-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathe2_surviveR_20thc_sweden.html
143 lines (113 loc) · 7.68 KB
/
e2_surviveR_20thc_sweden.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title> Surviver 20Thc Modern Swedenen</title>
<script src="library/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="library/bootstrap-3.3.5/css/paper.min.css" rel="stylesheet" />
<script src="library/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="library/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="library/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="library/navigation-1.1/tabsets.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
div.sourceCode { overflow-x: auto; }
table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode {
margin: 0; padding: 0; vertical-align: baseline; border: none; }
table.sourceCode { width: 100%; line-height: 100%; }
td.lineNumbers { text-align: right; padding-right: 4px; padding-left: 4px; color: #aaaaaa; border-right: 1px solid #aaaaaa; }
td.sourceCode { padding-left: 5px; }
code > span.kw { color: #007020; font-weight: bold; } /* Keyword */
code > span.dt { color: #902000; } /* DataType */
code > span.dv { color: #40a070; } /* DecVal */
code > span.bn { color: #40a070; } /* BaseN */
code > span.fl { color: #40a070; } /* Float */
code > span.ch { color: #4070a0; } /* Char */
code > span.st { color: #4070a0; } /* String */
code > span.co { color: #60a0b0; font-style: italic; } /* Comment */
code > span.ot { color: #007020; } /* Other */
code > span.al { color: #ff0000; font-weight: bold; } /* Alert */
code > span.fu { color: #06287e; } /* Function */
code > span.er { color: #ff0000; font-weight: bold; } /* Error */
code > span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
code > span.cn { color: #880000; } /* Constant */
code > span.sc { color: #4070a0; } /* SpecialChar */
code > span.vs { color: #4070a0; } /* VerbatimString */
code > span.ss { color: #bb6688; } /* SpecialString */
code > span.im { } /* Import */
code > span.va { color: #19177c; } /* Variable */
code > span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code > span.op { color: #666666; } /* Operator */
code > span.bu { } /* BuiltIn */
code > span.ex { } /* Extension */
code > span.pp { color: #bc7a00; } /* Preprocessor */
code > span.at { color: #7d9029; } /* Attribute */
code > span.do { color: #ba2121; font-style: italic; } /* Documentation */
code > span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code > span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
</style>
</head>
<body>
<div style="width:100%;height:200px;background-image:url('library/header/swed.jpg');background-size:cover;"></div>
<div class="container-fluid main-container"><div class="row"><div class="col-md-4"><a href="index.html"><i class="glyphicon glyphicon-th-list"></i> Back to index</a></div></div></div>
<div class="container-fluid main-container">
<div id="run-bernoulli-model-with-survival-to-15-on-cluster" class="section level1">
<h1>Run Bernoulli model with survival to 15 on cluster</h1>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(dplyr); <span class="kw">library</span>(brms)
<span class="kw">setwd</span>(<span class="st">"/usr/users/rarslan/updated_data/"</span>)
args =<span class="st"> </span><span class="kw">commandArgs</span>()
dataset =<span class="st"> </span>args[<span class="dv">6</span>]
uptobyear =<span class="st"> </span>args[<span class="dv">7</span>]
<span class="kw">load</span>(<span class="kw">paste0</span>(dataset, <span class="st">".rdata"</span>))
model_data =<span class="st"> </span><span class="kw">get</span>(<span class="kw">paste0</span>(dataset, <span class="st">".1"</span>)) %>%<span class="st"> </span><span class="kw">tbl_df</span>() %>%
<span class="st"> </span><span class="kw">filter</span>(survive1y ==<span class="st"> </span><span class="dv">1</span>) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(byear <<span class="st"> </span>uptobyear) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">select</span>(survive1y, surviveR, birth_cohort, male, maternalage.factor, paternalage.mean, paternalage, paternal_loss, maternal_loss, older_siblings, nr.siblings, last_born, idParents) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">na.omit</span>()
if (dataset ==<span class="st"> "swed_subset_survival"</span>) {
<span class="co"># switched the factor reference from later than 45 to unclear, because censoring means parental deaths later than age 45 are recorded as unclear/unknown</span>
model_data$maternal_loss =<span class="st"> </span><span class="kw">relevel</span>(model_data$maternal_loss, <span class="dt">ref =</span> <span class="st">"unclear"</span>)
model_data$paternal_loss =<span class="st"> </span><span class="kw">relevel</span>(model_data$paternal_loss, <span class="dt">ref =</span> <span class="st">"unclear"</span>)
dataset =<span class="st"> "swed"</span>
}
model =<span class="st"> </span><span class="kw">brm</span>( surviveR ~<span class="st"> </span>paternalage +<span class="st"> </span>birth_cohort +<span class="st"> </span>male +<span class="st"> </span>maternalage.factor +<span class="st"> </span>paternalage.mean +<span class="st"> </span>paternal_loss +<span class="st"> </span>maternal_loss +<span class="st"> </span>older_siblings +<span class="st"> </span>nr.siblings +<span class="st"> </span>last_born +<span class="st"> </span>(<span class="dv">1</span> |<span class="st"> </span>idParents),
<span class="dt">prior =</span> <span class="kw">c</span>(<span class="kw">set_prior</span>(<span class="st">"normal(0,70)"</span>, <span class="dt">class =</span> <span class="st">"b"</span>),
<span class="kw">set_prior</span>(<span class="st">"student_t(3, 0, 50)"</span>, <span class="dt">class =</span> <span class="st">"sd"</span>)),
<span class="dt">family =</span> <span class="kw">bernoulli</span>(<span class="dt">link =</span> <span class="st">"cauchit"</span>), <span class="dt">data =</span> model_data,
<span class="dt">chains =</span> <span class="dv">6</span>, <span class="dt">iter =</span> <span class="dv">1500</span>, <span class="dt">warmup =</span> <span class="dv">1000</span>, <span class="dt">cores =</span> <span class="dv">6</span>, <span class="dt">ranef =</span> <span class="ot">FALSE</span>)
<span class="kw">summary</span>(model)
<span class="kw">saveRDS</span>(model,<span class="dt">file =</span> <span class="kw">paste0</span>(<span class="st">"coefs/"</span>, dataset, <span class="st">"/e2_surviveR_wide_priors.rds"</span>))</code></pre></div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
$(document).ready(function () {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
});
</script>
</body>
</html>