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<!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" />
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<title>Compare Descriptives</title>
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<div class="col-md-4" style="background:black;text-align:center"><a href="index.html" style="color:white"><i class="glyphicon glyphicon-th-list"></i> Back to index</a></div>
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<div id="comparison-of-descriptives-across-populations" class="section level1 tab-content">
<h1>Comparison of descriptives across populations</h1>
<div id="loading-details" class="section level3 accordion">
<h3>Loading details</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">source</span>(<span class="st">"0__helpers.R"</span>)
opts_chunk$<span class="kw">set</span>(<span class="dt">render =</span> pander_handler,<span class="dt">warning=</span><span class="ot">FALSE</span>,<span class="dt">cache=</span><span class="ot">FALSE</span>,<span class="dt">tidy=</span><span class="ot">FALSE</span>,<span class="dt">autodep=</span><span class="ot">TRUE</span>,<span class="dt">dev=</span><span class="st">'png'</span>,<span class="dt">fig.width=</span><span class="dv">12</span>,<span class="dt">fig.height=</span><span class="fl">7.5</span>)
<span class="kw">load</span>(<span class="st">"rpqa.rdata"</span>)
<span class="kw">load</span>(<span class="st">"ddb.rdata"</span>)
<span class="kw">load</span>(<span class="st">"krmh.rdata"</span>)
<span class="kw">load</span>(<span class="st">"swed1.rdata"</span>)
<span class="kw">load</span>(<span class="st">"swed.rdata"</span>)
demo_mod_swed =<span class="st"> </span><span class="kw">aggDemoTrends</span>(swed)
demo_old_swed =<span class="st"> </span><span class="kw">aggDemoTrends</span>(ddb<span class="fl">.1</span>) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">Population =</span> <span class="st">"Historical Sweden"</span>) %>%
<span class="st"> </span><span class="kw">melt</span>(<span class="dt">id=</span><span class="kw">c</span>(<span class="st">"Population"</span>,<span class="st">"Year"</span>,<span class="st">"Parent"</span>)) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population,Parent,variable) %>%
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean</span>(value,<span class="dt">na.rm=</span>T))
<span class="kw">rm</span>(rpqa,ddb, krmh, swed)
desc_theme =<span class="st"> </span><span class="kw">theme_minimal</span>(<span class="dt">base_size =</span> <span class="dv">24</span>)
<span class="kw">update_geom_defaults</span>(<span class="st">"bar"</span>, <span class="kw">list</span>(<span class="dt">fill =</span> <span class="st">"#6c92b2"</span>, <span class="dt">alpha =</span> <span class="dv">1</span>/<span class="dv">2</span>))
mymin =<span class="st"> </span><span class="kw">theme_minimal</span>(<span class="dt">base_size =</span> <span class="dv">20</span>) +<span class="kw">theme</span>(<span class="dt">panel.grid.major.y =</span><span class="kw">element_blank</span>(),<span class="dt">panel.grid.major.x =</span> <span class="kw">element_line</span>(<span class="dt">colour=</span><span class="st">"#eeeeee"</span>))
rpqa<span class="fl">.1</span>$Population =<span class="st"> "Québec"</span>
ddb<span class="fl">.1</span>$Population =<span class="st"> "Historical Sweden"</span>
krmh<span class="fl">.1</span>$Population =<span class="st"> "Krummhörn"</span>
swed<span class="fl">.1</span>$Population =<span class="st"> "20th-century Sweden"</span>
all =<span class="st"> </span><span class="kw">rbind</span>(
rpqa<span class="fl">.1</span> %>%<span class="st"> </span><span class="kw">select</span>(paternalage, maternalage, age_at_1st_child, age_at_last_child, children, male, Population, survive1y,surviveR, ever_married),
ddb<span class="fl">.1</span> %>%<span class="st"> </span><span class="kw">select</span>(paternalage, maternalage, age_at_1st_child, age_at_last_child, children, male, Population, survive1y,surviveR, ever_married),
krmh<span class="fl">.1</span> %>%<span class="st"> </span><span class="kw">select</span>(paternalage, maternalage, age_at_1st_child, age_at_last_child, children, male, Population, survive1y,surviveR, ever_married),
swed<span class="fl">.1</span> %>%<span class="st"> </span><span class="kw">select</span>(paternalage, maternalage, age_at_1st_child, age_at_last_child, children, male, Population, survive1y,surviveR, ever_married)
)
<span class="kw">rm</span>(rpqa<span class="fl">.1</span>,ddb<span class="fl">.1</span>, krmh<span class="fl">.1</span>,swed<span class="fl">.1</span>)
all =<span class="st"> </span><span class="kw">data.table</span>(all)
all[, paternalage :<span class="er">=</span><span class="st"> </span><span class="dv">10</span> *<span class="st"> </span>paternalage]
all[, maternalage :<span class="er">=</span><span class="st"> </span><span class="dv">10</span> *<span class="st"> </span>maternalage]
