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3_stan_brms_by_item_cluster.html
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<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">bsub</span> -a openmpi -q mpi -W 48:00 -n 212,300 -R span[block=4] mpirun.lsf R --slave -f /usr/users/rarslan/relationship_dynamics/3_stan_brms_by_item_cluster.R</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">suppressPackageStartupMessages</span>(<span class="kw">library</span>(brms))
<span class="kw">suppressPackageStartupMessages</span>(<span class="kw">library</span>(dplyr))
args =<span class="st"> </span><span class="kw">commandArgs</span>()
outcome =<span class="st"> </span>args[<span class="dv">6</span>]
outcomes =<span class="st"> </span><span class="kw">list</span>(<span class="st">"communication_partner_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"communication_partner_2"</span> =<span class="st"> </span><span class="kw">categorical</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"mate_retention_1"</span> =<span class="st"> </span><span class="kw">bernoulli</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"relationship_satisfaction_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"mate_retention_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"sexual_intercourse_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"sexual_intercourse_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"sexual_intercourse_3"</span> =<span class="st"> </span><span class="kw">bernoulli</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"sexual_intercourse_satisfaction"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"sexual_intercourse_5"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_3"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_4"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_5"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_6"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_7"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"choice_of_clothing_8"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"self_esteem_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"desirability_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"desirability_partner"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"NARQ_admiration_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"NARQ_admiration_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"NARQ_admiration_3"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"NARQ_rivalry_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"NARQ_rivalry_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"NARQ_rivalry_3"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"jealousy_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"male_jealousy_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"male_jealousy_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"male_jealousy_3"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"male_mate_retention_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"male_mate_retention_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"mate_retention_3"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"mate_retention_4"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"mate_retention_5"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"mate_retention_6"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"attention_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"attention_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"male_attention_1"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_intimacy_sex"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_2"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_3"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_4"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_5"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_6"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_7"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_8"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_9"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_10"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_11"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_12"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>),
<span class="st">"extra_pair_13"</span> =<span class="st"> </span><span class="kw">cumulative</span>(<span class="dt">link =</span> <span class="st">"logit"</span>))
<span class="co"># cat(paste('bsub -q mpi -W 24:00 -n 4 -R span[block=4] Rscript "/usr/users/rarslan/relationship_dynamics/3_stan_brms_by_item_cluster.R"',names(outcomes)), sep = "\n")</span>
<span class="kw">load</span>(<span class="st">"full_data.rdata"</span>)
diary =<span class="st"> </span>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)
)
diary$extra_pair_intimacy_sex =<span class="st"> </span>diary$extra_pair_sex +<span class="st"> </span>diary$extra_pair_intimacy
twice =<span class="st"> </span><span class="kw">c</span>(<span class="st">"1"</span> =<span class="st"> </span><span class="dv">1</span>, <span class="st">"2"</span> =<span class="st"> </span><span class="dv">2</span>, <span class="st">"3"</span> =<span class="st"> </span><span class="dv">0</span>)
diary$sexual_intercourse_2 =<span class="st"> </span>twice[diary$sexual_intercourse_2]
diary$sexual_intercourse_5 =<span class="st"> </span>twice[diary$sexual_intercourse_5]
diary$mate_retention_2 =<span class="st"> </span>twice[diary$mate_retention_2]
diary$relationship_satisfaction_1 =<span class="st"> </span><span class="kw">as.integer</span>(diary$relationship_satisfaction_1)
diary$sexual_intercourse_satisfaction =<span class="st"> </span><span class="kw">as.integer</span>(diary$sexual_intercourse_satisfaction)
<span class="kw">message</span>(outcome, <span class="st">" begun"</span>)
family =<span class="st"> </span>outcomes[[outcome]]
model =<span class="st"> </span><span class="kw">brm</span>(<span class="kw">as.formula</span>(<span class="kw">paste</span>(outcome,<span class="st">"~ included * (menstruation + fertile) + fertile_mean + (1 + fertile + menstruation | person)"</span>)),
<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">family =</span> family, <span class="dt">data =</span> diary,
<span class="dt">chains =</span> <span class="dv">4</span>, <span class="dt">iter =</span> <span class="dv">2000</span>, <span class="dt">warmup =</span> <span class="dv">1000</span>, <span class="dt">cores =</span> <span class="dv">4</span>)
model =<span class="st"> </span><span class="kw">add_ic</span>(model, <span class="dt">pointwise =</span> <span class="ot">FALSE</span>)
<span class="kw">saveRDS</span>(model, <span class="dt">file =</span> <span class="kw">paste0</span>(<span class="st">"by_item/"</span>,outcome,<span class="st">".rds"</span>))
<span class="kw">message</span>(outcome, <span class="st">" fini"</span>)
<span class="kw">summary</span>(model)</code></pre></div>
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