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update documentations for multi-trait
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@reworkhow
reworkhow committed Feb 27, 2018
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120 changes: 94 additions & 26 deletions docs/2.2.Multivariate_Linear_Additive_Genetic_Model.ipynb
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Original file line number Diff line number Diff line change
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"text": [
"\n",
"\r",
"\u001b[32mcalculating inbreeding... 20%|█████ | ETA: 0:00:01\u001b[39m\r",
"\u001b[32mcalculating inbreeding... 20%|█████ | ETA: 0:00:00\u001b[39m\r",
"\u001b[32mcalculating inbreeding... 100%|█████████████████████████| Time: 0:00:00\u001b[39m\n"
]
}
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"output_type": "stream",
"text": [
"\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 0%| | ETA: 0:07:47\u001b[39m"
"\u001b[32mrunning MCMC for conventional (no markers)... 0%| | ETA: 0:07:55\u001b[39m"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Posterior means at iteration: 500\n",
"Residual covariance matrix: \n"
"Posterior means at iteration: 500"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 25%|█ | ETA: 0:00:02\u001b[39m"
"\u001b[32mrunning MCMC for conventional (no markers)... 25%|██ | ETA: 0:00:02\u001b[39m"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[104.124 26.2121; 26.2121 7.32556]\n",
"\n",
"Residual covariance matrix: \n",
"[38.2784 8.53017; 8.53017 2.54553]\n",
"Polygenic effects covariance matrix \n",
"[33.2182 4.31627; 4.31627 2.43989]\n",
"[120.265 26.6641; 26.6641 8.25117]\n",
"\n"
]
},
Expand All @@ -387,9 +388,9 @@
"\n",
"Posterior means at iteration: 1000\n",
"Residual covariance matrix: \n",
"[81.3315 20.3175; 20.3175 5.78435]\n",
"[40.7927 9.60445; 9.60445 2.88894]\n",
"Polygenic effects covariance matrix \n",
"[53.594 9.25546; 9.25546 3.74766]\n",
"[109.396 23.709; 23.709 7.38335]\n",
"\n"
]
},
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"output_type": "stream",
"text": [
"\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 89%|█████ | ETA: 0:00:00\u001b[39m\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 79%|█████ | ETA: 0:00:00\u001b[39m\r",
"\u001b[32mrunning MCMC for conventional (no markers)...100%|██████| Time: 0:00:01\u001b[39m\n"
]
}
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"data": {
"text/plain": [
"4×100 Array{Float64,2}:\n",
" 117.321 44.3716 90.1009 90.132 … 84.898 110.494 82.4971 \n",
" 19.8691 7.04933 23.8387 14.1878 19.2768 20.4771 20.563 \n",
" 19.8691 7.04933 23.8387 14.1878 19.2768 20.4771 20.563 \n",
" 3.59992 1.40274 6.57932 2.65989 4.76932 4.13422 5.29953"
" 140.286 165.117 27.4022 47.8215 … 100.707 114.361 87.6562 \n",
" 19.8049 48.1317 6.39921 9.76642 27.2255 23.6785 22.9175 \n",
" 19.8049 48.1317 6.39921 9.76642 27.2255 23.6785 22.9175 \n",
" 3.25893 14.6208 2.0417 2.35088 7.86628 5.32089 6.31246"
]
},
"execution_count": 15,
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"out[\"MCMC samples for residual covariance matrix\"]"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"100-element Array{Array{Float64,2},1}:\n",
" [140.286 19.8049; 19.8049 3.25893]\n",
" [165.117 48.1317; 48.1317 14.6208]\n",
" [27.4022 6.39921; 6.39921 2.0417] \n",
" [47.8215 9.76642; 9.76642 2.35088]\n",
" [32.3853 6.17495; 6.17495 1.50397]\n",
" [133.801 37.3524; 37.3524 10.6991]\n",
" [54.6587 12.1139; 12.1139 2.97054]\n",
" [147.844 48.5646; 48.5646 16.3886]\n",
" [92.846 27.3524; 27.3524 8.32298] \n",
" [92.0702 24.6955; 24.6955 6.7504] \n",
" [266.548 75.1539; 75.1539 21.5001]\n",
" [162.668 35.0212; 35.0212 7.80687]\n",
" [26.0195 9.02234; 9.02234 3.36369]\n",
" ⋮ \n",
" [90.9382 19.8054; 19.8054 4.45033]\n",
" [66.0173 17.1109; 17.1109 4.62523]\n",
" [93.3314 28.7019; 28.7019 9.23725]\n",
" [82.5146 24.6105; 24.6105 7.65399]\n",
" [129.921 36.5742; 36.5742 10.4571]\n",
" [69.667 18.2625; 18.2625 5.10302] \n",
" [84.0481 18.6961; 18.6961 4.36653]\n",
" [145.568 41.1245; 41.1245 12.0517]\n",
" [39.3698 13.6979; 13.6979 4.99284]\n",
" [100.707 27.2255; 27.2255 7.86628]\n",
" [114.361 23.6785; 23.6785 5.32089]\n",
" [87.6562 22.9175; 22.9175 6.31246]"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"using JWAS:misc\n",
"reformat(out[\"MCMC samples for residual covariance matrix\"])"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -449,7 +497,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -466,7 +514,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -476,7 +524,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -486,7 +534,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 20,
"metadata": {},
"outputs": [
{
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"marker effect variances: 4.000\n",
"\n",
"\n",
"\n",
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 23%|█ | ETA: 0:00:00\u001b[39m"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Posterior means at iteration: 500\n",
"Residual covariance matrix: \n",
"[150.715 34.6499; 34.6499 8.54643]\n",
"[127.85 29.8952; 29.8952 7.57724]\n",
"Polygenic effects covariance matrix \n",
"[5.23974 1.01862 0.159582; 1.01862 0.907634 -0.037244; 0.159582 -0.037244 0.651138]\n",
"[6.51745 1.40374 0.121162; 1.40374 1.02113 -0.007159; 0.121162 -0.007159 0.416418]\n",
"\n"
]
},
Expand All @@ -548,7 +610,7 @@
"output_type": "stream",
"text": [
"\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 20%|█ | ETA: 0:00:00\u001b[39m"
"\u001b[32mrunning MCMC for conventional (no markers)... 50%|███ | ETA: 0:00:00\u001b[39m"
]
},
{
Expand All @@ -558,9 +620,9 @@
"\n",
"Posterior means at iteration: 1000\n",
"Residual covariance matrix: \n",
"[161.705 37.4924; 37.4924 9.2784]\n",
"[133.3 31.3482; 31.3482 7.94058]\n",
"Polygenic effects covariance matrix \n",
"[4.6876 0.922553 0.112737; 0.922553 0.865759 -0.026022; 0.112737 -0.026022 0.537082]\n",
"[5.91959 1.24817 0.140792; 1.24817 0.984565 0.035887; 0.140792 0.035887 0.43876]\n",
"\n"
]
},
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"output_type": "stream",
"text": [
"\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 52%|███ | ETA: 0:00:00\u001b[39m\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 84%|█████ | ETA: 0:00:00\u001b[39m\r",
"\u001b[32mrunning MCMC for conventional (no markers)... 76%|█████ | ETA: 0:00:00\u001b[39m\r",
"\u001b[32mrunning MCMC for conventional (no markers)...100%|██████| Time: 0:00:00\u001b[39m\n"
]
}
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"source": [
"keys(out)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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