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[Previously saved workspace restored] > setwd('C:/Users/mapjg/Dropbox/KinMixLou/test3/website') # set to the same directory as all the scripts and data files > > source('Preamble.R') Loading required package: KinMix Loading required package: DNAmixtures Loading required package: RHugin Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Rgraphviz Loading required package: grid This version of the RHugin package has been modified by Therese Graversen. Any issues should be reported to graversen@math.ku.dk Attaching package: ‘RHugin’ The following object is masked from ‘package:BiocGenerics’: score Loading required package: Rsolnp Loading required package: numDeriv Loading required package: Matrix Loading required package: ribd Loading required package: pedtools Attaching package: ‘pedtools’ The following object is masked from ‘package:Rgraphviz’: name The following object is masked from ‘package:graph’: leaves > > source('Toothbrush data and parameters.R') Reading Toothbrush data markers used in mixture: Marker01 Marker02 Marker03 Marker04 Marker05 Marker06 Marker07 Marker08 Marker09 Marker10 Marker11 Marker12 Marker13 Marker14 Marker15 Marker16 Marker17 Marker18 Marker19 Marker20 Parameters set to rho eta xi phi.U1 phi.U2 1 8.964 265.6 0 0.9264 0.07356 mu 2381.032 sigma 0.06135822 vanilla model log likelihood: -520.9942 > > # any of the following can be done in any order > > source('Table 3.R') log10 LR for U1 10.97424 log10 LR for U2 4.530725 > source('Table 4.R') # takes a long time! Using peak heights Marker01 log10 LR 0.6850491 ; LR 4.842272 Marker02 log10 LR 1.038119 ; LR 10.9174 Marker03 log10 LR 1.110182 ; LR 12.88788 Marker04 log10 LR 0.5700872 ; LR 3.716099 Marker05 log10 LR 0.7130608 ; LR 5.164886 Marker06 log10 LR 0.5240292 ; LR 3.342175 Marker07 log10 LR 0.2005535 ; LR 1.586914 Marker08 log10 LR 0.7052239 ; LR 5.072521 Marker09 log10 LR 0.2103224 ; LR 1.623015 Marker10 log10 LR 0.3327775 ; LR 2.151679 Marker11 log10 LR 1.038148 ; LR 10.91812 Marker12 log10 LR 0.2979572 ; LR 1.985899 Marker13 log10 LR 0.3560494 ; LR 2.270123 Marker14 log10 LR 0.1791453 ; LR 1.510586 Marker15 log10 LR 0.4041013 ; LR 2.53572 Marker16 log10 LR 0.790522 ; LR 6.173365 Marker17 log10 LR 0.37829 ; LR 2.389406 Marker18 log10 LR 0.8302818 ; LR 6.765218 Marker19 log10 LR 0.5187422 ; LR 3.301735 Marker20 log10 LR 0.09160004 ; LR 1.23481 all trace all marker overall log10 LR 10.97424 LR 94241336178 Time difference of 2.634471 secs Using presence only Marker01 log10 LR 0.4934383 ; LR 3.114858 Marker02 log10 LR 0.8901811 ; LR 7.765709 Marker03 log10 LR 0.9917479 ; LR 9.811782 Marker04 log10 LR 0.5577429 ; LR 3.61196 Marker05 log10 LR 0.692927 ; LR 4.930909 Marker06 log10 LR 0.4111992 ; LR 2.577503 