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<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">filter</span>(minimum_cycle_length_diary <=<span class="st"> </span><span class="dv">36</span>, minimum_cycle_length_diary ><span class="st"> </span><span class="dv">20</span>) %>%
<span class="st"> </span><span class="kw">filter</span>(!<span class="kw">is.na</span>(fertile), !<span class="kw">is.na</span>(included), RCD ><span class="st"> </span>-<span class="dv">1</span> *<span class="st"> </span>minimum_cycle_length_diary, RCD ><span class="st"> </span>-<span class="dv">40</span>) %>%
<span class="st"> </span><span class="kw">select</span>(person, menstruation, fertile_mean, RCD_inferred, 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, -RCD_inferred, -included)
model =<span class="st"> </span><span class="kw">brm</span>(value ~<span class="st"> </span>included +<span class="st"> </span><span class="kw">s</span>(RCD_inferred, <span class="dt">by =</span> included) +<span class="st"> </span>fertile_mean +<span class="st"> </span>(<span class="dv">1</span>|person) +<span class="st"> </span>(<span class="dv">1</span> +<span class="st"> </span>included |<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_rcd_no_mens.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> F)
<span class="kw">saveRDS</span>(model, <span class="dt">file =</span> <span class="st">"3_brms_extra_pair_long_rcd_no_mens.rds"</span>)
<span class="kw">summary</span>(model)</code></pre></div>
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