R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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 an HTML browser interface to help. Type 'q()' to quit R. [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 > epgT<-epg > parsT<-pars > baselineT<-baseline > 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 > epgR<-epg > parsR<-pars > baselineR<-baseline > > cat('sum of baselines:',baselineT+baselineR,'\n') sum of baselines: -1113.667 > > source('Table 7.R') ... baseline: -1113.667 rho eta xi phi.U1 phi.U2 1 8.964 265.6 0.00000 0.9264 0.07356 2 4.071 393.5 0.01182 0.5001 0.49994 ... log10LR for same 2 contribs: 23.56212 ... log10LR for same 2 contribs, U1=parent of D: 34.53625 rho eta xi phi.U1 phi.U2 phi.U3 1 8.964 265.6 0.00000 0.9264 0.07356 0.0000 2 4.071 393.5 0.01182 0.5001 0.00000 0.4999 ... log10LR for U1=U2, indpt U3: 16.52503 ... log10LR for U1=U2=parent of D, indpt U3: 27.49925 rho eta xi phi.U1 phi.U2 phi.U3 1 8.964 265.6 0.00000 0.9264 0.07356 0.0000 2 4.071 393.5 0.01182 0.5001 0.00000 0.4999 ... log10LR for T = F&M of D, RB = F of D and unknown: 34.45957 rho eta xi phi.U1 phi.U2 phi.U3 1 8.964 265.6 0.00000 0.9264 0.07356 0.0000 2 4.071 393.5 0.01182 0.0000 0.50006 0.4999 ... log10LR for T = M&F of D, RB = F of D and unknown: 25.54383 >