all[, age_at_1st_child :<span class="er">=</span><span class="st"> </span><span class="dv">10</span> *<span class="st"> </span>age_at_1st_child]
all[, age_at_last_child :<span class="er">=</span><span class="st"> </span><span class="dv">10</span> *<span class="st"> </span>age_at_last_child]
mean_sd =<span class="st"> </span>function(x) { <span class="kw">paste0</span>(<span class="kw">round</span>(<span class="kw">mean</span>(x, <span class="dt">na.rm=</span>T),<span class="dv">2</span>), <span class="st">" ("</span>,<span class="kw">round</span>(<span class="kw">sd</span>(x,<span class="dt">na.rm=</span>T),<span class="dv">2</span>),<span class="st">")"</span>) }
mean_sd_bin =<span class="st"> </span>function(x) {
m=<span class="st"> </span><span class="kw">mean</span>(x, <span class="dt">na.rm=</span>T)
<span class="kw">sprintf</span>(<span class="st">"%.3f (%.3f)"</span>,m,m*(<span class="dv">1</span>-m))
}
nodot =<span class="st"> </span>function(x) {
<span class="kw">names</span>(x) =<span class="st"> </span>stringr::<span class="kw">str_replace_all</span>(<span class="kw">names</span>(x),stringr::<span class="kw">fixed</span>(<span class="st">"."</span>),<span class="st">" "</span>)
x
}
all[, sex :<span class="er">=</span><span class="st"> </span><span class="kw">factor</span>(<span class="kw">ifelse</span>(male==<span class="dv">1</span>,<span class="st">"male"</span>,<span class="st">"female"</span>))]
all[, reproductive_timespan :<span class="er">=</span><span class="st"> </span>age_at_last_child -<span class="st"> </span>age_at_1st_child]
all =<span class="st"> </span>all[!<span class="kw">is.na</span>(sex), ]
all =<span class="st"> </span><span class="kw">data.frame</span>(all)</code></pre></div>
</div>
<div id="reproductive-timing" class="section level2">
<h2>Reproductive timing</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">demo_mod_swed$Population =<span class="st"> "20th-century Sweden"</span>
demo_mod_swed$lty =<span class="st"> </span><span class="kw">factor</span>(<span class="st">"all"</span>, <span class="dt">levels =</span> <span class="kw">c</span>(<span class="st">"first"</span>,<span class="st">"all"</span>,<span class="st">"last"</span>))
rep_timing_comp =<span class="st"> </span><span class="kw">ggplot</span>(<span class="dt">data =</span> demo_mod_swed) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_line</span>(<span class="kw">aes</span>(<span class="dt">x=</span> Year, <span class="dt">y =</span> first, <span class="dt">colour =</span> Population, <span class="dt">linetype =</span> <span class="st">"first"</span>), <span class="dt">colour =</span> <span class="st">"#8A846C"</span>, <span class="dt">size =</span> <span class="dv">1</span>) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_line</span>(<span class="kw">aes</span>(<span class="dt">x =</span> Year, <span class="dt">y =</span> all, <span class="dt">colour =</span> Population, <span class="dt">linetype =</span> <span class="st">"all"</span>), <span class="dt">size =</span> <span class="dv">1</span>) +
<span class="st"> </span><span class="kw">geom_line</span>(<span class="kw">aes</span>(<span class="dt">x=</span> Year, <span class="dt">y =</span> last, <span class="dt">colour =</span> Population,<span class="dt">linetype =</span> <span class="st">"last"</span>), <span class="dt">colour =</span> <span class="st">"#8A846C"</span>, <span class="dt">size =</span> <span class="dv">1</span>) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_hline</span>(<span class="kw">aes</span>(<span class="dt">yintercept =</span> value, <span class="dt">colour =</span> Population,<span class="dt">linetype =</span> variable), <span class="dt">data =</span> demo_old_swed, <span class="dt">size =</span> <span class="dv">1</span>) +
<span class="st"> </span><span class="kw">geom_text</span>(<span class="kw">aes</span>(<span class="dt">x =</span> <span class="dv">1980</span> +<span class="st"> </span><span class="kw">ifelse</span>(variable ==<span class="st"> "all"</span>, <span class="dv">0</span>, <span class="kw">ifelse</span>(variable ==<span class="st"> "first"</span>, -<span class="dv">33</span>, <span class="dv">0</span>)),
<span class="dt">y =</span> value +<span class="st"> </span><span class="fl">0.3</span>, <span class="dt">colour =</span> Population,
<span class="dt">label =</span> <span class="kw">paste</span>(variable,<span class="st">"births in Sweden 1737-1880"</span>)), <span class="dt">data =</span> demo_old_swed) +<span class="st"> </span>
<span class="st"> </span>pop_colour +<span class="st"> </span>
<span class="st"> </span><span class="kw">scale_linetype_manual</span>(<span class="st">"Birth"</span>, <span class="dt">breaks =</span> <span class="kw">c</span>(<span class="st">"last"</span>, <span class="st">"all"</span>,<span class="st">"first"</span>), <span class="dt">values =</span> <span class="kw">c</span>( <span class="st">"solid"</span>,<span class="st">"dashed"</span>, <span class="st">"dotted"</span>)) +
