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<!DOCTYPE html>
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<title>Québec Data Wrangling</title>
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<div style="width:100%;height:200px;background-image:url('library/header/rpqa.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>
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<div id="rpqa-data-wrangling" class="section level1 tab-content">
<h1>RPQA Data wrangling</h1>
<div id="description-of-data" class="section level2">
<h2>description of data</h2>
<p>Data from the « Registre de la Population du Québec Ancien » of the Programme de Recherche en Démographie Historique, Demography Department, Université de Montréal</p>
<p>January 2012</p>
<p>The data is «Family reconstitution data» based on the systematic transcription of names, place and dates of catholic Baptisms, Marriages and Burials registered in Quebec for the period 1621-1799. Data also include death information of the 1800-1850 for people born before 1750. There are two distinct numerotations: one for couples, one for individuals.</p>
<p>The data is presented in two files:</p>
<p>1- A couple’s file, giving for each couple</p>
<ul>
<li>its id number and the id numbers of the spouses</li>
<li>a date followed by a one digit code (1= marriage date; 2 = marriage contract date, used to replace missing marriage date, contracts being normally signed a few days before the actual marriage; 4 = first mention of the couple in the documents (baptism of a child, remarriage of a spouse, etc.); the couple can have married outside Quebec and migrated in, or it can be a couple formed in Quebec for which the marriage was lost and no contract found to replace)</li>
<li>a place: parish were the marriage was celebrated, “000” if a marriage contract (meaning somewhere in Quebec), or a place outside Quebec or no place at all)</li>
</ul>
<p>2- A file of individuals, giving for each:</p>
<ul>
<li>Id number and id numbers of parents</li>
<li>A code of one’s ethnic origin (for certain immigrants: 911 = German, 795 = born in USA, 901 = British, 794 = “English” (American or British)</li>
<li>A flag identifying Indians</li>
<li>A flag identifying Immigrants (= anyone born outside Quebec; mostly born in France but could be born out West (fur trading country) from Quebec parents…</li>
<li>A flag identifying those having died outside Quebec (out-migrants)</li>
<li>Date of birth, followed by a one digit code (1 = date of birth; 2 = date of baptism, can be used as equivalent to date of birth), = 3 or 4: child died soon after birth, before having received formal baptism; = 5 or 6: approximate year of birth, usually from an age declaration; = 7 missing info</li>
<li>Place of birth: usually parish of baptism</li>
<li>Date of death, followed by a one digit code (1 = date of death; 2 = date of burial; 3 or 4 = date found from another source; 5 = missing info)</li>
<li>Place of death: normally: parish of burial</li>
<li>Flag identifying among those who married those who could sign (= 1) and those who could not (= 2)</li>
</ul>
<p>For all place codes: numbers from 0000 to 6909 correspond to Quebec parishes. 3901 = Montreal; 4501 = Quebec city; 6001 = Trois-Rivieres. They are the only urban areas, with Trois-Rivieres being more a village than a town. The Administration and the merchants and such lived either in Montreal or Quebec. All other parishes are rural. 5 digit codes (10011…) correspond to places in France. 7801 to 789 to areas out West (“Pays-d’en-Haut”, outposts for military reasons and fur trade).</p>
