 8 -1.2037243 8.856519e-01 FALSE 9 0.7971977 2.126681e-01 FALSE 10 -0.7538303 7.745245e-01 FALSE 11 -0.7336100 7.684068e-01 FALSE 12 -0.4097014 6.589875e-01 FALSE 13 0.0738261 4.705744e-01 FALSE Summary statistics: Total Chi squared = 36.93278 Total degreed of freedom = 11 p = 1.222729e-09 Sum of counts = 1097 Levels: V1 V2 V3 V4 2 2 2 2 > > > > cleanEx(); ..nameEx <- "hier.cfa" > > ### * hier.cfa > > flush(stderr()); flush(stdout()) > > ### Name: hier.cfa > ### Title: Hierachical analysis of configuration frequencies > ### Aliases: hier.cfa > ### Keywords: multivariate htest > > ### ** Examples > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > hier.cfa(configs,counts) *** Hierarchical CFA *** Overall chi squared df p order V1 V3 V4 22.9903336 4 0.0001271905 3 V2 V3 V4 17.2251999 4 0.0017475767 3 V1 V2 V4 16.5362030 4 0.0023779347 3 V1 V3 10.4129150 1 0.0012513706 2 V1 V3 10.4129150 1 0.0012513706 2 V3 V4 8.6523726 1 0.0032663575 2 V3 V4 8.6523726 1 0.0032663575 2 V1 V2 V3 8.6071090 4 0.0717062583 3 V1 V2 5.3987739 1 0.0201509035 2 V1 V2 5.3987739 1 0.0201509035 2 V1 V4 3.4154458 1 0.0645889662 2 V1 V4 3.4154458 1 0.0645889662 2 V2 V3 1.9496936 1 0.1626198715 2 V2 V3 1.9496936 1 0.1626198715 2 V2 V4 0.2902919 1 0.5900335348 2 V2 V4 0.2902919 1 0.5900335348 2 > > > > cleanEx(); ..nameEx <- "mcfa" > > ### * mcfa > > flush(stderr()); flush(stdout()) > > ### Name: mcfa > ### Title: Two or more-sample CFA > ### Aliases: mcfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts1<-trunc(runif(250)*10) > counts2<-trunc(runif(250)*10) > mcfa(configs,cbind(counts1,counts2)) $labels [1] "B C E G" "A D E G" "A C E G" "A C E G" "A C F G" "A C F G" "A D F G" [8] "B C E G" "A C E G" "A D E G" "B C E G" "B C E G" "B C E G" "B C E G" [15] "A D E G" "A D F G" "B C E G" "A C E G" "A C E G" "A C E G" "A C F G" [22] "A C E G" "B C F G" "A C F G" "A C F G" "A C E G" "A C F H" "A C E G" [29] "A D E G" "A C F G" "A C F H" "A C E G" "A C F G" "A C E G" "A C E H" [36] "B C F G" "A D E G" "A C E G" "A C E G" "B C E G" "A C E H" "B C E G" [43] "A C E G" "B C E G" "A C E G" "A C E G" "B C E G" "A C E G" "A C E G" [50] "A C F G" "B C E G" "A C E G" "A C E G" "B C F G" "B C F G" "A C F G" [57] "A C F G" "A C E H" "A C F H" "A C E G" "A C E G" "A C E G" "A D E H" [64] "A C E G" "A C E G" "A D E G" "A C E G" "A C E G" "A C F H" "A C E G" [71] "A C F G" "A D F G" "B C F G" "A D E G" "B C E G" "B C E H" "A C F G" [78] "A C F G" "B C F G" "A D E G" "B C E G" "A C F G" "A C E G" "A C F H" [85] "B C F H" "B C F G" "A C E G" "A C E G" "A C E G" "A C F G" "A C E G" [92] "A C E G" "A C E G" "B C F H" "A D F G" "B C F G" "A C E G" "B C E G" [99] "A C F G" "A C E G" "A C E G" "A C E H" "A D E G" "A C E G" "A C E G" [106] "B C F G" "A C E G" "A C E H" "B C E G" "A C E G" "A D E H" "B D E G" [113] "A C E G" "A C E G" "A C E G" "A C F G" "B C E G" "A C E G" "A C E G" [120] "B C F G" "A C E G" "A C E G" "B C F G" "B C F H" "A C E G" "A C F G" [127] "A C E G" "B C E G" "B C F G" "B C E G" "A C E G" "A C E G" "A D F G" [134] "A C E G" "A C E H" "A C F G" "A C E G" "A C E G" "B C F G" "B C E G" [141] "B C E G" "B C E G" "A C E G" "A D F G" "A D E G" "A D F G" "A C E H" [148] "B C F G" "A C E G" "B C E G" "A D F G" "A C E G" "B C E G" "A C F H" [155] "B C E G" "A C E G" "A C E G" "A C E G" "A C E G" "A C E H" "A C E G" [162] "A C F G" "B C E G" "B C E G" "A C E G" "A D F G" "A C E G" "A C F G" [169] "A C E G" "A C E G" "B D E H" "A C E G" "A C E G" "A D E G" "A C F H" [176] "A C F H" "A C E G" "A C F G" "B C E G" "B D E G" "A C E G" "A C F G" [183] "B C E G" "A C E G" "B C F G" "A C E G" "A C E G" "B C E G" "A C E G" [190] "A D E G" "A C E G" "A C E G" "A C F G" "A C E G" "B C E G" "A C E G" [197] "B C E G" "A D E G" "A C E H" "B C E G" "A C E G" "B C E H" "B D E G" [204] "A C F G" "A C F G" "A C E G" "A C F G" "B C E G" "A D E G" "B C E G" [211] "B C F G" "B C E G" "B C E G" "B C E G" "A C F G" "A C E G" "A C E G" [218] "B C E G" "A C F G" "A C F G" "A C F H" "A C E G" "A C F G" "A C E G" [225] "B C E G" "B C E H" "A C F G" "A C E G" "B C E G" "A C F G" "A C F H" [232] "A C F G" "B C E G" "A C F G" "A C E H" "B C F G" "A C E G" "B C E G" [239] "B C E G" "A C F G" "A C E H" "B C F G" "A C E G" "A D E G" "A C E G" [246] "A C F G" "A C E G" "A C E G" "A C F G" "B C E H" $counts counts1 counts2 [1,] 0 0 [2,] 0 0 [3,] 0 0 [4,] 0 0 [5,] 0 9 [6,] 9 0 [7,] 9 0 [8,] 0 8 [9,] 0 8 [10,] 0 8 [11,] 0 8 [12,] 0 8 [13,] 0 8 [14,] 0 8 [15,] 8 0 [16,] 8 0 [17,] 0 7 [18,] 7 0 [19,] 1 9 [20,] 1 9 [21,] 0 6 [22,] 9 1 [23,] 9 1 [24,] 9 1 [25,] 9 1 [26,] 6 0 [27,] 6 0 [28,] 6 0 [29,] 6 0 [30,] 1 8 [31,] 8 1 [32,] 8 1 [33,] 0 5 [34,] 5 0 [35,] 5 0 [36,] 1 7 [37,] 1 7 [38,] 1 7 [39,] 2 9 [40,] 2 9 [41,] 7 1 [42,] 7 1 [43,] 7 1 [44,] 7 1 [45,] 9 2 [46,] 9 2 [47,] 0 4 [48,] 0 4 [49,] 0 4 [50,] 0 4 [51,] 4 0 [52,] 4 0 [53,] 2 8 [54,] 2 8 [55,] 2 8 [56,] 2 8 [57,] 2 8 [58,] 1 6 [59,] 1 6 [60,] 1 6 [61,] 8 2 [62,] 6 1 [63,] 6 1 [64,] 3 9 [65,] 3 9 [66,] 0 3 [67,] 0 3 [68,] 3 0 [69,] 3 0 [70,] 3 0 [71,] 3 0 [72,] 3 0 [73,] 3 0 [74,] 9 3 [75,] 9 3 [76,] 1 5 [77,] 1 5 [78,] 7 2 [79,] 7 2 [80,] 5 1 [81,] 5 1 [82,] 5 1 [83,] 5 1 [84,] 3 8 [85,] 3 8 [86,] 3 8 [87,] 8 3 [88,] 8 3 [89,] 8 3 [90,] 8 3 [91,] 8 3 [92,] 2 6 [93,] 2 6 [94,] 4 9 [95,] 0 2 [96,] 0 2 [97,] 2 0 [98,] 2 0 [99,] 1 4 [100,] 1 4 [101,] 1 4 [102,] 9 4 [103,] 9 4 [104,] 9 4 [105,] 3 7 [106,] 3 7 [107,] 3 7 [108,] 4 1 [109,] 4 1 [110,] 4 1 [111,] 4 1 [112,] 7 3 [113,] 7 3 [114,] 4 8 [115,] 8 4 [116,] 8 4 [117,] 8 4 [118,] 5 2 [119,] 5 2 [120,] 1 3 [121,] 1 3 [122,] 1 3 [123,] 1 3 [124,] 1 3 [125,] 1 3 [126,] 0 1 [127,] 0 1 [128,] 0 1 [129,] 0 1 [130,] 1 0 [131,] 1 0 [132,] 1 0 [133,] 3 1 [134,] 3 1 [135,] 3 1 [136,] 4 7 [137,] 4 7 [138,] 7 4 [139,] 2 4 [140,] 6 9 [141,] 6 9 [142,] 6 9 [143,] 4 2 [144,] 4 2 [145,] 4 2 [146,] 4 2 [147,] 4 2 [148,] 4 2 [149,] 8 5 [150,] 8 5 [151,] 3 5 [152,] 3 5 [153,] 3 5 [154,] 3 5 [155,] 3 5 [156,] 3 5 [157,] 9 6 [158,] 9 6 [159,] 9 6 [160,] 5 3 [161,] 5 3 [162,] 5 3 [163,] 5 3 [164,] 5 7 [165,] 5 7 [166,] 1 2 [167,] 1 2 [168,] 6 8 [169,] 6 8 [170,] 6 8 [171,] 6 8 [172,] 6 4 [173,] 7 9 [174,] 7 9 [175,] 7 9 [176,] 2 1 [177,] 2 1 [178,] 2 1 [179,] 2 1 [180,] 7 5 [181,] 7 5 [182,] 7 5 [183,] 8 6 [184,] 8 6 [185,] 2 3 [186,] 2 3 [187,] 2 3 [188,] 2 3 [189,] 9 7 [190,] 9 7 [191,] 9 7 [192,] 9 7 [193,] 9 7 [194,] 3 4 [195,] 3 4 [196,] 3 4 [197,] 3 2 [198,] 4 5 [199,] 4 5 [200,] 4 5 [201,] 4 5 [202,] 5 6 [203,] 5 6 [204,] 5 6 [205,] 5 6 [206,] 5 6 [207,] 4 3 [208,] 4 3 [209,] 4 3 [210,] 4 3 [211,] 6 7 [212,] 6 7 [213,] 6 7 [214,] 6 7 [215,] 7 8 [216,] 7 8 [217,] 7 8 [218,] 7 8 [219,] 8 9 [220,] 8 9 [221,] 8 9 [222,] 5 4 [223,] 6 5 [224,] 7 6 [225,] 7 6 [226,] 7 6 [227,] 7 6 [228,] 9 9 [229,] 9 9 [230,] 9 9 [231,] 9 9 [232,] 9 9 [233,] 9 9 [234,] 8 8 [235,] 8 8 [236,] 7 7 [237,] 6 6 [238,] 6 6 [239,] 5 5 [240,] 5 5 [241,] 4 4 [242,] 4 4 [243,] 3 3 [244,] 3 3 [245,] 3 3 [246,] 2 2 [247,] 2 2 [248,] 2 2 [249,] 1 1 [250,] 1 1 $expected [,1] [,2] [1,] 0.000000 0.000000 [2,] 0.000000 0.000000 [3,] 0.000000 0.000000 [4,] 0.000000 0.000000 [5,] 4.564494 4.435506 [6,] 4.564494 4.435506 [7,] 4.564494 4.435506 [8,] 4.057328 3.942672 [9,] 4.057328 3.942672 [10,] 4.057328 3.942672 [11,] 4.057328 3.942672 [12,] 4.057328 3.942672 [13,] 4.057328 3.942672 [14,] 4.057328 3.942672 [15,] 4.057328 3.942672 [16,] 4.057328 3.942672 [17,] 3.550162 3.449838 [18,] 3.550162 3.449838 [19,] 5.071660 4.928340 [20,] 5.071660 4.928340 [21,] 3.042996 2.957004 [22,] 5.071660 4.928340 [23,] 5.071660 4.928340 [24,] 5.071660 4.928340 [25,] 5.071660 4.928340 [26,] 3.042996 2.957004 [27,] 3.042996 2.957004 [28,] 3.042996 2.957004 [29,] 3.042996 2.957004 [30,] 4.564494 4.435506 [31,] 4.564494 4.435506 [32,] 4.564494 4.435506 [33,] 2.535830 2.464170 [34,] 2.535830 2.464170 [35,] 2.535830 2.464170 [36,] 4.057328 3.942672 [37,] 4.057328 3.942672 [38,] 4.057328 3.942672 [39,] 5.578826 5.421174 [40,] 5.578826 5.421174 [41,] 4.057328 3.942672 [42,] 4.057328 3.942672 [43,] 4.057328 3.942672 [44,] 4.057328 3.942672 [45,] 5.578826 5.421174 [46,] 5.578826 5.421174 [47,] 2.028664 1.971336 [48,] 2.028664 1.971336 [49,] 2.028664 1.971336 [50,] 2.028664 1.971336 [51,] 2.028664 1.971336 [52,] 2.028664 1.971336 [53,] 5.071660 4.928340 [54,] 5.071660 4.928340 [55,] 5.071660 4.928340 [56,] 5.071660 4.928340 [57,] 5.071660 4.928340 [58,] 3.550162 3.449838 [59,] 3.550162 3.449838 [60,] 3.550162 3.449838 [61,] 5.071660 4.928340 [62,] 3.550162 3.449838 [63,] 3.550162 3.449838 [64,] 6.085992 5.914008 [65,] 6.085992 5.914008 [66,] 1.521498 1.478502 [67,] 1.521498 1.478502 [68,] 1.521498 1.478502 [69,] 1.521498 1.478502 [70,] 1.521498 1.478502 [71,] 1.521498 1.478502 [72,] 1.521498 1.478502 [73,] 1.521498 1.478502 [74,] 6.085992 5.914008 [75,] 6.085992 5.914008 [76,] 3.042996 2.957004 [77,] 3.042996 2.957004 [78,] 4.564494 4.435506 [79,] 4.564494 4.435506 [80,] 3.042996 2.957004 [81,] 3.042996 2.957004 [82,] 3.042996 2.957004 [83,] 3.042996 2.957004 [84,] 5.578826 5.421174 [85,] 5.578826 5.421174 [86,] 5.578826 5.421174 [87,] 5.578826 5.421174 [88,] 5.578826 5.421174 [89,] 5.578826 5.421174 [90,] 5.578826 5.421174 [91,] 5.578826 5.421174 [92,] 4.057328 3.942672 [93,] 4.057328 3.942672 [94,] 6.593158 6.406842 [95,] 1.014332 0.985668 [96,] 1.014332 0.985668 [97,] 1.014332 0.985668 [98,] 1.014332 0.985668 [99,] 2.535830 2.464170 [100,] 2.535830 2.464170 [101,] 2.535830 2.464170 [102,] 6.593158 6.406842 [103,] 6.593158 6.406842 [104,] 6.593158 6.406842 [105,] 5.071660 4.928340 [106,] 5.071660 4.928340 [107,] 5.071660 4.928340 [108,] 2.535830 2.464170 [109,] 2.535830 2.464170 [110,] 2.535830 2.464170 [111,] 2.535830 2.464170 [112,] 5.071660 4.928340 [113,] 5.071660 4.928340 [114,] 6.085992 5.914008 [115,] 6.085992 5.914008 [116,] 6.085992 5.914008 [117,] 6.085992 5.914008 [118,] 3.550162 3.449838 [119,] 3.550162 3.449838 [120,] 2.028664 1.971336 [121,] 2.028664 1.971336 [122,] 2.028664 1.971336 [123,] 2.028664 1.971336 [124,] 2.028664 1.971336 [125,] 2.028664 1.971336 [126,] 0.507166 0.492834 [127,] 0.507166 0.492834 [128,] 0.507166 0.492834 [129,] 0.507166 0.492834 [130,] 0.507166 0.492834 [131,] 0.507166 0.492834 [132,] 0.507166 0.492834 [133,] 2.028664 1.971336 [134,] 2.028664 1.971336 [135,] 