<span class="st"> </span><span class="kw">geom_text</span>(<span class="kw">aes</span>(<span class="dt">x =</span> Year, <span class="dt">y =</span> all +<span class="st"> </span><span class="fl">0.3</span>,
<span class="dt">label =</span> <span class="kw">ifelse</span>(Year ><span class="st"> </span><span class="dv">1670</span> &<span class="st"> </span>Year %%<span class="st"> </span><span class="dv">15</span> ==<span class="st"> </span><span class="dv">0</span>, <span class="kw">round</span>(all), <span class="ot">NA</span>))) +<span class="st"> </span>
<span class="st"> </span><span class="kw">facet_wrap</span>(~<span class="st"> </span>Parent,<span class="dt">scales =</span> <span class="st">"free_y"</span>) +
<span class="st"> </span>desc_theme +<span class="st"> </span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="st">"Parental age at birth"</span>, <span class="dt">limits =</span> <span class="kw">c</span>(<span class="dv">23</span>,<span class="dv">40</span>)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.box =</span> <span class="st">"horizontal"</span>,
<span class="dt">panel.margin =</span> <span class="kw">unit</span>(<span class="dv">2</span>, <span class="st">"lines"</span>))
rep_timing_comp</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-1-1.png" alt="plot of chunk unnamed-chunk-1" /></p>
</div>
<div id="age-at-first-child" class="section level2">
<h2>Age at first child</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(age_at_1st_child)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population) %>%<span class="st"> </span><span class="kw">na.omit</span>()</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="29%" />
<col width="26%" />
<col width="17%" />
<col width="17%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">25.02 (5.09)</td>
<td align="center">25.85 (4.84)</td>
<td align="center">26.58 (4.44)</td>
<td align="center">23.65 (4.87)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">28.07 (5.6)</td>
<td align="center">28.13 (5.18)</td>
<td align="center">29.29 (5.36)</td>
<td align="center">28.69 (6.01)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">age_at_1st_child =</span> <span class="kw">ifelse</span>(Population ==<span class="st"> "20th-century Sweden"</span>, age_at_1st_child +<span class="st"> </span><span class="kw">runif</span>(<span class="kw">n</span>())-<span class="fl">0.5</span>, age_at_1st_child)) -><span class="st"> </span>all <span class="co"># want smooth density even though we only have ages at year granularity</span>
<span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> age_at_1st_child, <span class="dt">group =</span> <span class="kw">interaction</span>(Population,sex))) +<span class="st"> </span>
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Age at first child"</span>) +
<span class="st"> </span><span class="kw">geom_violin</span>(<span class="kw">aes</span>(<span class="dt">linetype =</span> sex), <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-2-1.png" alt="plot of chunk unnamed-chunk-2" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> age_at_1st_child, <span class="dt">fill =</span> Population)) +
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Density"</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Age at first child"</span>) +
<span class="st"> </span><span class="kw">facet_grid</span>( sex ~<span class="st"> </span>. )+
<span class="st"> </span><span class="kw">geom_density</span>(<span class="dt">alpha =</span> <span class="fl">0.5</span>, <span class="dt">position =</span> <span class="kw">position_identity</span>(), <span class="dt">colour =</span> <span class="ot">NA</span>)+
<span class="st"> </span>mymin +<span class="st"> </span>pop_colour +<span class="st"> </span>pop_fill +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>)) ->
<span class="st"> </span>gg_age_at_1st_child
gg_age_at_1st_child</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-2-2.png" alt="plot of chunk unnamed-chunk-2" /></p>
</div>
<div id="age-at-last-child" class="section level2">
<h2>Age at last child</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(age_at_last_child)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="29%" />
<col width="26%" />
<col width="17%" />
<col width="17%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">30.34 (5.41)</td>
<td align="center">34.79 (7.2)</td>
<td align="center">35.95 (6.34)</td>
<td align="center">37.27 (6.88)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">33.57 (6.14)</td>
<td align="center">37.52 (8.29)</td>
<td align="center">39.61 (7.5)</td>
<td align="center">43.9 (8.95)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">age_at_last_child =</span> <span class="kw">ifelse</span>(Population ==<span class="st"> "20th-century Sweden"</span>, age_at_last_child +<span class="st"> </span><span class="kw">runif</span>(<span class="kw">n</span>())-<span class="fl">0.5</span>, age_at_last_child)) -><span class="st"> </span>all <span class="co"># want smooth density even though we only have ages at year granularity</span>