<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$<span class="kw">set</span>(<span class="dt">cache=</span><span class="ot">FALSE</span>,<span class="dt">tidy=</span><span class="ot">FALSE</span>,<span class="dt">autodep=</span><span class="ot">TRUE</span>,<span class="dt">fig.width=</span><span class="dv">12</span>,<span class="dt">fig.height=</span><span class="fl">7.5</span>)
<span class="co"># rpqa_fam</span>
<span class="co"># gebkk 1, 2 gebfk, gebmk. 1 datum genau bekannt, 2 = 15. juni eines jahrs, jahrgenau</span>
<span class="co"># rpqa_unions # alle ehen</span>
<span class="co"># unbekanntes schicksal = Nbirth - infantD/1y - childD/1-15y - adultD/15+</span>
<span class="co">#eheF == 1 und eheM == 1 erstehen</span>
<span class="co"># auswahl_id_f == alle ehen der frau, vv</span>
<span class="co"># ehebekannt: kennen anfang und ende der ehe, bei ehebekannt==1 mehr geburten pro ehe</span>
<span class="co"># 1670-1750</span></code></pre></div>
</div>
</div>
<div id="transforming-data" class="section level2">
<h2>Transforming data</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa.individuals =<span class="st"> </span>foreign::<span class="kw">read.dta</span>(<span class="st">"data/RPQA_29Oct2014/RPQA-family.dta"</span>)
rpqa.unions =<span class="st"> </span>foreign::<span class="kw">read.dta</span>(<span class="st">"data/RPQA_29Oct2014/RPQA-union4.dta"</span>)
rpqa.unions =<span class="st"> </span>rpqa.unions %>%<span class="st"> </span><span class="kw">select</span>(id, id_m, id_f, dat, dateMannee, dateMmois, dateMjour, qualiteDateM, codeLieuM, ehebekannt)
rpqa.unions$idParents =<span class="st"> </span><span class="kw">str_c</span>(rpqa.unions$id_m, <span class="st">'_'</span>, rpqa.unions$id_f)
rpqa.unions$idParents[<span class="kw">which</span>(rpqa.unions$idParents==<span class="st">"NA_NA"</span>)] =<span class="st"> </span><span class="ot">NA</span>
rpqa.individuals$idParents =<span class="st"> </span><span class="kw">str_c</span>(rpqa.individuals$idPere, <span class="st">'_'</span>, rpqa.individuals$idMere)
rpqa.individuals$idParents[<span class="kw">which</span>(rpqa.individuals$idParents==<span class="st">"NA_NA"</span>)] =<span class="st"> </span><span class="ot">NA</span>
rpqa =<span class="st"> </span>rpqa.individuals
rpqa$immigrant =<span class="st"> </span><span class="kw">factor</span>(rpqa$immigrant,<span class="dt">levels=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>),<span class="dt">labels=</span><span class="kw">c</span>(<span class="st">'NO'</span>,<span class="st">''</span>))
rpqa$emigrant =<span class="st"> </span><span class="kw">factor</span>(rpqa$emigrant,<span class="dt">levels=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>),<span class="dt">labels=</span><span class="kw">c</span>(<span class="st">'NO'</span>,<span class="st">''</span>))
rpqa$amerindien =<span class="st"> </span><span class="kw">factor</span>(rpqa$amerindien,<span class="dt">levels=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>),<span class="dt">labels=</span><span class="kw">c</span>(<span class="st">'NO'</span>,<span class="st">''</span>))
rpqa$sexe =<span class="st"> </span>car::<span class="kw">Recode</span>(rpqa$sexe,<span class="st">"'M'='m';'x'=NA"</span>)
rpqa$male =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$sexe ==<span class="st"> 'm'</span>,<span class="dv">1</span>,<span class="dv">0</span>)
rpqa$bdate =<span class="st"> </span><span class="kw">as.Date</span>(rpqa$gebk)
rpqa$byear =<span class="st"> </span><span class="kw">year</span>(rpqa$bdate)
rpqa$ddate =<span class="st"> </span><span class="kw">as.Date</span>(rpqa$todk)
rpqa$dyear =<span class="st"> </span><span class="kw">year</span>(rpqa$ddate)
rpqa$bdate.Father =<span class="st"> </span><span class="kw">as.Date</span>(rpqa$gebm)