Marker07 log10 LR 0.02945267 ; LR 1.07017 Marker08 log10 LR 0.7426844 ; LR 5.529481 Marker09 log10 LR 0.07354052 ; LR 1.184515 Marker10 log10 LR 0.3691207 ; LR 2.339487 Marker11 log10 LR 0.802564 ; LR 6.346934 Marker12 log10 LR 0.2342334 ; LR 1.714879 Marker13 log10 LR 0.3533503 ; LR 2.256058 Marker14 log10 LR 0.3257552 ; LR 2.117168 Marker15 log10 LR 0.3906867 ; LR 2.458593 Marker16 log10 LR 0.7196317 ; LR 5.243626 Marker17 log10 LR 0.239347 ; LR 1.73519 Marker18 log10 LR 0.5460124 ; LR 3.515705 Marker19 log10 LR 0.4928944 ; LR 3.11096 Marker20 log10 LR 0.17436 ; LR 1.494032 all trace all marker overall log10 LR 9.53087 LR 3395234481 Time difference of 2.644453 secs Using peak heights, omitting Markers 8 and 10 Marker01 log10 LR 0.6850491 ; LR 4.842272 Marker02 log10 LR 1.038119 ; LR 10.9174 Marker03 log10 LR 1.110182 ; LR 12.88788 Marker04 log10 LR 0.5700872 ; LR 3.716099 Marker05 log10 LR 0.7130608 ; LR 5.164886 Marker06 log10 LR 0.5240292 ; LR 3.342175 Marker07 log10 LR 0.2005535 ; LR 1.586914 Marker09 log10 LR 0.2103224 ; LR 1.623015 Marker11 log10 LR 1.038148 ; LR 10.91812 Marker12 log10 LR 0.2979572 ; LR 1.985899 Marker13 log10 LR 0.3560494 ; LR 2.270123 Marker14 log10 LR 0.1791453 ; LR 1.510586 Marker15 log10 LR 0.4041013 ; LR 2.53572 Marker16 log10 LR 0.790522 ; LR 6.173365 Marker17 log10 LR 0.37829 ; LR 2.389406 Marker18 log10 LR 0.8302818 ; LR 6.765218 Marker19 log10 LR 0.5187422 ; LR 3.301735 Marker20 log10 LR 0.09160004 ; LR 1.23481 all trace all marker overall log10 LR 9.93624 LR 8634556962 Time difference of 2.036826 secs Using presence only, omitting Markers 8 and 10 Marker01 log10 LR 0.4934383 ; LR 3.114858 Marker02 log10 LR 0.8901811 ; LR 7.765709 Marker03 log10 LR 0.9917479 ; LR 9.811782 Marker04 log10 LR 0.5577429 ; LR 3.61196 Marker05 log10 LR 0.692927 ; LR 4.930909 Marker06 log10 LR 0.4111992 ; LR 2.577503 Marker07 log10 LR 0.02945267 ; LR 1.07017 Marker09 log10 LR 0.07354052 ; LR 1.184515 Marker11 log10 LR 0.802564 ; LR 6.346934 Marker12 log10 LR 0.2342334 ; LR 1.714879 Marker13 log10 LR 0.3533503 ; LR 2.256058 Marker14 log10 LR 0.3257552 ; LR 2.117168 Marker15 log10 LR 0.3906867 ; LR 2.458593 Marker16 log10 LR 0.7196317 ; LR 5.243626 Marker17 log10 LR 0.239347 ; LR 1.73519 Marker18 log10 LR 0.5460124 ; LR 3.515705 Marker19 log10 LR 0.4928944 ; LR 3.11096 Marker20 log10 LR 0.17436 ; LR 1.494032 all trace all marker overall log10 LR 8.419065 LR 262460967 Time difference of 2.057052 secs Using relMix Marker01 3.01965 Marker02 7.178708 Marker03 9.234993 Marker04 3.544825 Marker05 4.747475 Marker06 2.546122 Marker07 1.076776 Marker09 1.262897 Marker11 6.303686 Marker12 1.709233 Marker13 2.249096 Marker14 2.085075 Marker15 2.390977 Marker16 5.022736 Marker17 1.887014 Marker18 3.476996 Marker19 3.008855 Marker20 