<span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> age_at_last_child, <span class="dt">group =</span> <span class="kw">interaction</span>(Population,sex))) +<span class="st"> </span>
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Age at last child"</span>) +
<span class="st"> </span><span class="kw">geom_violin</span>(<span class="kw">aes</span>(<span class="dt">linetype =</span> sex), <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-3-1.png" alt="plot of chunk unnamed-chunk-3" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> age_at_last_child, <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Density"</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Age at last child"</span>) +
<span class="st"> </span><span class="kw">facet_grid</span>( sex ~<span class="st"> </span>. )+
<span class="st"> </span><span class="kw">geom_density</span>(<span class="dt">alpha =</span> <span class="fl">0.5</span>, <span class="dt">position =</span> <span class="kw">position_identity</span>(), <span class="dt">colour =</span> <span class="ot">NA</span>)+
<span class="st"> </span>mymin +<span class="st"> </span>pop_colour +<span class="st"> </span>pop_fill +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>)) ->
<span class="st"> </span>gg_age_at_last_child
gg_age_at_last_child</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-3-2.png" alt="plot of chunk unnamed-chunk-3" /></p>
</div>
<div id="reproductive-timespan" class="section level2">
<h2>Reproductive timespan</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(reproductive_timespan)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="29%" />
<col width="26%" />
<col width="17%" />
<col width="17%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">5.32 (4.74)</td>
<td align="center">8.94 (6.94)</td>
<td align="center">9.37 (6.61)</td>
<td align="center">13.62 (7.54)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">5.5 (5.4)</td>
<td align="center">9.39 (7.4)</td>
<td align="center">10.32 (6.97)</td>
<td align="center">15.21 (8.54)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">reproductive_timespan =</span> <span class="kw">ifelse</span>(Population ==<span class="st"> "20th-century Sweden"</span>, reproductive_timespan +<span class="st"> </span><span class="kw">runif</span>(<span class="kw">n</span>())-<span class="fl">0.5</span>, reproductive_timespan)) -><span class="st"> </span>all <span class="co"># want smooth density even though we only have ages at year granularity</span>
all %>%<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">reproductive_timespan =</span> <span class="kw">ifelse</span>(reproductive_timespan<<span class="dv">0</span>,<span class="dv">0</span>,reproductive_timespan)) -><span class="st"> </span>all
<span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> reproductive_timespan, <span class="dt">group =</span> <span class="kw">interaction</span>(Population,sex))) +
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Reproductive timespan"</span>) +
<span class="st"> </span><span class="kw">geom_violin</span>(<span class="kw">aes</span>(<span class="dt">linetype =</span> sex),<span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-4-1.png" alt="plot of chunk unnamed-chunk-4" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> reproductive_timespan, <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Density"</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Reproductive timespan"</span>) +
<span class="st"> </span><span class="kw">facet_grid</span>( sex ~<span class="st"> </span>. )+
<span class="st"> </span><span class="kw">geom_density</span>(<span class="dt">alpha =</span> <span class="fl">0.5</span>, <span class="dt">position =</span> <span class="kw">position_identity</span>(), <span class="dt">colour =</span> <span class="ot">NA</span>)+
<span class="st"> </span>mymin +<span class="st"> </span>pop_colour +<span class="st"> </span>pop_fill +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-4-2.png" alt="plot of chunk unnamed-chunk-4" /></p>
</div>
<div id="paternal-age" class="section level2">
<h2>Paternal age</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(paternalage)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> . ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="5%" />
<col width="30%" />
<col width="27%" />
<col width="18%" />
<col width="18%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">.</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">.</td>
<td align="center">31.84 (7.05)</td>
<td align="center">34.37 (7.69)</td>
<td align="center">35.23 (7.56)</td>
<td align="center">36.33 (8.49)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">paternalage =</span> <span class="kw">ifelse</span>(Population ==<span class="st"> "20th-century Sweden"</span>, paternalage +<span class="st"> </span><span class="kw">runif</span>(<span class="kw">n</span>())-<span class="fl">0.5</span>, paternalage)) -><span class="st"> </span>all <span class="co"># want smooth density even though we only have ages at year granularity</span>
