-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path3_brms_extra_pair_long_by_item_person.html
194 lines (163 loc) · 8.4 KB
/
3_brms_extra_pair_long_by_item_person.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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
<!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></title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/paper.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
div.sourceCode { overflow-x: visible; }
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">
body {
margin-top: 45px;
}
.main-container {
max-width: 1400px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
</style>
<script src="library/auto_tab_first_section.js"></script>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<script>
$(document).ready(function () {
window.initializeCodeFolding("show" === "show");
});
</script>
</head>
<body>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Fertility diary</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="1_power_analysis.html">Power analysis</a>
</li>
<li>
<a href="1_researcher_df_analysis.html">Researcher degree of freedom simulation</a>
</li>
<li>
<a href="1_wrangle_data.html">Data wrangling</a>
</li>
<li>
<a href="2_descriptives.html">Descriptives</a>
</li>
<li>
<a href="3_fertility_as_prereg.html">Preregistered analyses</a>
</li>
<li>
<a href="3_fertility_robustness.html">Robustness tests</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="container-fluid main-container">
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(brms)
<span class="kw">load</span>(<span class="st">"full_data.rdata"</span>)
<span class="kw">library</span>(lubridate)
<span class="kw">library</span>(dplyr)
diary_long =<span class="st"> </span>diary %>%
<span class="st"> </span><span class="kw">mutate</span>(
<span class="dt">included =</span> included_all,
<span class="dt">fertile =</span> <span class="kw">if_else</span>(<span class="kw">is.na</span>(prc_stirn_b_squished), prc_stirn_b_backward_inferred, prc_stirn_b_squished)
) %>%<span class="st"> </span><span class="kw">group_by</span>(person) %>%
<span class="st"> </span><span class="kw">mutate</span>(
<span class="dt">fertile_mean =</span> <span class="kw">mean</span>(fertile, <span class="dt">na.rm =</span> T)
) %>%
<span class="st"> </span><span class="kw">select</span>(person, menstruation, fertile_mean, fertile, included, extra_pair_2, extra_pair_3, extra_pair_4, extra_pair_5, extra_pair_6, extra_pair_7, extra_pair_8, extra_pair_9, extra_pair_10, extra_pair_11, extra_pair_12, extra_pair_13) %>%
<span class="st"> </span>tidyr::<span class="kw">gather</span>(variable, value, -person, -menstruation, -fertile_mean, -fertile, -included)
model =<span class="st"> </span><span class="kw">brm</span>(value ~<span class="st"> </span>included *<span class="st"> </span>(menstruation +<span class="st"> </span>fertile) +<span class="st"> </span>fertile_mean +<span class="st"> </span>(<span class="dv">1</span> +<span class="st"> </span>menstruation +<span class="st"> </span>fertile |<span class="st"> </span>person) +<span class="st"> </span>(<span class="dv">1</span> +<span class="st"> </span>included *<span class="st"> </span>(menstruation +<span class="st"> </span>fertile) |<span class="st"> </span>variable),
<span class="dt">data =</span> diary_long,
<span class="dt">prior =</span> <span class="kw">c</span>(<span class="kw">set_prior</span>(<span class="st">"student_t(3, 0, 1)"</span>, <span class="dt">class =</span> <span class="st">"b"</span>),
<span class="kw">set_prior</span>(<span class="st">"cauchy(0, 2)"</span>, <span class="dt">class =</span> <span class="st">"sd"</span>)),
<span class="dt">chains =</span> <span class="dv">6</span>,
<span class="dt">cores =</span> <span class="dv">6</span>,
<span class="dt">iter =</span> <span class="dv">1500</span>,
<span class="dt">warmup =</span> <span class="dv">500</span>,
<span class="dt">family =</span> <span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="dt">control =</span> <span class="kw">list</span>(<span class="dt">adapt_delta =</span> <span class="fl">0.9</span>)
)
<span class="kw">saveRDS</span>(model, <span class="dt">file =</span> <span class="st">"3_brms_extra_pair_long_fab_by_item_person.rds"</span>)
model =<span class="st"> </span><span class="kw">add_ic</span>(model, <span class="dt">ic =</span> <span class="kw">c</span>(<span class="st">"loo"</span>), <span class="dt">pointwise =</span> <span class="ot">FALSE</span>)
<span class="kw">saveRDS</span>(model, <span class="dt">file =</span> <span class="st">"3_brms_extra_pair_long_fab_by_item_person.rds"</span>)
<span class="kw">summary</span>(model)</code></pre></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>