2.028664 1.971336 [136,] 5.578826 5.421174 [137,] 5.578826 5.421174 [138,] 5.578826 5.421174 [139,] 3.042996 2.957004 [140,] 7.607490 7.392510 [141,] 7.607490 7.392510 [142,] 7.607490 7.392510 [143,] 3.042996 2.957004 [144,] 3.042996 2.957004 [145,] 3.042996 2.957004 [146,] 3.042996 2.957004 [147,] 3.042996 2.957004 [148,] 3.042996 2.957004 [149,] 6.593158 6.406842 [150,] 6.593158 6.406842 [151,] 4.057328 3.942672 [152,] 4.057328 3.942672 [153,] 4.057328 3.942672 [154,] 4.057328 3.942672 [155,] 4.057328 3.942672 [156,] 4.057328 3.942672 [157,] 7.607490 7.392510 [158,] 7.607490 7.392510 [159,] 7.607490 7.392510 [160,] 4.057328 3.942672 [161,] 4.057328 3.942672 [162,] 4.057328 3.942672 [163,] 4.057328 3.942672 [164,] 6.085992 5.914008 [165,] 6.085992 5.914008 [166,] 1.521498 1.478502 [167,] 1.521498 1.478502 [168,] 7.100324 6.899676 [169,] 7.100324 6.899676 [170,] 7.100324 6.899676 [171,] 7.100324 6.899676 [172,] 5.071660 4.928340 [173,] 8.114656 7.885344 [174,] 8.114656 7.885344 [175,] 8.114656 7.885344 [176,] 1.521498 1.478502 [177,] 1.521498 1.478502 [178,] 1.521498 1.478502 [179,] 1.521498 1.478502 [180,] 6.085992 5.914008 [181,] 6.085992 5.914008 [182,] 6.085992 5.914008 [183,] 7.100324 6.899676 [184,] 7.100324 6.899676 [185,] 2.535830 2.464170 [186,] 2.535830 2.464170 [187,] 2.535830 2.464170 [188,] 2.535830 2.464170 [189,] 8.114656 7.885344 [190,] 8.114656 7.885344 [191,] 8.114656 7.885344 [192,] 8.114656 7.885344 [193,] 8.114656 7.885344 [194,] 3.550162 3.449838 [195,] 3.550162 3.449838 [196,] 3.550162 3.449838 [197,] 2.535830 2.464170 [198,] 4.564494 4.435506 [199,] 4.564494 4.435506 [200,] 4.564494 4.435506 [201,] 4.564494 4.435506 [202,] 5.578826 5.421174 [203,] 5.578826 5.421174 [204,] 5.578826 5.421174 [205,] 5.578826 5.421174 [206,] 5.578826 5.421174 [207,] 3.550162 3.449838 [208,] 3.550162 3.449838 [209,] 3.550162 3.449838 [210,] 3.550162 3.449838 [211,] 6.593158 6.406842 [212,] 6.593158 6.406842 [213,] 6.593158 6.406842 [214,] 6.593158 6.406842 [215,] 7.607490 7.392510 [216,] 7.607490 7.392510 [217,] 7.607490 7.392510 [218,] 7.607490 7.392510 [219,] 8.621822 8.378178 [220,] 8.621822 8.378178 [221,] 8.621822 8.378178 [222,] 4.564494 4.435506 [223,] 5.578826 5.421174 [224,] 6.593158 6.406842 [225,] 6.593158 6.406842 [226,] 6.593158 6.406842 [227,] 6.593158 6.406842 [228,] 9.128988 8.871012 [229,] 9.128988 8.871012 [230,] 9.128988 8.871012 [231,] 9.128988 8.871012 [232,] 9.128988 8.871012 [233,] 9.128988 8.871012 [234,] 8.114656 7.885344 [235,] 8.114656 7.885344 [236,] 7.100324 6.899676 [237,] 6.085992 5.914008 [238,] 6.085992 5.914008 [239,] 5.071660 4.928340 [240,] 5.071660 4.928340 [241,] 4.057328 3.942672 [242,] 4.057328 3.942672 [243,] 3.042996 2.957004 [244,] 3.042996 2.957004 [245,] 3.042996 2.957004 [246,] 2.028664 1.971336 [247,] 2.028664 1.971336 [248,] 2.028664 1.971336 [249,] 1.014332 0.985668 [250,] 1.014332 0.985668 $chisq [1] NaN NaN NaN NaN 9.2617260788 [6] 8.7456700091 8.7456700091 8.2326454034 8.2326454034 8.2326454034 [11] 8.2326454034 8.2326454034 8.2326454034 8.2326454034 7.7739288970 [16] 7.7739288970 7.2035647280 6.8021877849 6.6327275821 6.6327275821 [21] 6.1744840525 6.1740110757 6.1740110757 6.1740110757 6.1740110757 [26] 5.8304466727 5.8304466727 5.8304466727 5.8304466727 5.6481004821 [31] 5.2467235390 5.2467235390 5.1454033771 4.8587055606 4.8587055606 [36] 4.6745867760 4.6745867760 4.6745867760 4.6584090143 4.6584090143 [41] 4.3305493962 4.3305493962 4.3305493962 4.3305493962 4.2570320712 [46] 4.2570320712 4.1163227017 4.1163227017 4.1163227017 4.1163227017 [51] 3.8869644485 3.8869644485 3.7748127676 3.7748127676 3.7748127676 [56] 3.7748127676 3.7748127676 3.7169493468 3.7169493468 3.7169493468 [61] 3.4307753878 3.4302515303 3.4302515303 3.1751003932 3.1751003932 [66] 3.0872420263 3.0872420263 2.9152233364 2.9152233364 2.9152233364 [71] 2.9152233364 2.9152233364 2.9152233364 2.8310630134 2.8310630134 [76] 2.7831263329 2.7831263329 2.6368485773 2.6368485773 2.5537680798 [81] 2.5537680798 2.5537680798 2.5537680798 2.4188030215 2.4188030215 [86] 2.4188030215 2.1321052050 2.1321052050 2.1321052050 2.1321052050 [91] 2.1321052050 2.1167335955 2.1167335955 2.0694917310 2.0581613508 [96] 2.0581613508 1.9434822242 1.9434822242 1.8874063838 1.8874063838 [101] 1.8874063838 1.7827939145 1.7827939145 1.7827939145 1.7170623105 [106] 1.7170623105 1.7170623105 1.7153876939 1.7153876939 1.7153876939 [111] 1.7153876939 1.4877040573 1.4877040573 1.4507517518 1.2213934986 [116] 1.2213934986 1.2213934986 1.2014072150 1.2014072150 1.0583667977 [121] 1.0583667977 1.0583667977 1.0583667977 1.0583667977 1.0583667977 [126] 1.0290806754 1.0290806754 1.0290806754 1.0290806754 0.9717411121 [131] 0.9717411121 0.9717411121 0.9436876711 0.9436876711 0.9436876711 [136] 0.9066191718 0.9066191718 0.7346004819 0.7253758759 0.6892143164 [141] 0.6892143164 0.6892143164 0.6106967493 0.6106967493 0.6106967493 [146] 0.6106967493 0.6106967493 0.6106967493 0.6091113893 0.6091113893 [151] 0.5590858618 0.5590858618 0.5590858618 0.5590858618 0.5590858618 [156] 0.5590858618 0.5171956265 0.5171956265 0.5171956265 0.4444067352 [161] 