<span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> paternalage)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Paternal age"</span>) +
<span class="st"> </span><span class="kw">geom_violin</span>() +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="fl">0.4</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="fl">0.4</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-5-1.png" alt="plot of chunk unnamed-chunk-5" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> paternalage), <span class="dt">data =</span> all) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="dt">binwidth=</span><span class="dv">1</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Paternal age"</span>) +
<span class="st"> </span><span class="kw">facet_wrap</span>(~<span class="st"> </span>Population, <span class="dt">scale =</span> <span class="st">"free_y"</span>) +<span class="st"> </span>
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-5-2.png" alt="plot of chunk unnamed-chunk-5" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> paternalage, <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Density"</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Paternal age"</span>) +
<span class="st"> </span><span class="kw">geom_density</span>(<span class="dt">alpha =</span> <span class="fl">0.5</span>, <span class="dt">position =</span> <span class="kw">position_identity</span>(), <span class="dt">colour =</span> <span class="ot">NA</span>)+
<span class="st"> </span>mymin +<span class="st"> </span>pop_colour +<span class="st"> </span>pop_fill +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-5-3.png" alt="plot of chunk unnamed-chunk-5" /></p>
</div>
<div id="maternal-age" class="section level2">
<h2>Maternal age</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(maternalage)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> . ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="5%" />
<col width="30%" />
<col width="27%" />
<col width="18%" />
<col width="18%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">.</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">.</td>
<td align="center">28.34 (6.11)</td>
<td align="center">31.54 (6.32)</td>
<td align="center">31.53 (5.88)</td>
<td align="center">29.57 (6.68)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">maternalage =</span> <span class="kw">ifelse</span>(Population ==<span class="st"> "20th-century Sweden"</span>, maternalage +<span class="st"> </span><span class="kw">runif</span>(<span class="kw">n</span>())-<span class="fl">0.5</span>, maternalage)) -><span class="st"> </span>all <span class="co"># want smooth density even though we only have ages at year granularity</span>
<span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> maternalage)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Maternal age"</span>) +
<span class="st"> </span><span class="kw">geom_violin</span>() +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="fl">0.4</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="fl">0.4</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-6-1.png" alt="plot of chunk unnamed-chunk-6" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> maternalage), <span class="dt">data =</span> all) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="dt">binwidth=</span><span class="dv">1</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Maternal age"</span>) +
<span class="st"> </span><span class="kw">facet_wrap</span>(~<span class="st"> </span>Population, <span class="dt">scale =</span> <span class="st">"free_y"</span>) +<span class="st"> </span>
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-6-2.png" alt="plot of chunk unnamed-chunk-6" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> maternalage, <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Density"</span>) +
<span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Maternal age"</span>) +
<span class="st"> </span><span class="kw">geom_density</span>(<span class="dt">alpha =</span> <span class="fl">0.5</span>, <span class="dt">position =</span> <span class="kw">position_identity</span>(), <span class="dt">colour =</span> <span class="ot">NA</span>)+
<span class="st"> </span>mymin +<span class="st"> </span>pop_colour +<span class="st"> </span>pop_fill +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-6-3.png" alt="plot of chunk unnamed-chunk-6" /></p>
</div>
<div id="number-of-children" class="section level2">
<h2>Number of children</h2>
<div id="only-those-who-married" class="section level3">
<h3>only those who married</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(ever_married ==<span class="st"> </span><span class="dv">1</span>) %>%
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(children)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table style="width:97%;">
<colgroup>
<col width="9%" />
<col width="30%" />
<col width="27%" />
<col width="16%" />
<col width="12%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">2.15 (1.11)</td>
