
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)

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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 
> 
> 
