> 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('Razorblade data and parameters.R') Reading Razorblade 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 4.071 393.5 0.01182 0.5001 0.4999 mu 1601.682 sigma 0.05041438 vanilla model log likelihood: -592.673 > > # the following can be done in any order > > source('Table 3.R') log10 LR for U1 8.443148 log10 LR for U2 8.443664 > source('Table 5.R') Relationship: monozygotic twins Marker01 log10 LR -2.640932 ; LR 0.002285957 Marker02 log10 LR -Inf ; LR 0 Marker03 log10 LR -Inf ; LR 0 Marker04 log10 LR -2.938444 ; LR 0.001152275 Marker05 log10 LR 1.202624 ; LR 15.945 Marker06 log10 LR -Inf ; LR 0 Marker07 log10 LR -1.053447 ; LR 0.08842051 Marker08 log10 LR -Inf ; LR 0 Marker09 log10 LR -Inf ; LR 0 Marker10 log10 LR -1.156481 ; LR 0.06974594 Marker11 log10 LR -Inf ; LR 0 Marker12 log10 LR -1.769617 ; LR 0.01699741 Marker13 log10 LR -0.4029052 ; LR 0.395453 Marker14 log10 LR 0.4986865 ; LR 3.152728 Marker15 log10 LR -0.9630761 ; LR 0.1088739 Marker16 log10 LR -3.59601 ; LR 0.0002535069 Marker17 log10 LR -0.519361 ; LR 0.3024398 Marker18 log10 LR -Inf ; LR 0 Marker19 log10 LR -3.250213 ; LR 0.0005620656 Marker20 log10 LR -3.99664 ; LR 0.0001007767 all trace all marker overall log10 LR -Inf LR 0 Relationship: parent-child Marker01 log10 LR -0.03460664 ; LR 0.9234074 Marker02 log10 LR -2.494572 ; LR 0.00320205 Marker03 log10 LR 0.1970806 ; LR 1.574275 Marker04 log10 LR 0.2814662 ; LR 1.911905 Marker05 log10 LR 0.49716 ; LR 3.141666 Marker06 log10 LR -0.04099574 ; LR 0.9099222 Marker07 log10 LR -0.246981 ; LR 0.566264 Marker08 log10 LR -Inf ; LR 0 Marker09 log10 LR -0.05221802 ; LR 0.8867108 Marker10 log10 LR -0.02168391 ; LR 0.9512969 Marker11 log10 LR -1.466223 ; LR 0.03418038 Marker12 log10 LR -0.03692915 ; LR 0.9184824 Marker13 log10 LR 0.2795689 ; LR 1.90357 Marker14 log10 LR 0.1792077 ; LR 1.510803 Marker15 log10 LR 0.001571007 ; LR 1.003624 Marker16 log10 LR -1.254807 ; LR 0.05561507 Marker17 log10 LR 0.1146138 ; LR 1.302008 Marker18 log10 LR 0.1821677 ; LR 1.521135 Marker19 log10 LR -0.3127435 ; LR 0.4866945 Marker20 log10 LR -0.3683967 ; LR 0.4281572 all trace all marker overall log10 LR -Inf LR 0 Relationship: sibs Marker01 log10 LR -0.1473522 ; LR 0.7122752 Marker02 log10 LR -0.5992876 ; LR 0.251601 Marker03 log10 LR 0.01583631 ; LR 1.037137 Marker04 log10 LR 0.08143387 ; LR 1.20624 Marker05 log10 LR 0.7639579 ; LR 5.807082 Marker06 log10 LR -0.1518348 ; LR 0.7049611 Marker07 log10 LR -0.2555215 ; LR 0.5552371 Marker08 log10 LR -0.60206 ; LR 0.25 Marker09 log10 LR -0.1590441 ; LR 0.6933554 Marker10 log10 LR -0.1289615 ; LR 0.7430849 Marker11 log10 