<td align="center">3.66 (3.18)</td>
<td align="center">3.66 (2.89)</td>
<td align="center">7.3 (4.6)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">2.17 (1.18)</td>
<td align="center">4.04 (3.22)</td>
<td align="center">4.09 (2.95)</td>
<td align="center">8 (4.97)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(ever_married ==<span class="st"> </span><span class="dv">1</span>) %>%
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> children, <span class="dt">group =</span> <span class="kw">interaction</span>(Population,sex))) +
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">geom_violin</span>(<span class="kw">aes</span>(<span class="dt">linetype =</span> sex),<span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-7-1.png" alt="plot of chunk unnamed-chunk-7" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(ever_married ==<span class="st"> </span><span class="dv">1</span>) %>%
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> children, <span class="dt">y =</span> ..density.., <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="kw">aes</span>(<span class="dt">y =</span> ..density..), <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width =</span> <span class="dv">1</span>),<span class="dt">binwidth=</span><span class="fl">1.1</span>) +
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">breaks =</span> <span class="kw">seq</span>(<span class="dv">0</span>,<span class="dv">25</span>,<span class="dt">by=</span><span class="dv">2</span>)) +
<span class="st"> </span>mymin +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-7-2.png" alt="plot of chunk unnamed-chunk-7" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(ever_married ==<span class="st"> </span><span class="dv">1</span>) %>%
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> children)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="dt">binwidth=</span><span class="dv">1</span>) +
<span class="st"> </span><span class="kw">facet_wrap</span>(~<span class="st"> </span>Population, <span class="dt">scale =</span> <span class="st">"free_y"</span>) +<span class="st"> </span>
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-7-3.png" alt="plot of chunk unnamed-chunk-7" /></p>
</div>
<div id="only-those-who-had-children-at-all" class="section level3">
<h3>only those who had children at all</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(children ><span class="st"> </span><span class="dv">0</span>) %>%
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(children)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="30%" />
<col width="27%" />
<col width="16%" />
<col width="16%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">2.29 (0.95)</td>
<td align="center">4.53 (2.9)</td>
<td align="center">4.41 (2.6)</td>
<td align="center">7.97 (4.2)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">2.33 (1.01)</td>
<td align="center">4.68 (3)</td>
<td align="center">4.76 (2.63)</td>
<td align="center">8.66 (4.58)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(children ><span class="st"> </span><span class="dv">0</span>) %>%
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> children, <span class="dt">group =</span> <span class="kw">interaction</span>(Population,sex))) +
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">geom_violin</span>(<span class="kw">aes</span>(<span class="dt">linetype =</span> sex),<span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-8-1.png" alt="plot of chunk unnamed-chunk-8" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(children ><span class="st"> </span><span class="dv">0</span>) %>%
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> children, <span class="dt">y =</span> ..density.., <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="kw">aes</span>(<span class="dt">y =</span> ..density..), <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width =</span> <span class="dv">1</span>),<span class="dt">binwidth=</span><span class="fl">1.1</span>) +
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">breaks =</span> <span class="kw">seq</span>(<span class="dv">0</span>,<span class="dv">25</span>,<span class="dt">by=</span><span class="dv">2</span>)) +
<span class="st"> </span>mymin +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-8-2.png" alt="plot of chunk unnamed-chunk-8" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(children ><span class="st"> </span><span class="dv">0</span>) %>%
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> children)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="dt">binwidth=</span><span class="dv">1</span>) +
<span class="st"> </span><span class="kw">facet_wrap</span>(~<span class="st"> </span>Population, <span class="dt">scale =</span> <span class="st">"free_y"</span>) +<span class="st"> </span>
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-8-3.png" alt="plot of chunk unnamed-chunk-8" /></p>
</div>
<div id="all-included-including-those-who-died-in-childhood" class="section level3">