1.603116 all trace all marker overall log10 LR: 8.350256 LR: 224004272 Time difference of 17.83516 mins > source('Table 5.R') Relationship: monozygotic twins Marker01 log10 LR -Inf ; LR 0 Marker02 log10 LR -Inf ; LR 0 Marker03 log10 LR -Inf ; LR 0 Marker04 log10 LR 0.4488577 ; LR 2.81098 Marker05 log10 LR 0.6196396 ; LR 4.165236 Marker06 log10 LR -3.798504 ; LR 0.0001590363 Marker07 log10 LR -Inf ; LR 0 Marker08 log10 LR -Inf ; LR 0 Marker09 log10 LR -Inf ; LR 0 Marker10 log10 LR -Inf ; LR 0 Marker11 log10 LR -Inf ; LR 0 Marker12 log10 LR -5.049543 ; LR 8.921889e-06 Marker13 log10 LR 0.416403 ; LR 2.608573 Marker14 log10 LR -4.878776 ; LR 1.321977e-05 Marker15 log10 LR -Inf ; LR 0 Marker16 log10 LR -Inf ; LR 0 Marker17 log10 LR -Inf ; LR 0 Marker18 log10 LR -Inf ; LR 0 Marker19 log10 LR 0.2545793 ; LR 1.797129 Marker20 log10 LR 0.4033447 ; LR 2.531307 all trace all marker overall log10 LR -Inf LR 0 Relationship: parent-child Marker01 log10 LR -0.07395222 ; LR 0.8434275 Marker02 log10 LR -0.07108158 ; LR 0.849021 Marker03 log10 LR 0.1122314 ; LR 1.294886 Marker04 log10 LR 0.2295031 ; LR 1.696302 Marker05 log10 LR 0.3098291 ; LR 2.040935 Marker06 log10 LR -0.07792525 ; LR 0.8357469 Marker07 log10 LR -0.2397287 ; LR 0.5757995 Marker08 log10 LR 0.05290242 ; LR 1.129542 Marker09 log10 LR -0.1106614 ; LR 0.7750659 Marker10 log10 LR -0.1036514 ; LR 0.7876777 Marker11 log10 LR -Inf ; LR 0 Marker12 log10 LR -0.08130209 ; LR 0.8292737 Marker13 log10 LR 0.2049453 ; LR 1.603043 Marker14 log10 LR -0.08873589 ; LR 0.8151999 Marker15 log10 LR -0.1142709 ; LR 0.7686508 Marker16 log10 LR -0.01570329 ; LR 0.9644877 Marker17 log10 LR -0.03520135 ; LR 0.9221438 Marker18 log10 LR -5.330476 ; LR 4.67223e-06 Marker19 log10 LR 0.1361537 ; LR 1.368213 Marker20 log10 LR 0.1993942 ; LR 1.582684 all trace all marker overall log10 LR -Inf LR 0 Relationship: sibs Marker01 log10 LR -0.1728157 ; LR 0.6717138 Marker02 log10 LR -0.1710113 ; LR 0.6745105 Marker03 log10 LR -0.0469932 ; LR 0.8974429 Marker04 log10 LR 0.2554886 ; LR 1.800896 Marker05 log10 LR 0.3639458 ; LR 2.311776 Marker06 log10 LR -0.17528 ; LR 0.6679132 Marker07 log10 LR -0.2692986 ; LR 0.5378998 Marker08 log10 LR -0.08896442 ; LR 0.814771 Marker09 log10 LR -0.1954974 ; LR 0.6375329 Marker10 log10 LR -0.1912228 ; LR 0.6438389 Marker11 log10 LR -0.60206 ; LR 0.25 Marker12 log10 LR -0.1774141 ; LR 0.6646391 Marker13 log10 LR 0.2313842 ; LR 1.703665 Marker14 log10 LR -0.182036 ; LR 0.6576033 Marker15 log10 LR -0.1976879 ; LR 0.6343254 Marker16 log10 LR -0.1353443 ; LR 0.7322439 Marker17 log10 LR -0.1480865 ; LR 0.7110719 Marker18 log10 LR -0.6020559 ; LR 0.2500023 Marker19 log10 LR 0.1409443 ; LR 1.383389 Marker20 log10 LR 0.2237992 ; LR 1.674169 all trace all marker overall log10 LR -2.140206 LR 