rpqa$byear.Father =<span class="st"> </span><span class="kw">year</span>(rpqa$bdate.Father)
rpqa$ddate.Father =<span class="st"> </span><span class="kw">as.Date</span>(rpqa$todm)
rpqa$dyear.Father =<span class="st"> </span><span class="kw">year</span>(rpqa$ddate.Father)
rpqa$bdate.Mother =<span class="st"> </span><span class="kw">as.Date</span>(rpqa$gebf)
rpqa$byear.Mother =<span class="st"> </span><span class="kw">year</span>(rpqa$bdate.Mother)
rpqa$ddate.Mother =<span class="st"> </span><span class="kw">as.Date</span>(rpqa$todf)
rpqa$dyear.Mother =<span class="st"> </span><span class="kw">year</span>(rpqa$ddate.Mother)
rpqa$age.days =<span class="st"> </span><span class="kw">as.numeric</span>(rpqa$ddate -<span class="st"> </span>rpqa$bdate)
rpqa$age.days =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age.days <<span class="st"> </span><span class="dv">0</span>, <span class="dv">0</span>, rpqa$age.days)
<span class="co"># head(data.frame(as.numeric(rpqa$ddate - rpqa$bdate)/365, rpqa$ddate, rpqa$bdate))</span>
rpqa$age.days.Father =<span class="st"> </span><span class="kw">as.numeric</span>(rpqa$ddate.Father -<span class="st"> </span>rpqa$bdate.Father)
rpqa$age.days.Mother =<span class="st"> </span><span class="kw">as.numeric</span>(rpqa$ddate.Mother -<span class="st"> </span>rpqa$bdate.Mother)
rpqa$age =<span class="st"> </span>rpqa$age.days /<span class="st"> </span><span class="dv">365</span>/<span class="dv">10</span>
<span class="kw">qplot</span>(rpqa$age *<span class="st"> </span><span class="dv">10</span>)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/transform.data-1.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$age *<span class="st"> </span><span class="dv">10</span>) +<span class="st"> </span><span class="kw">xlim</span>(<span class="dv">1</span>,<span class="ot">NA</span>)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/transform.data-2.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># qplot(rpqa.individuals$age.days)</span>
rpqa$paternalage =<span class="st"> </span><span class="kw">as.numeric</span>(rpqa$bdate -<span class="st"> </span>rpqa$bdate.Father)/<span class="dv">365</span>/<span class="dv">10</span>
<span class="kw">qplot</span>(rpqa$paternalage *<span class="dv">10</span>)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/transform.data-3.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">head</span>(<span class="kw">sort</span>(rpqa$paternalage *<span class="dv">10</span>),<span class="dv">20</span>)</code></pre></div>
<pre><code>## [1] 14.84 15.05 15.47 15.90 15.92 15.92 16.01 16.01 16.13 16.18 16.30
## [12] 16.33 16.35 16.45 16.45 16.52 16.57 16.60 16.60 16.61</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tail</span>(<span class="kw">sort</span>(rpqa$paternalage *<span class="dv">10</span>),<span class="dv">20</span>)</code></pre></div>
<pre><code>## [1] 78.92 79.98 80.00 80.00 80.76 80.87 81.08 81.18 81.20 81.76 81.91
## [12] 81.99 82.00 82.69 83.04 83.43 83.46 84.79 85.20 85.44</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$maternalage =<span class="st"> </span><span class="kw">as.numeric</span>(rpqa$bdate -<span class="st"> </span>rpqa$bdate.Mother)/<span class="dv">365</span>/<span class="dv">10</span>
<span class="kw">qplot</span>(rpqa$maternalage *<span class="dv">10</span>)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/transform.data-4.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">table</span>(rpqa$age.Mother <<span class="st"> </span>(rpqa$maternalage -<span class="st"> </span><span class="fl">0.1</span>)) <span class="co"># zombie moms</span></code></pre></div>