0.4444067352 0.4444067352 0.4444067352 0.3932067416 0.3932067416 [166] 0.3626879379 0.3626879379 0.3459888045 0.3459888045 0.3459888045 [171] 0.3459888045 0.3447970843 0.3106780752 0.3106780752 0.3106780752 [176] 0.3053483746 0.3053483746 0.3053483746 0.3053483746 0.2785276150 [181] 0.2785276150 0.2785276150 0.2313096779 0.2313096779 0.2297381055 [186] 0.2297381055 0.2297381055 0.2297381055 0.1959989486 0.1959989486 [191] 0.1959989486 0.1959989486 0.1959989486 0.1729944023 0.1729944023 [196] 0.1729944023 0.1723985422 0.1416527422 0.1416527422 0.1416527422 [201] 0.1416527422 0.1218574653 0.1218574653 0.1218574653 0.1218574653 [206] 0.1218574653 0.1156548390 0.1156548390 0.1156548390 0.1156548390 [211] 0.1082794717 0.1082794717 0.1082794717 0.1082794717 0.0984318481 [216] 0.0984318481 0.0984318481 0.0984318481 0.0909979932 0.0909979932 [221] 0.0909979932 0.0843131789 0.0645179020 0.0509399084 0.0509399084 [226] 0.0509399084 0.0509399084 0.0036980440 0.0036980440 0.0036980440 [231] 0.0036980440 0.0036980440 0.0036980440 0.0032871502 0.0032871502 [236] 0.0028762564 0.0024653626 0.0024653626 0.0020544689 0.0020544689 [241] 0.0016435751 0.0016435751 0.0012326813 0.0012326813 0.0012326813 [246] 0.0008217875 0.0008217875 0.0008217875 0.0004108938 0.0004108938 > > > > cleanEx(); ..nameEx <- "plot.bcfa" > > ### * plot.bcfa > > flush(stderr()); flush(stdout()) > > ### Name: plot.bcfa > ### Title: Plotting method for a bcfa object > ### Aliases: plot.bcfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > plot(boot.cfa(configs,counts,runs=25)) > > > > cleanEx(); ..nameEx <- "plot.hcfa" > > ### * plot.hcfa > > flush(stderr()); flush(stdout()) > > ### Name: plot.hcfa > ### Title: Plotting method for a hcfa object > ### Aliases: plot.hcfa > ### Keywords: multivariate htest > > ### ** Examples > > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > plot(hier.cfa(configs,counts)) > > > > cleanEx(); ..nameEx <- "plot.mcfa" > > ### * plot.mcfa > > flush(stderr()); flush(stdout()) > > ### Name: plot.mcfa > ### Title: Plotting method for a mcfa object > ### Aliases: plot.mcfa > ### Keywords: multivariate htest > > ### ** Examples > > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts1<-trunc(runif(250)*10) > counts2<-trunc(runif(250)*10) > > plot(cfa(configs,cbind(counts1,counts2))) > > > > > cleanEx(); ..nameEx <- "plot.scfa" > > ### * plot.scfa > > flush(stderr()); flush(stdout()) > > ### Name: plot.scfa > ### Title: Plotting method for a scfa object > ### Aliases: plot.scfa > ### Keywords: multivariate htest > > ### ** Examples > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > plot(cfa(configs,counts)) > > > > cleanEx(); ..nameEx <- "print.bcfa" > > ### * print.bcfa > > flush(stderr()); flush(stdout()) > > ### Name: print.bcfa > ### Title: Print an object of the class hcfa > ### Aliases: print.bcfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > result<-boot.cfa(configs,counts,runs=25) > print(result) cnt.antitype cnt.type pct.types cnt.sig pct.cnt.sig B D E H 3 22 88 3 12 B D E G 25 0 0 0 0 B C F H 19 6 24 3 12 B C F G 25 0 0 0 0 B C E H 16 9 36 1 4 B C E G 0 25 100 0 0 A D F G 0 25 100 0 0 A D E H 25 0 0 1 4 A D E G 3 22 88 0 0 A C F H 14 11 44 1 4 A C F G 2 23 92 0 0 A C E H 11 14 56 1 4 A C E G 24 1 4 0 0 > > > > cleanEx(); ..nameEx <- "print.hcfa" > > ### * print.hcfa > > flush(stderr()); flush(stdout()) > > ### Name: print.hcfa > ### Title: Print an object of the class hcfa > ### Aliases: print.hcfa > ### Keywords: multivariate htest > > ### ** Examples > > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > result<-hier.cfa(configs,counts) > print(result) *** Hierarchical CFA *** Overall chi squared df p order V1 V3 V4 22.9903336 4 0.0001271905 3 V2 V3 V4 17.2251999 4 0.0017475767 3 V1 V2 V4 16.5362030 4 0.0023779347 3 V1 V3 10.4129150 1 0.0012513706 2 V1 V3 10.4129150 1 0.0012513706 2 V3 V4 8.6523726 1 0.0032663575 2 V3 V4 8.6523726 1 0.0032663575 2 V1 V2 V3 8.6071090 4 0.0717062583 3 V1 V2 5.3987739 1 0.0201509035 2 V1 V2 5.3987739 1 0.0201509035 2 V1 V4 3.4154458 1 0.0645889662 2 V1 V4 3.4154458 1 0.0645889662 2 V2 V3 1.9496936 1 0.1626198715 2 V2 V3 1.9496936 1 0.1626198715 2 V2 V4 0.2902919 1 0.5900335348 2 V2 V4 0.2902919 1 0.5900335348 2 Overall chi squared df p order V1 V3 V4 22.9903336 4 0.0001271905 3 V2 V3 V4 17.2251999 4 0.0017475767 3 V1 V2 V4 16.5362030 4 0.0023779347 3 V1 V3 10.4129150 1 0.0012513706 2 V1 V3 10.4129150 1 0.0012513706 2 V3 V4 8.6523726 1 0.0032663575 2 V3 V4 8.6523726 1 0.0032663575 2 V1 V2 V3 8.6071090 4 0.0717062583 3 V1 V2 5.3987739 1 0.0201509035 2 V1 V2 5.3987739 1 0.0201509035 2 V1 V4 3.4154458 1 0.0645889662 2 V1 V4 3.4154458 1 0.0645889662 2 V2 V3 1.9496936 1 0.1626198715 2 V2 V3 1.9496936 1 0.1626198715 2 V2 V4 0.2902919 1 0.5900335348 2 V2 V4 0.2902919 1 0.5900335348 2 > > > > cleanEx(); ..nameEx <- "print.mcfa" > > ### * print.mcfa > > flush(stderr()); flush(stdout()) > > ### Name: print.mcfa > ### Title: Print an object of the class mcfa > ### Aliases: print.mcfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts1<-trunc(runif(250)*10) > counts2<-trunc(runif(250)*10) > result<-cfa(configs,cbind(counts1,counts2)) > print(result) *** Repeated