0.007240923 Relationship: double first cousins Marker01 log10 LR -0.0561172 ; LR 0.8787853 Marker02 log10 LR -0.05508184 ; LR 0.8808829 Marker03 log10 LR 0.02039532 ; LR 1.048082 Marker04 log10 LR 0.1380813 ; LR 1.374299 Marker05 log10 LR 0.2008991 ; LR 1.588178 Marker06 log10 LR -0.05753803 ; LR 0.875915 Marker07 log10 LR -0.1087833 ; LR 0.7784248 Marker08 log10 LR -0.006088607 ; LR 0.9860783 Marker09 log10 LR -0.06897475 ; LR 0.8531497 Marker10 log10 LR -0.06657389 ; LR 0.8578791 Marker11 log10 LR -0.2498775 ; LR 0.5625 Marker12 log10 LR -0.05874792 ; LR 0.8734782 Marker13 log10 LR 0.1227652 ; LR 1.326677 Marker14 log10 LR -0.06137983 ; LR 0.8682008 Marker15 log10 LR -0.07020108 ; LR 0.850744 Marker16 log10 LR -0.03424207 ; LR 0.9241829 Marker17 log10 LR -0.04176881 ; LR 0.9083039 Marker18 log10 LR -0.2498761 ; LR 0.5625018 Marker19 log10 LR 0.07478006 ; LR 1.1879 Marker20 log10 LR 0.1186658 ; LR 1.314213 all trace all marker overall log10 LR -0.5096641 LR 0.3092687 Relationship: quadruple-half-first-cousins Marker01 log10 LR -0.04563709 ; LR 0.9002496 Marker02 log10 LR -0.04445815 ; LR 0.9026967 Marker03 log10 LR 0.04050839 ; LR 1.097762 Marker04 log10 LR 0.13393 ; LR 1.361225 Marker05 log10 LR 0.1915411 ; LR 1.554323 Marker06 log10 LR -0.04725878 ; LR 0.8968942 Marker07 log10 LR -0.1061482 ; LR 0.7831623 Marker08 log10 LR 0.01090376 ; LR 1.025425 Marker09 log10 LR -0.06031039 ; LR 0.8703413 Marker10 log10 LR -0.0575658 ; LR 0.875859 Marker11 log10 LR -0.2747011 ; LR 0.53125 Marker12 log10 LR -0.04863453 ; LR 0.8940575 Marker13 log10 LR 0.1186282 ; LR 1.314099 Marker14 log10 LR -0.05163577 ; LR 0.8879004 Marker15 log10 LR -0.06171313 ; LR 0.8675347 Marker16 log10 LR -0.02080987 ; LR 0.9532134 Marker17 log10 LR -0.02933338 ; LR 0.9346879 Marker18 log10 LR -0.2746994 ; LR 0.531252 Marker19 log10 LR 0.07408597 ; LR 1.186004 Marker20 log10 LR 0.1148703 ; LR 1.302778 all trace all marker overall log10 LR -0.4384378 LR 0.3643864 Relationship: half-sibs Marker01 log10 LR -0.03540392 ; LR 0.9217138 Marker02 log10 LR -0.03408816 ; LR 0.9245105 Marker03 log10 LR 0.05973107 ; LR 1.147443 Marker04 log10 LR 0.1297385 ; LR 1.348151 Marker05 log10 LR 0.1819771 ; LR 1.520467 Marker06 log10 LR -0.0372172 ; LR 0.9178734 Marker07 log10 LR -0.103529 ; LR 0.7878998 Marker08 log10 LR 0.02725623 ; LR 1.064771 Marker09 log10 LR -0.05181552 ; LR 0.8875329 Marker10 log10 LR -0.04874077 ; LR 0.8938389 Marker11 log10 LR -0.30103 ; LR 0.5 Marker12 log10 LR -0.0387513 ; LR 0.9146369 Marker13 log10 LR 0.1144514 ; LR 1.301522 Marker14 log10 LR -0.04210554 ; LR 0.9075999 Marker15 log10 LR -0.0533879 ; LR 0.8843254 Marker16 log10 LR -0.007780672 ; LR 0.9822439 Marker17 log10 LR -0.01724412 ; LR 0.9610719 Marker18 log10 LR -0.301028 ; LR 0.5000023 Marker19 log10 