<h3>all included, including those who died in childhood</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd</span>(children)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="30%" />
<col width="27%" />
<col width="16%" />
<col width="16%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">1.91 (1.22)</td>
<td align="center">1.04 (2.36)</td>
<td align="center">1.78 (2.72)</td>
<td align="center">3.93 (4.96)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">1.79 (1.32)</td>
<td align="center">0.96 (2.32)</td>
<td align="center">1.62 (2.73)</td>
<td align="center">3.68 (5.22)</td>
</tr>
</tbody>
</table>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> Population, <span class="dt">y =</span> children, <span class="dt">group =</span> <span class="kw">interaction</span>(Population,sex))) +
<span class="st"> </span><span class="kw">coord_flip</span>()+
<span class="st"> </span><span class="kw">geom_violin</span>(<span class="kw">aes</span>(<span class="dt">linetype =</span> sex),<span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_linerange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"median_hilow"</span>, <span class="dt">colour =</span> <span class="st">"#aec05d"</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span><span class="kw">geom_pointrange</span>(<span class="dt">stat =</span> <span class="st">"summary"</span>, <span class="dt">fun.data=</span><span class="st">"mean_cl_boot"</span>,<span class="dt">colour =</span> <span class="st">"#6c92b2"</span>, <span class="dt">size =</span> <span class="dv">1</span>, <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width=</span><span class="dv">1</span>)) +
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-9-1.png" alt="plot of chunk unnamed-chunk-9" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(all, <span class="kw">aes</span>(<span class="dt">x =</span> children, <span class="dt">y =</span> ..density.., <span class="dt">fill =</span> Population)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="kw">aes</span>(<span class="dt">y =</span> ..density..), <span class="dt">position =</span> <span class="kw">position_dodge</span>(<span class="dt">width =</span> <span class="dv">1</span>),<span class="dt">binwidth=</span><span class="fl">1.1</span>) +
<span class="st"> </span>mymin +
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),
<span class="dt">legend.justification =</span> <span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-9-2.png" alt="plot of chunk unnamed-chunk-9" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggplot</span>(<span class="kw">aes</span>(<span class="dt">x =</span> children), <span class="dt">data =</span> all) +<span class="st"> </span>
<span class="st"> </span><span class="kw">geom_histogram</span>(<span class="dt">binwidth=</span><span class="dv">1</span>) +
<span class="st"> </span><span class="kw">facet_wrap</span>(~<span class="st"> </span>Population, <span class="dt">scale =</span> <span class="st">"free_y"</span>) +<span class="st"> </span>
<span class="st"> </span>mymin</code></pre></div>
<p><img src="1_compare_descriptives/figure/unnamed-chunk-9-3.png" alt="plot of chunk unnamed-chunk-9" /></p>
</div>
</div>
<div id="child-mortality" class="section level2">
<h2>Child mortality</h2>
<div id="number-of-children-surviving-their-first-year" class="section level3">
<h3>number of children surviving their first year</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">opts_chunk$<span class="kw">set</span>(<span class="dt">message=</span><span class="ot">FALSE</span>,<span class="dt">warning=</span><span class="ot">FALSE</span>)
<span class="kw">load</span>(<span class="st">"swed2.rdata"</span>)
swed<span class="fl">.2</span>$Population =<span class="st"> "20th-century Sweden"</span>
all =<span class="st"> </span><span class="kw">data.table</span>(all)
all =<span class="st"> </span><span class="kw">rbind</span>(
all[Population !=<span class="st"> "20th-century Sweden"</span>, <span class="kw">list</span>(paternalage, maternalage, age_at_1st_child, age_at_last_child, children, male, Population, survive1y,surviveR)],
swed<span class="fl">.2</span>[byear <<span class="st"> </span><span class="dv">1990</span>, <span class="kw">list</span>(paternalage, maternalage, age_at_1st_child, age_at_last_child, children, male, Population, survive1y,surviveR)]
)
<span class="kw">rm</span>(swed<span class="fl">.2</span>)
all =<span class="st"> </span><span class="kw">setDF</span>(all)
all$sex =<span class="st"> </span><span class="kw">factor</span>(<span class="kw">ifelse</span>(all$male==<span class="dv">1</span>,<span class="st">"male"</span>,<span class="st">"female"</span>))
all$reproductive_timespan =<span class="st"> </span>all$age_at_last_child -<span class="st"> </span>all$age_at_1st_child
all$<span class="st">`</span><span class="dt">Birth outcome</span><span class="st">`</span> =<span class="st"> </span><span class="dv">1</span>+all$survive1y+all$surviveR