analysis of configuration frequencies (MCFA) *** label n.counts1 n.counts2 expected.1 expected.2 chisq p.chisq 1 B C E G 0 0 0.000000 0.000000 NaN NaN 2 A D E G 0 0 0.000000 0.000000 NaN NaN 3 A C E G 0 0 0.000000 0.000000 NaN NaN 4 A C E G 0 0 0.000000 0.000000 NaN NaN 5 A C F G 0 9 4.564494 4.435506 9.2617260788 0.002339924 6 A C F G 9 0 4.564494 4.435506 8.7456700091 0.003103381 7 A D F G 9 0 4.564494 4.435506 8.7456700091 0.003103381 8 B C E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 9 A C E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 10 A D E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 11 B C E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 12 B C E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 13 B C E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 14 B C E G 0 8 4.057328 3.942672 8.2326454034 0.004114352 15 A D E G 8 0 4.057328 3.942672 7.7739288970 0.005300564 16 A D F G 8 0 4.057328 3.942672 7.7739288970 0.005300564 17 B C E G 0 7 3.550162 3.449838 7.2035647280 0.007275891 18 A C E G 7 0 3.550162 3.449838 6.8021877849 0.009104624 19 A C E G 1 9 5.071660 4.928340 6.6327275821 0.010012184 20 A C E G 1 9 5.071660 4.928340 6.6327275821 0.010012184 21 A C F G 0 6 3.042996 2.957004 6.1744840525 0.012960570 22 A C E G 9 1 5.071660 4.928340 6.1740110757 0.012964035 23 B C F G 9 1 5.071660 4.928340 6.1740110757 0.012964035 24 A C F G 9 1 5.071660 4.928340 6.1740110757 0.012964035 25 A C F G 9 1 5.071660 4.928340 6.1740110757 0.012964035 26 A C E G 6 0 3.042996 2.957004 5.8304466727 0.015751124 27 A C F H 6 0 3.042996 2.957004 5.8304466727 0.015751124 28 A C E G 6 0 3.042996 2.957004 5.8304466727 0.015751124 29 A D E G 6 0 3.042996 2.957004 5.8304466727 0.015751124 30 A C F G 1 8 4.564494 4.435506 5.6481004821 0.017474291 31 A C F H 8 1 4.564494 4.435506 5.2467235390 0.021988136 32 A C E G 8 1 4.564494 4.435506 5.2467235390 0.021988136 33 A C F G 0 5 2.535830 2.464170 5.1454033771 0.023307995 34 A C E G 5 0 2.535830 2.464170 4.8587055606 0.027506967 35 A C E H 5 0 2.535830 2.464170 4.8587055606 0.027506967 36 B C F G 1 7 4.057328 3.942672 4.6745867760 0.030612066 37 A D E G 1 7 4.057328 3.942672 4.6745867760 0.030612066 38 A C E G 1 7 4.057328 3.942672 4.6745867760 0.030612066 39 A C E G 2 9 5.578826 5.421174 4.6584090143 0.030901813 40 B C E G 2 9 5.578826 5.421174 4.6584090143 0.030901813 41 A C E H 7 1 4.057328 3.942672 4.3305493962 0.037434161 42 B C E G 7 1 4.057328 3.942672 4.3305493962 0.037434161 43 A C E G 7 1 4.057328 3.942672 4.3305493962 0.037434161 44 B C E G 7 1 4.057328 3.942672 4.3305493962 0.037434161 45 A C E G 9 2 5.578826 5.421174 4.2570320712 0.039088157 46 A C E G 9 2 5.578826 5.421174 4.2570320712 0.039088157 47 B C E G 0 4 2.028664 1.971336 4.1163227017 0.042471302 48 A C E G 0 4 2.028664 1.971336 4.1163227017 0.042471302 49 A C E G 0 4 2.028664 1.971336 4.1163227017 0.042471302 50 A C F G 0 4 2.028664 1.971336 4.1163227017 0.042471302 51 B C E G 4 0 2.028664 1.971336 3.8869644485 0.048662302 52 A C E G 4 0 2.028664 1.971336 3.8869644485 0.048662302 53 A C E G 2 8 5.071660 4.928340 3.7748127676 0.052029724 54 B C F G 2 8 5.071660 4.928340 3.7748127676 0.052029724 55 B C F G 2 8 5.071660 4.928340 3.7748127676 0.052029724 56 A C F G 2 8 5.071660 4.928340 3.7748127676 0.052029724 57 A C F G 2 8 5.071660 4.928340 3.7748127676 0.052029724 58 A C E H 1 6 3.550162 3.449838 3.7169493468 0.053862696 59 A C F H 1 6 3.550162 3.449838 3.7169493468 0.053862696 60 A C E G 1 6 3.550162 3.449838 3.7169493468 0.053862696 61 A C E G 8 2 5.071660 4.928340 3.4307753878 0.063992050 62 A C E G 6 1 3.550162 3.449838 3.4302515303 0.064012351 63 A D E H 6 1 3.550162 3.449838 3.4302515303 0.064012351 64 A C E G 3 9 6.085992 5.914008 3.1751003932 0.074768617 65 A C E G 3 9 6.085992 5.914008 3.1751003932 0.074768617 66 A D E G 0 3 1.521498 1.478502 3.0872420263 0.078908447 67 A C E G 0 3 1.521498 1.478502 3.0872420263 0.078908447 68 A C E G 3 0 1.521498 1.478502 2.9152233364 0.087747264 69 A C F H 3 0 1.521498 1.478502 2.9152233364 0.087747264 70 A C E G 3 0 1.521498 1.478502 2.9152233364 0.087747264 71 A C F G 3 0 1.521498 1.478502 2.9152233364 0.087747264 72 A D F G 3 0 1.521498 1.478502 2.9152233364 0.087747264 73 B C F G 3 0 1.521498 1.478502 2.9152233364 0.087747264 74 A D E G 9 3 6.085992 5.914008 2.8310630134 0.092457142 75 B C E G 9 3 6.085992 5.914008 2.8310630134 0.092457142 76 B C E H 1 5 3.042996 2.957004 2.7831263329 0.095262049 77 A C F G 1 5 3.042996 2.957004 2.7831263329 0.095262049 78 A C F G 7 2 4.564494 4.435506 2.6368485773 0.104410471 79 B C F G 7 2 4.564494 4.435506 2.6368485773 0.104410471 80 A D E G 5 1 3.042996 2.957004 2.5537680798 0.110031552 81 B C E G 5 1 3.042996 2.957004 2.5537680798 0.110031552 82 A C F G 5 1 3.042996 2.957004 2.5537680798 0.110031552 83 A C E G 5 1 3.042996 2.957004 2.5537680798 0.110031552 84 A C F H 3 8 5.578826 5.421174 2.4188030215 0.119886505 85 B C F H 3 8 5.578826 5.421174 2.4188030215 0.119886505 86 B C F G 3 8 5.578826 5.421174 2.4188030215 0.119886505 