LR 0.07339077 ; LR 1.184107 Marker20 log10 LR 0.1110413 ; LR 1.291342 all trace all marker overall log10 LR -0.3745357 LR 0.4221475 Relationship: cousins Marker01 log10 LR -0.01734129 ; LR 0.9608569 Marker02 log10 LR -0.01670971 ; LR 0.9622552 Marker03 log10 LR 0.03089162 ; LR 1.073721 Marker04 log10 LR 0.069696 ; LR 1.174075 Marker05 log10 LR 0.1004511 ; LR 1.260234 Marker06 log10 LR -0.01821005 ; LR 0.9589367 Marker07 log10 LR -0.04868683 ; LR 0.8939499 Marker08 log10 LR 0.0138419 ; LR 1.032386 Marker09 log10 LR -0.02513545 ; LR 0.9437665 Marker10 log10 LR -0.02368697 ; LR 0.9469194 Marker11 log10 LR -0.1249387 ; LR 0.75 Marker12 log10 LR -0.01894358 ; LR 0.9573184 Marker13 log10 LR 0.06098509 ; LR 1.150761 Marker14 log10 LR -0.02054269 ; LR 0.9538 Marker15 log10 LR -0.02587409 ; LR 0.9421627 Marker16 log10 LR -0.003872912 ; LR 0.9911219 Marker17 log10 LR -0.00853648 ; LR 0.9805359 Marker18 log10 LR -0.1249381 ; LR 0.7500012 Marker19 log10 LR 0.03824382 ; LR 1.092053 Marker20 log10 LR 0.05905992 ; LR 1.145671 all trace all marker overall log10 LR -0.1042474 LR 0.7865975 Relationship: half-cousins Marker01 log10 LR -0.008584098 ; LR 0.9804284 Marker02 log10 LR -0.008274497 ; LR 0.9811276 Marker03 log10 LR 0.01572042 ; LR 1.036861 Marker04 log10 LR 0.03624461 ; LR 1.087038 Marker05 log10 LR 0.05312334 ; LR 1.130117 Marker06 log10 LR -0.00900959 ; LR 0.9794684 Marker07 log10 LR -0.02366151 ; LR 0.9469749 Marker08 log10 LR 0.006976096 ; LR 1.016193 Marker09 log10 LR -0.01238591 ; LR 0.9718832 Marker10 log10 LR -0.01168202 ; LR 0.9734597 Marker11 log10 LR -0.05799195 ; LR 0.875 Marker12 log10 LR -0.009368509 ; LR 0.9786592 Marker13 log10 LR 0.03156213 ; LR 1.07538 Marker14 log10 LR -0.0101499 ; LR 0.9769 Marker15 log10 LR -0.01274439 ; LR 0.9710813 Marker16 log10 LR -0.001932139 ; LR 0.995561 Marker17 log10 LR -0.004247266 ; LR 0.990268 Marker18 log10 LR -0.05799166 ; LR 0.8750006 Marker19 log10 LR 0.01954274 ; LR 1.046027 Marker20 log10 LR 0.03053313 ; LR 1.072835 all trace all marker overall log10 LR -0.03432095 LR 0.9240151 > source('Table 6.R') log10 LR U2 father of D and U1 mother of D vs U1, U2 and D all unrelated 17.93456 log10 LR U2 father of D and U1 unrelated vs U1, U2 and D all unrelated 4.530725 log10 LR U1 mother of D and U2 unrelated vs U1, U2 and D all unrelated 10.97424 log10 LR U2 father of D and U1 maternal aunt of D vs U1, U2 and D all unrelated 14.0284 log10 LR U1 maternal aunt of D and U2 unrelated vs U1, U2 and D all unrelated 7.452493 log10 LR U2 paternal uncle of D and U1 mother of D vs U1, U2 and D all unrelated 15.57922 log10 LR U2 paternal uncle of D and U1 unrelated vs U1, U2 and D all unrelated 2.795748 log10 LR U2 paternal uncle of D and U1 maternal aunt of D vs U1, U2 and D all unrelated 11.76286 > >