<pre><code>## < table of extent 0 ></code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">table</span>(rpqa$age.Father <<span class="st"> </span>(rpqa$paternalage -<span class="st"> </span><span class="fl">0.1</span>)) <span class="co"># zombie dads</span></code></pre></div>
<pre><code>## < table of extent 0 ></code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">head</span>(<span class="kw">sort</span>(rpqa$maternalage *<span class="dv">10</span>),<span class="dv">20</span>) <span class="co"># 10y old may be possible</span></code></pre></div>
<pre><code>## [1] 9.953 12.008 12.482 13.008 13.049 13.140 13.156 13.238 13.247 13.247
## [11] 13.299 13.337 13.381 13.405 13.408 13.441 13.458 13.510 13.559 13.581</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tail</span>(<span class="kw">sort</span>(rpqa$maternalage *<span class="dv">10</span>),<span class="dv">40</span>) <span class="co"># but 69y old. something wrong with that.</span></code></pre></div>
<pre><code>## [1] 51.01 51.03 51.04 51.05 51.09 51.16 51.24 51.40 51.56 51.62 51.63
## [12] 51.72 51.72 51.92 52.03 52.12 52.12 52.16 52.35 52.35 52.38 52.49
## [23] 52.85 52.92 53.03 53.23 53.60 54.35 54.73 54.85 54.90 55.03 55.04
## [34] 55.68 55.93 56.04 56.70 57.58 59.60 69.27</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(maternalage*<span class="dv">10</span>,paternalage*<span class="dv">10</span>,<span class="dt">data=</span>rpqa,<span class="dt">geom=</span><span class="st">"jitter"</span>,<span class="dt">alpha=</span><span class="kw">I</span>(<span class="fl">0.1</span>),<span class="dt">shape=</span><span class="kw">I</span>(<span class="st">"."</span>)) +<span class="st"> </span><span class="kw">xlim</span>(<span class="dv">12</span>,<span class="dv">50</span>) +<span class="st"> </span><span class="kw">geom_smooth</span>()</code></pre></div>
<pre><code>## `geom_smooth()` using method = 'gam'</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/transform.data-5.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">cor.test</span>(rpqa$maternalage,rpqa$paternalage)</code></pre></div>
<pre><code>##
## Pearson's product-moment correlation
##
## data: rpqa$maternalage and rpqa$paternalage
## t = 510, df = 390000, p-value <2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.6309 0.6346
## sample estimates:
## cor
## 0.6328</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">xtabs</span>(~<span class="st"> </span><span class="kw">is.na</span>(idMere) +<span class="st"> </span><span class="kw">is.na</span>(idPere), <span class="dt">data =</span> rpqa.individuals)</code></pre></div>
<pre><code>## is.na(idPere)
## is.na(idMere) FALSE TRUE
## FALSE 427016 509
## TRUE 265 31801</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># rpqa = merge(rpqa, spouses, by.x = "idIndividu",by.y="id", all.x =T)</span></code></pre></div>
</div>
<div id="count-kids-and-spouses" class="section level2">
<h2>count kids and spouses</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">count_and_merge =<span class="st"> </span>function(df, what, wt_var) {
counted.dad =<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">data=</span> df[,<span class="kw">c</span>(<span class="st">'idPere'</span>,wt_var)],<span class="dt">formula =</span> idPere ~<span class="st"> </span>.,<span class="dt">fun.aggregate =</span> sum, <span class="dt">na.rm=</span>T,<span class="dt">value.var =</span> wt_var)
counted.mom =<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">data=</span> df[,<span class="kw">c</span>(<span class="st">'idMere'</span>,wt_var)],<span class="dt">formula =</span> idMere ~<span class="st"> </span>.,<span class="dt">fun.aggregate =</span> sum, <span class="dt">na.rm=</span>T, <span class="dt">value.var =</span> wt_var)
