R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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Platform: i386-w64-mingw32/i386 (32-bit)

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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 
> 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 
>