87 A C E G 8 3 5.578826 5.421174 2.1321052050 0.144242532 88 A C E G 8 3 5.578826 5.421174 2.1321052050 0.144242532 89 A C E G 8 3 5.578826 5.421174 2.1321052050 0.144242532 90 A C F G 8 3 5.578826 5.421174 2.1321052050 0.144242532 91 A C E G 8 3 5.578826 5.421174 2.1321052050 0.144242532 92 A C E G 2 6 4.057328 3.942672 2.1167335955 0.145696987 93 A C E G 2 6 4.057328 3.942672 2.1167335955 0.145696987 94 B C F H 4 9 6.593158 6.406842 2.0694917310 0.150271594 95 A D F G 0 2 1.014332 0.985668 2.0581613508 0.151392748 96 B C F G 0 2 1.014332 0.985668 2.0581613508 0.151392748 97 A C E G 2 0 1.014332 0.985668 1.9434822242 0.163290938 98 B C E G 2 0 1.014332 0.985668 1.9434822242 0.163290938 99 A C F G 1 4 2.535830 2.464170 1.8874063838 0.169494746 100 A C E G 1 4 2.535830 2.464170 1.8874063838 0.169494746 101 A C E G 1 4 2.535830 2.464170 1.8874063838 0.169494746 102 A C E H 9 4 6.593158 6.406842 1.7827939145 0.181806624 103 A D E G 9 4 6.593158 6.406842 1.7827939145 0.181806624 104 A C E G 9 4 6.593158 6.406842 1.7827939145 0.181806624 105 A C E G 3 7 5.071660 4.928340 1.7170623105 0.190071630 106 B C F G 3 7 5.071660 4.928340 1.7170623105 0.190071630 107 A C E G 3 7 5.071660 4.928340 1.7170623105 0.190071630 108 A C E H 4 1 2.535830 2.464170 1.7153876939 0.190287834 109 B C E G 4 1 2.535830 2.464170 1.7153876939 0.190287834 110 A C E G 4 1 2.535830 2.464170 1.7153876939 0.190287834 111 A D E H 4 1 2.535830 2.464170 1.7153876939 0.190287834 112 B D E G 7 3 5.071660 4.928340 1.4877040573 0.222573030 113 A C E G 7 3 5.071660 4.928340 1.4877040573 0.222573030 114 A C E G 4 8 6.085992 5.914008 1.4507517518 0.228407366 115 A C E G 8 4 6.085992 5.914008 1.2213934986 0.269087351 116 A C F G 8 4 6.085992 5.914008 1.2213934986 0.269087351 117 B C E G 8 4 6.085992 5.914008 1.2213934986 0.269087351 118 A C E G 5 2 3.550162 3.449838 1.2014072150 0.273040603 119 A C E G 5 2 3.550162 3.449838 1.2014072150 0.273040603 120 B C F G 1 3 2.028664 1.971336 1.0583667977 0.303587976 121 A C E G 1 3 2.028664 1.971336 1.0583667977 0.303587976 122 A C E G 1 3 2.028664 1.971336 1.0583667977 0.303587976 123 B C F G 1 3 2.028664 1.971336 1.0583667977 0.303587976 124 B C F H 1 3 2.028664 1.971336 1.0583667977 0.303587976 125 A C E G 1 3 2.028664 1.971336 1.0583667977 0.303587976 126 A C F G 0 1 0.507166 0.492834 1.0290806754 0.310374688 127 A C E G 0 1 0.507166 0.492834 1.0290806754 0.310374688 128 B C E G 0 1 0.507166 0.492834 1.0290806754 0.310374688 129 B C F G 0 1 0.507166 0.492834 1.0290806754 0.310374688 130 B C E G 1 0 0.507166 0.492834 0.9717411121 0.324246334 131 A C E G 1 0 0.507166 0.492834 0.9717411121 0.324246334 132 A C E G 1 0 0.507166 0.492834 0.9717411121 0.324246334 133 A D F G 3 1 2.028664 1.971336 0.9436876711 0.331331268 134 A C E G 3 1 2.028664 1.971336 0.9436876711 0.331331268 135 A C E H 3 1 2.028664 1.971336 0.9436876711 0.331331268 136 A C F G 4 7 5.578826 5.421174 0.9066191718 0.341013046 137 A C E G 4 7 5.578826 5.421174 0.9066191718 0.341013046 138 A C E G 7 4 5.578826 5.421174 0.7346004819 0.391396046 139 B C F G 2 4 3.042996 2.957004 0.7253758759 0.394386166 140 B C E G 6 9 7.607490 7.392510 0.6892143164 0.406431749 141 B C E G 6 9 7.607490 7.392510 0.6892143164 0.406431749 142 B C E G 6 9 7.607490 7.392510 0.6892143164 0.406431749 143 A C E G 4 2 3.042996 2.957004 0.6106967493 0.434525592 144 A D F G 4 2 3.042996 2.957004 0.6106967493 0.434525592 145 A D E G 4 2 3.042996 2.957004 0.6106967493 0.434525592 146 A D F G 4 2 3.042996 2.957004 0.6106967493 0.434525592 147 A C E H 4 2 3.042996 2.957004 0.6106967493 0.434525592 148 B C F G 4 2 3.042996 2.957004 0.6106967493 0.434525592 149 A C E G 8 5 6.593158 6.406842 0.6091113893 0.435122584 150 B C E G 8 5 6.593158 6.406842 0.6091113893 0.435122584 151 A D F G 3 5 4.057328 3.942672 0.5590858618 0.454628797 152 A C E G 3 5 4.057328 3.942672 0.5590858618 0.454628797 153 B C E G 3 5 4.057328 3.942672 0.5590858618 0.454628797 154 A C F H 3 5 4.057328 3.942672 0.5590858618 0.454628797 155 B C E G 3 5 4.057328 3.942672 0.5590858618 0.454628797 156 A C E G 3 5 4.057328 3.942672 0.5590858618 0.454628797 157 A C E G 9 6 7.607490 7.392510 0.5171956265 0.472040406 158 A C E G 9 6 7.607490 7.392510 0.5171956265 0.472040406 159 A C E G 9 6 7.607490 7.392510 0.5171956265 0.472040406 160 A C E H 5 3 4.057328 3.942672 0.4444067352 0.505003145 161 A C E G 5 3 4.057328 3.942672 0.4444067352 0.505003145 162 A C F G 5 3 4.057328 3.942672 0.4444067352 0.505003145 163 B C E G 5 3 4.057328 3.942672 0.4444067352 0.505003145 164 B C E G 5 7 6.085992 5.914008 0.3932067416 0.530618600 165 A C E G 5 7 6.085992 5.914008 0.3932067416 0.530618600 166 A D F G 1 2 1.521498 1.478502 0.3626879379 0.547017200 167 A C E G 1 2 1.521498 1.478502 0.3626879379 0.547017200 168 A C F G 6 8 7.100324 6.899676 0.3459888045 0.556392601 169 A C E G 6 8 7.100324 6.899676 0.3459888045 0.556392601 170 A C E G 6 8 7.100324 6.899676 0.3459888045 0.556392601 171 B D E H 6 8 7.100324 6.899676 0.3459888045 0.556392601 172 A C E G 6 4 5.071660 4.928340 0.3447970843 0.557073255 173 A C E G 7 9 8.114656 7.885344 0.3106780752 0.577264389 