LR -0.5733421 ; LR 0.2670902 Marker12 log10 LR -0.1466118 ; LR 0.7134906 Marker13 log10 LR 0.1141599 ; LR 1.300648 Marker14 log10 LR 0.2537215 ; LR 1.793583 Marker15 log10 LR -0.1084456 ; LR 0.7790304 Marker16 log10 LR -0.5561569 ; LR 0.2778709 Marker17 log10 LR -0.01027701 ; LR 0.9766141 Marker18 log10 LR 0.004565276 ; LR 1.010567 Marker19 log10 LR -0.3067236 ; LR 0.4934878 Marker20 log10 LR -0.3333849 ; LR 0.4641038 all trace all marker overall log10 LR -2.845329 LR 0.001427813 Relationship: double first cousins Marker01 log10 LR -0.04147403 ; LR 0.9089207 Marker02 log10 LR -0.2489514 ; LR 0.5637008 Marker03 log10 LR 0.06177397 ; LR 1.152853 Marker04 log10 LR 0.1070526 ; LR 1.279536 Marker05 log10 LR 0.4373045 ; LR 2.737187 Marker06 log10 LR -0.04396571 ; LR 0.9037208 Marker07 log10 LR -0.1076965 ; LR 0.7803753 Marker08 log10 LR -0.2498775 ; LR 0.5625 Marker09 log10 LR -0.04816894 ; LR 0.8950165 Marker10 log10 LR -0.03451821 ; LR 0.9235955 Marker11 log10 LR -0.2400923 ; LR 0.5753176 Marker12 log10 LR -0.04191738 ; LR 0.9079932 Marker13 log10 LR 0.1142955 ; LR 1.301055 Marker14 log10 LR 0.1225751 ; LR 1.326096 Marker15 log10 LR -0.02426333 ; LR 0.9456636 Marker16 log10 LR -0.2340548 ; LR 0.5833715 Marker17 log10 LR 0.02924397 ; LR 1.069656 Marker18 log10 LR 0.05420137 ; LR 1.132926 Marker19 log10 LR -0.1278172 ; LR 0.7450456 Marker20 log10 LR -0.1408225 ; LR 0.7230652 all trace all marker overall log10 LR -0.6571727 LR 0.2202051 Relationship: quadruple-half-first-cousins Marker01 log10 LR -0.02904341 ; LR 0.9353122 Marker02 log10 LR -0.2735573 ; LR 0.5326509 Marker03 log10 LR 0.08635814 ; LR 1.219995 Marker04 log10 LR 0.1360049 ; LR 1.367744 Marker05 log10 LR 0.3809363 ; LR 2.40401 Marker06 log10 LR -0.03182492 ; LR 0.929341 Marker07 log10 LR -0.1069301 ; LR 0.7817536 Marker08 log10 LR -0.2747011 ; LR 0.53125 Marker09 log10 LR -0.03659662 ; LR 0.919186 Marker10 log10 LR -0.02244925 ; LR 0.949622 Marker11 log10 LR -0.2626452 ; LR 0.5462039 Marker12 log10 LR -0.02983114 ; LR 0.9336172 Marker13 log10 LR 0.1387509 ; LR 1.37642 Marker14 log10 LR 0.1108418 ; LR 1.290749 Marker15 log10 LR -0.01155798 ; LR 0.9737378 Marker16 log10 LR -0.255246 ; LR 0.5555895 Marker17 log10 LR 0.04545203 ; LR 1.11033 Marker18 log10 LR 0.07800215 ; LR 1.196746 Marker19 log10 LR -0.1283124 ; LR 0.7441964 Marker20 log10 LR -0.1435298 ; LR 0.7185719 all trace all marker overall log10 LR -0.629879 LR 0.2344882 Relationship: half-sibs Marker01 log10 LR -0.01695871 ; LR 0.9617037 Marker02 log10 LR -0.2996416 ; LR 0.501601 Marker03 log10 LR 0.1096249 ; LR 1.287137 Marker04 log10 LR 0.1631472 ; LR 1.455952 Marker05 log10 LR 0.3161451 ; LR 2.070833 Marker06 log10 LR -0.02001432 ; LR 0.9549611 Marker07 log10 LR -0.106165 ; LR 0.783132 Marker08 log10 LR -0.30103 ; LR 0.5 Marker09 log10 LR -0.02532467 ; LR 0.9433554 Marker10 log10 LR -0.01070664 ; LR 0.9756485 Marker11 log10 LR -0.2864337 ; LR 0.5170902 Marker12 log10 LR -0.01807217 ; LR 0.9592412 Marker13 log10 LR 0.1619023 ; LR 1.451785 Marker14 log10 LR 0.09878257 ; LR 1.255401 Marker15 log10 LR 0.0007862139 ; LR 1.001812 Marker16 log10 LR -0.2775244 ; LR 0.5278075 Marker17 log10 LR 0.06107689 ; LR 1.151004 Marker18 log10 LR 0.1005661 ; LR 1.260567 Marker19 log10 LR -0.1288082 ; LR 0.7433473 Marker20 log10 LR -0.146254 ; LR 0.7140786 all trace all marker overall log10 LR -0.6249023 LR 0.2371907 Relationship: cousins Marker01 log10 LR -0.008396583 ; LR 0.9808519 Marker02 log10 LR -0.1244754 ; LR 0.7508005 Marker03 log10 LR 0.05826227 ; LR 1.143569 Marker04 log10 LR 0.08918994 ; LR 1.227976 Marker05 log10 LR 0.1862262 ; LR 1.535416 Marker06 log10 LR -0.009891876 ; LR 0.9774805 Marker07 log10 LR -0.0498465 ; LR 0.891566 Marker08 log10 LR -0.1249387 ; LR 0.75 Marker09 log10 LR -0.01247777 ; LR 0.9716777 Marker10 log10 LR -0.005320326 ; LR 0.9878242 Marker11 log10 LR -0.1200186 ; LR 0.7585451 Marker12 log10 LR -0.008942088 ; LR 0.9796206 Marker13 log10 LR 0.0884524 ; LR 1.225893 Marker14 log10 LR 0.05219383 ; LR 1.127701 Marker15 log10 LR 0.0003932849 ; LR 1.000906 Marker16 log10 LR -0.1169613 ; LR 0.7639038 Marker17 log10 LR 0.03161125 ; LR 1.075502 Marker18 log10 LR 0.05318746 ; LR 1.130284 Marker19 log10 LR -0.05964609 ; LR 0.8716736 Marker20 log10 LR -0.06699926 ; LR 0.8570393 all trace all marker overall log10 LR -0.148398 LR 0.7105621 Relationship: half-cousins Marker01 log10 LR -0.004177999 ; LR 0.9904259 Marker02 log10 LR -0.05779333 ; LR 0.8754003 Marker03 log10 LR 0.03010742 ; LR 1.071784 Marker04 log10 LR 0.04688055 ; LR 1.113988 Marker05 log10 LR 0.1030193 ; LR 1.267708 Marker06 log10 LR -0.004917775 ; LR 0.9887403 Marker07 log10 LR -0.0242085 ; LR 0.945783 Marker08 log10 LR -0.05799195 ; LR 0.875 Marker09 log10 LR -0.006194073 ; LR 0.9858388 Marker10 log10 LR -0.002652016 ; LR 0.9939121 Marker11 log10 LR -0.05587649 ; LR 0.8792725 Marker12 log10 LR -0.00444803 ; LR 0.9898103 Marker13 log10 LR 0.0464742 ; LR 1.112946 Marker14 log10 LR 0.02688053 ; LR 1.06385 Marker15 log10 LR 0.000196687 ; LR 1.000453 Marker16 log10 LR -0.05455511 ; LR 0.8819519 Marker17 log10 LR 0.01609318 ; LR 1.037751 Marker18 log10 LR 0.02740745 ; LR 1.065142 Marker19 log10 LR -0.02879987 ; LR 0.9358368 Marker20 log10 LR -0.0322089 ; LR 0.9285197 all trace all marker overall log10 LR -0.03676473 LR 0.9188302 >