all =<span class="st"> </span>all[!<span class="kw">is.na</span>(all$sex), ]
<span class="kw">library</span>(formr)
in_100 =<span class="st"> </span>function(x) {
x =<span class="st"> </span><span class="kw">na.omit</span>(x)
prop =<span class="st"> </span><span class="kw">round</span>(<span class="kw">mean</span>(x) *<span class="st"> </span><span class="dv">100</span>)
<span class="kw">c</span>(<span class="kw">rep</span>(<span class="st">"lived to 1 year"</span>, prop), <span class="kw">rep</span>(<span class="st">"died"</span>, <span class="dv">100</span>-prop))
}
counts_unit =<span class="st"> </span>function(x, <span class="dt">unit =</span> <span class="dv">1000</span>) {
x =<span class="st"> </span><span class="kw">na.omit</span>(x)
bigger_units =<span class="st"> </span><span class="kw">round</span>(<span class="kw">table</span>(x)/unit)
bins =<span class="st"> </span><span class="kw">paste</span>(unit,<span class="kw">names</span>(bigger_units))
<span class="kw">factor</span>(<span class="kw">rep</span>(bins,bigger_units), <span class="dt">levels =</span> bins)
}
qwaffle =<span class="st"> </span>function(Pop, <span class="dt">unit =</span> <span class="dv">1000</span>) {
all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">filter</span>(Population ==<span class="st"> </span>Pop) %>%<span class="st"> </span>
<span class="st"> </span>.[, <span class="st">"Birth outcome"</span>] %>%
<span class="st"> </span><span class="kw">counts_unit</span>(., unit) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">qplot_waffle_tile</span>() +<span class="st"> </span>
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">text =</span> <span class="kw">element_text</span>(<span class="dt">size =</span> <span class="dv">30</span>)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">scale_fill_manual</span>(<span class="kw">paste</span>(unit, <span class="st">"births"</span>),<span class="dt">breaks=</span><span class="dv">1</span>:<span class="dv">3</span>,<span class="dt">labels=</span><span class="kw">c</span>(<span class="st">"births who lived up to 1y"</span>,<span class="st">"births who lived 1y-15y"</span>,<span class="st">"births who lived 15y+"</span>), <span class="dt">values=</span><span class="kw">c</span>(<span class="st">"darkred"</span>,<span class="st">"red"</span>,<span class="st">"gray90"</span>)) +<span class="st"> </span>
<span class="st"> </span><span class="kw">ggtitle</span>(Pop)
}
all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">value =</span> <span class="kw">mean_sd_bin</span>(survive1y)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="28%" />
<col width="25%" />
<col width="18%" />
<col width="18%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">0.995 (0.005)</td>
<td align="center">0.880 (0.105)</td>
<td align="center">0.889 (0.099)</td>
<td align="center">0.793 (0.164)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">0.993 (0.007)</td>
<td align="center">0.859 (0.121)</td>
<td align="center">0.871 (0.113)</td>
<td align="center">0.775 (0.174)</td>
</tr>
</tbody>
</table>
</div>
<div id="number-of-children-surviving-to-15" class="section level3">
<h3>number of children surviving to 15</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(Population, sex) %>%<span class="st"> </span>
<span class="st"> </span><span class="kw">summarise</span>(<span class="dt">surviveR =</span> <span class="kw">mean_sd_bin</span>(surviveR)) %>%
<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">formula =</span> sex ~<span class="st"> </span>Population)</code></pre></div>
<table>
<colgroup>
<col width="9%" />
<col width="28%" />
<col width="25%" />
<col width="18%" />
<col width="18%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">sex</th>
<th align="center">20th-century Sweden</th>
<th align="center">Historical Sweden</th>
<th align="center">Krummhörn</th>
<th align="center">Québec</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">female</td>
<td align="center">0.992 (0.008)</td>
<td align="center">0.724 (0.200)</td>
<td align="center">0.741 (0.192)</td>
<td align="center">0.674 (0.220)</td>
</tr>
<tr class="even">
<td align="center">male</td>
<td align="center">0.990 (0.010)</td>
<td align="center">0.688 (0.215)</td>
<td align="center">0.727 (0.198)</td>
<td align="center">0.668 (0.222)</td>
</tr>
</tbody>
</table>
<div class="row">
<div class="col-md-6">
<p><img src="1_compare_descriptives/figure/unnamed-chunk-12-1.png" alt="plot of chunk unnamed-chunk-12" /></p>
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<div class="col-md-6">
<p><img src="1_compare_descriptives/figure/unnamed-chunk-13-1.png" alt="plot of chunk unnamed-chunk-13" /></p>
</div>
</div>
<div class="row">
<div class="col-md-6">
<p><img src="1_compare_descriptives/figure/unnamed-chunk-14-1.png" alt="plot of chunk unnamed-chunk-14" /></p>
</div>
<div class="col-md-6">
<p><img src="1_compare_descriptives/figure/unnamed-chunk-15-1.png" alt="plot of chunk unnamed-chunk-15" /></p>
</div>
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