174 A D E G 7 9 8.114656 7.885344 0.3106780752 0.577264389 175 A C F H 7 9 8.114656 7.885344 0.3106780752 0.577264389 176 A C F H 2 1 1.521498 1.478502 0.3053483746 0.580548736 177 A C E G 2 1 1.521498 1.478502 0.3053483746 0.580548736 178 A C F G 2 1 1.521498 1.478502 0.3053483746 0.580548736 179 B C E G 2 1 1.521498 1.478502 0.3053483746 0.580548736 180 B D E G 7 5 6.085992 5.914008 0.2785276150 0.597667898 181 A C E G 7 5 6.085992 5.914008 0.2785276150 0.597667898 182 A C F G 7 5 6.085992 5.914008 0.2785276150 0.597667898 183 B C E G 8 6 7.100324 6.899676 0.2313096779 0.630554418 184 A C E G 8 6 7.100324 6.899676 0.2313096779 0.630554418 185 B C F G 2 3 2.535830 2.464170 0.2297381055 0.631718087 186 A C E G 2 3 2.535830 2.464170 0.2297381055 0.631718087 187 A C E G 2 3 2.535830 2.464170 0.2297381055 0.631718087 188 B C E G 2 3 2.535830 2.464170 0.2297381055 0.631718087 189 A C E G 9 7 8.114656 7.885344 0.1959989486 0.657969949 190 A D E G 9 7 8.114656 7.885344 0.1959989486 0.657969949 191 A C E G 9 7 8.114656 7.885344 0.1959989486 0.657969949 192 A C E G 9 7 8.114656 7.885344 0.1959989486 0.657969949 193 A C F G 9 7 8.114656 7.885344 0.1959989486 0.657969949 194 A C E G 3 4 3.550162 3.449838 0.1729944023 0.677464184 195 B C E G 3 4 3.550162 3.449838 0.1729944023 0.677464184 196 A C E G 3 4 3.550162 3.449838 0.1729944023 0.677464184 197 B C E G 3 2 2.535830 2.464170 0.1723985422 0.677988886 198 A D E G 4 5 4.564494 4.435506 0.1416527422 0.706643460 199 A C E H 4 5 4.564494 4.435506 0.1416527422 0.706643460 200 B C E G 4 5 4.564494 4.435506 0.1416527422 0.706643460 201 A C E G 4 5 4.564494 4.435506 0.1416527422 0.706643460 202 B C E H 5 6 5.578826 5.421174 0.1218574653 0.727028585 203 B D E G 5 6 5.578826 5.421174 0.1218574653 0.727028585 204 A C F G 5 6 5.578826 5.421174 0.1218574653 0.727028585 205 A C F G 5 6 5.578826 5.421174 0.1218574653 0.727028585 206 A C E G 5 6 5.578826 5.421174 0.1218574653 0.727028585 207 A C F G 4 3 3.550162 3.449838 0.1156548390 0.733795804 208 B C E G 4 3 3.550162 3.449838 0.1156548390 0.733795804 209 A D E G 4 3 3.550162 3.449838 0.1156548390 0.733795804 210 B C E G 4 3 3.550162 3.449838 0.1156548390 0.733795804 211 B C F G 6 7 6.593158 6.406842 0.1082794717 0.742111500 212 B C E G 6 7 6.593158 6.406842 0.1082794717 0.742111500 213 B C E G 6 7 6.593158 6.406842 0.1082794717 0.742111500 214 B C E G 6 7 6.593158 6.406842 0.1082794717 0.742111500 215 A C F G 7 8 7.607490 7.392510 0.0984318481 0.753719655 216 A C E G 7 8 7.607490 7.392510 0.0984318481 0.753719655 217 A C E G 7 8 7.607490 7.392510 0.0984318481 0.753719655 218 B C E G 7 8 7.607490 7.392510 0.0984318481 0.753719655 219 A C F G 8 9 8.621822 8.378178 0.0909979932 0.762912227 220 A C F G 8 9 8.621822 8.378178 0.0909979932 0.762912227 221 A C F H 8 9 8.621822 8.378178 0.0909979932 0.762912227 222 A C E G 5 4 4.564494 4.435506 0.0843131789 0.771535244 223 A C F G 6 5 5.578826 5.421174 0.0645179020 0.799492666 224 A C E G 7 6 6.593158 6.406842 0.0509399084 0.821435760 225 B C E G 7 6 6.593158 6.406842 0.0509399084 0.821435760 226 B C E H 7 6 6.593158 6.406842 0.0509399084 0.821435760 227 A C F G 7 6 6.593158 6.406842 0.0509399084 0.821435760 228 A C E G 9 9 9.128988 8.871012 0.0036980440 0.951509296 229 B C E G 9 9 9.128988 8.871012 0.0036980440 0.951509296 230 A C F G 9 9 9.128988 8.871012 0.0036980440 0.951509296 231 A C F H 9 9 9.128988 8.871012 0.0036980440 0.951509296 232 A C F G 9 9 9.128988 8.871012 0.0036980440 0.951509296 233 B C E G 9 9 9.128988 8.871012 0.0036980440 0.951509296 234 A C F G 8 8 8.114656 7.885344 0.0032871502 0.954279396 235 A C E H 8 8 8.114656 7.885344 0.0032871502 0.954279396 236 B C F G 7 7 7.100324 6.899676 0.0028762564 0.957229364 237 A C E G 6 6 6.085992 5.914008 0.0024653626 0.960399374 238 B C E G 6 6 6.085992 5.914008 0.0024653626 0.960399374 239 B C E G 5 5 5.071660 4.928340 0.0020544689 0.963847265 240 A C F G 5 5 5.071660 4.928340 0.0020544689 0.963847265 241 A C E H 4 4 4.057328 3.942672 0.0016435751 0.967661797 242 B C F G 4 4 4.057328 3.942672 0.0016435751 0.967661797 243 A C E G 3 3 3.042996 2.957004 0.0012326813 0.971992377 244 A D E G 3 3 3.042996 2.957004 0.0012326813 0.971992377 245 A C E G 3 3 3.042996 2.957004 0.0012326813 0.971992377 246 A C F G 2 2 2.028664 1.971336 0.0008217875 0.977130306 247 A C E G 2 2 2.028664 1.971336 0.0008217875 0.977130306 248 A C E G 2 2 2.028664 1.971336 0.0008217875 0.977130306 249 A C F G 1 1 1.014332 0.985668 0.0004108938 0.983827577 250 B C E H 1 1 1.014332 0.985668 0.0004108938 0.983827577 p.chisq.sig 1 NA 2 NA 3 NA 4 NA 5 FALSE 6 FALSE 7 FALSE 8 FALSE 9 FALSE 10 FALSE 11 FALSE 12 FALSE 13 FALSE 14 FALSE 15 FALSE 16 FALSE 17 FALSE 18 FALSE 19 FALSE 20 FALSE 21 FALSE 22 FALSE 23 FALSE 24 FALSE 25 FALSE 26 FALSE 27 FALSE 28 FALSE 29 FALSE 30 FALSE 31 FALSE 32 FALSE 33 FALSE 34 FALSE 35 FALSE 36 FALSE 37 FALSE 38 FALSE 39 FALSE 40 FALSE 41 FALSE 42 FALSE 43 FALSE 44 FALSE 45 FALSE 46 FALSE 47 FALSE 48 FALSE 49 FALSE 50 FALSE 51 FALSE 52 FALSE 53 FALSE 54 FALSE 55 FALSE 56 FALSE 57 FALSE 58 FALSE 59 FALSE 60 FALSE 61 FALSE 62 FALSE 63 FALSE 64 FALSE 65 FALSE 66 FALSE 67 FALSE 68 FALSE 69 FALSE 70 FALSE 71 FALSE 72 FALSE 73 FALSE 74 FALSE 75 FALSE 76 FALSE 77 FALSE 78 FALSE 79 FALSE 80 FALSE 81 FALSE 82 FALSE 83 FALSE 84 FALSE 85 FALSE 86 FALSE 87 FALSE 88 FALSE 89 FALSE 90 FALSE 91 FALSE 92 FALSE 93 FALSE 94 FALSE 95 FALSE 96 FALSE 97 FALSE 98 FALSE 99 FALSE 100 FALSE 101 FALSE 102 FALSE 103 FALSE 104 FALSE 105 FALSE 106 FALSE 107 FALSE 108 FALSE 109 FALSE 110 FALSE 111 FALSE 112 FALSE 113 FALSE 114 FALSE 115 FALSE 116 FALSE 117 FALSE 118 FALSE 119 FALSE 120 FALSE 121 FALSE 122 FALSE 123 FALSE 124 FALSE 125 FALSE 126 FALSE 127 FALSE 128 FALSE 129 FALSE 130 FALSE 131 FALSE 132 FALSE 133 FALSE 134 FALSE 135 FALSE 136 FALSE 137 FALSE 138 FALSE 139 FALSE 140 FALSE 141 FALSE 142 FALSE 143 FALSE 144 FALSE 145 FALSE 146 FALSE 147 FALSE 148 FALSE 149 FALSE 150 FALSE 151 FALSE 152 FALSE 153 FALSE 154 FALSE 155 FALSE 156 FALSE 157 FALSE 158 FALSE 159 FALSE 160 FALSE 161 FALSE 162 FALSE 163 FALSE 164 FALSE 165 FALSE 166 FALSE 167 FALSE 168 FALSE 169 FALSE 170 FALSE 171 FALSE 172 FALSE 173 FALSE 174 FALSE 175 FALSE 176 FALSE 177 FALSE 178 FALSE 179 FALSE 180 FALSE 181 FALSE 182 FALSE 183 FALSE 184 FALSE 185 FALSE 186 FALSE 187 FALSE 188 FALSE 189 FALSE 190 FALSE 191 FALSE 192 FALSE 193 FALSE 194 FALSE 195 FALSE 196 FALSE 197 FALSE 198 FALSE 199 FALSE 200 FALSE 201 FALSE 202 FALSE 203 FALSE 204 FALSE 205 FALSE 206 FALSE 207 FALSE 208 FALSE 209 FALSE 210 FALSE 211 FALSE 212 FALSE 213 FALSE 214 FALSE 215 FALSE 216 FALSE 217 FALSE 218 FALSE 219 FALSE 220 FALSE 221 FALSE 222 FALSE 223 FALSE 224 FALSE 225 FALSE 226 FALSE 227 FALSE 228 FALSE 229 FALSE 230 FALSE 231 FALSE 232 FALSE 233 FALSE 234 FALSE 235 FALSE 236 FALSE 237 FALSE 238 FALSE 239 FALSE 240 FALSE 241 FALSE 242 FALSE 243 FALSE 244 FALSE 245 FALSE 246 FALSE 247 FALSE 248 FALSE 249 FALSE 250 FALSE Summary statistics: Total Chi squared = 494.1466 Total degrees of freedom = 1.809251e+75 p = 0 Sum of counts = 2163 > > > > cleanEx(); ..nameEx <- "print.scfa" > > ### * print.scfa > > flush(stderr()); flush(stdout()) > > ### Name: print.scfa > ### Title: Print an object of the class scfa > ### Aliases: print.scfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > result<-cfa(configs,counts) > print(result) *** Analysis of configuration frequencies (CFA) *** label n expected Q chisq p.chisq sig.chisq 1 A C F H 50 27.745523 0.0208130786 17.85015097 2.390003e-05 TRUE 2 B C E G 182 151.626973 0.0321280867 6.08414666 1.364002e-02 FALSE 3 B C E H 14 22.545581 0.0079534145 3.23908086 7.190096e-02 FALSE 4 A D F G 35 27.074299 0.0074077112 2.32016088 1.277068e-01 FALSE 5 B D E H 6 3.271227 0.0024949263 2.27627104 1.313674e-01 FALSE 6 A C E H 54 63.931701 0.0096137894 1.54287598 2.141902e-01 FALSE 7 B C F G 57 65.804124 0.0085377809 1.17792931 2.777780e-01 FALSE 8 A C E G 411 429.963201 0.0284290175 0.83635759 3.604406e-01 FALSE 9 A D E G 69 62.385057 0.0063936276 0.70140942 4.023105e-01 FALSE 10 B D E G 19 22.000156 0.0027908431 0.40913052 5.224112e-01 FALSE 11 B C F H 8 9.784488 0.0016413375 0.32545353 5.683486e-01 FALSE 12 A C F G 182 186.598409 0.0050509674 0.11332017 7.363954e-01 FALSE 13 A D E H 10 9.276103 0.0006655156 0.05649217 8.121287e-01 FALSE z p.z sig.z 1 4.1832611 1.436785e-05 TRUE 2 2.6133207 4.483356e-03 FALSE 3 -1.9249306 9.728810e-01 FALSE 4 1.4450582 7.422078e-02 FALSE 5 1.2341243 1.085783e-01 FALSE 6 -1.3444226 9.105941e-01 FALSE 7 -1.1829917 8.815938e-01 FALSE 8 -1.2037243 8.856519e-01 FALSE 9 0.7971977 2.126681e-01 FALSE 10 -0.7538303 7.745245e-01 FALSE 11 -0.7336100 7.684068e-01 FALSE 12 -0.4097014 6.589875e-01 FALSE 13 0.0738261 4.705744e-01 FALSE Summary statistics: Total Chi squared = 36.93278 Total degreed of freedom = 11 p = 1.222729e-09 Sum of counts = 1097 Levels: V1 V2 V3 V4 2 2 2 2 > > > > cleanEx(); ..nameEx <- "scfa" > > ### * scfa > > flush(stderr()); flush(stdout()) > > ### Name: scfa > ### Title: One sample CFA > ### Aliases: scfa > ### Keywords: multivariate htest > > ### ** Examples > > # library(cfa) if not yet loaded > # Some random configurations: > configs<-cbind(c("A","B")[rbinom(250,1,0.3)+1],c("C","D")[rbinom(250,1,0.1)+1], + c("E","F")[rbinom(250,1,0.3)+1],c("G","H")[rbinom(250,1,0.1)+1]) > counts<-trunc(runif(250)*10) > scfa(configs,counts) $labels [1] "A C F H" "B C E G" "B C E H" "A D F G" "B D E H" "A C E H" "B C F G" [8] "A C E G" "A D E G" "B D E G" "B C F H" "A C F G" "A D E H" $n.levels [1] 2 2 2 2 $sums V1 V2 V3 V4 A C F H 811 958 332 142 B C E G 286 958 765 955 B C E H 286 958 765 142 A D F G 811 139 332 955 B D E H 286 139 765 142 A C E H 811 958 765 142 B C F G 286 958 332 955 A C E G 811 958 765 955 A D E G 811 139 765 955 B D E G 286 139 765 955 B C F H 286 958 332 142 A C F G 811 958 332 955 A D E H 811 139 765 142 $counts [1] 50 182 14 35 6 54 57 411 69 19 8 182 10 $expected [1] 27.745523 151.626973 22.545581 27.074299 3.271227 63.931701 [7] 65.804124 429.963201 62.385057 22.000156 9.784488 186.598409 [13] 9.276103 $chisq [1] 17.85015097 6.08414666 3.23908086 2.32016088 2.27627104 1.54287598 [7] 1.17792931 0.83635759 0.70140942 0.40913052 0.32545353 0.11332017 [13] 0.05649217 > > > > ### *