<span class="kw">names</span>(counted.dad) =<span class="st"> </span><span class="kw">names</span>(counted.mom) =<span class="st"> </span><span class="kw">c</span>(<span class="st">'idIndividu'</span>,what)
counted =<span class="st"> </span><span class="kw">rbind</span>(counted.dad,counted.mom)
df =<span class="st"> </span><span class="kw">merge</span>(df,counted,<span class="dt">by=</span><span class="st">'idIndividu'</span>,<span class="dt">all.x=</span>T)
df[,what] =<span class="st"> </span>car::<span class="kw">Recode</span>(df[,what],<span class="st">'NA=0'</span>)
df
}
rpqa.unions =<span class="st"> </span>rpqa.unions[<span class="kw">order</span>(rpqa.unions$id_m,rpqa.unions$dat),]
rpqa.unions$marriage.order.Father =<span class="st"> </span><span class="kw">ave</span>(<span class="kw">rep</span>(<span class="ot">NA</span>, <span class="kw">nrow</span>(rpqa.unions)), rpqa.unions$id_m, <span class="dt">FUN =</span> seq_along)
rpqa.unions =<span class="st"> </span>rpqa.unions[<span class="kw">order</span>(rpqa.unions$id_f,rpqa.unions$dat),]
rpqa.unions$marriage.order.Mother =<span class="st"> </span><span class="kw">ave</span>(<span class="kw">rep</span>(<span class="ot">NA</span>, <span class="kw">nrow</span>(rpqa.unions)), rpqa.unions$id_f, <span class="dt">FUN =</span> seq_along)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, rpqa.unions, <span class="dt">by=</span><span class="st">"idParents"</span>,<span class="dt">all.x=</span>T, <span class="dt">suffixes =</span> <span class="kw">c</span>(<span class="st">""</span>, <span class="st">".Parents"</span>))
rpqa$ehebekannt =<span class="st"> </span><span class="kw">ifelse</span>(<span class="kw">is.na</span>(rpqa$ehebekannt), <span class="dv">0</span>, <span class="dv">1</span>)
rpqa$first.marriage =<span class="st"> </span>(rpqa$marriage.order.Mother +<span class="st"> </span>rpqa$marriage.order.Father) ==<span class="st"> </span><span class="dv">2</span>
<span class="kw">table</span>(rpqa$first.marriage,<span class="dt">exclude=</span><span class="ot">NULL</span>)</code></pre></div>
<pre><code>##
## FALSE TRUE <NA>
## 63206 350838 45547</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">count_spouses =<span class="st"> </span>function(df, df2, what, wt_var) {
counted.husband =<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">data=</span> df2[,<span class="kw">c</span>(<span class="st">'id_m'</span>,wt_var)],<span class="dt">formula =</span> id_m ~<span class="st"> </span>.,<span class="dt">fun.aggregate =</span> sum, <span class="dt">na.rm=</span>T, <span class="dt">value.var =</span> wt_var)
counted.wive =<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">data=</span> df2[,<span class="kw">c</span>(<span class="st">'id_f'</span>,wt_var)],<span class="dt">formula =</span> id_f ~<span class="st"> </span>.,<span class="dt">fun.aggregate =</span> sum, <span class="dt">na.rm=</span>T, <span class="dt">value.var =</span> wt_var)
<span class="kw">names</span>(counted.husband) =<span class="st"> </span><span class="kw">names</span>(counted.wive) =<span class="st"> </span><span class="kw">c</span>(<span class="st">'idIndividu'</span>,what)
counted =<span class="st"> </span><span class="kw">rbind</span>(counted.husband,counted.wive)
df =<span class="st"> </span><span class="kw">merge</span>(df,counted,<span class="dt">by=</span><span class="st">'idIndividu'</span>,<span class="dt">all.x=</span>T)
df[,what] =<span class="st"> </span>car::<span class="kw">Recode</span>(df[,what],<span class="st">'NA=0'</span>)
df
}
rpqa$born =<span class="st"> </span><span class="dv">1</span>; rpqa.unions$born =<span class="st"> </span><span class="dv">1</span>
rpqa =<span class="st"> </span><span class="kw">count_spouses</span>(rpqa,rpqa.unions, <span class="st">'spouses'</span>, <span class="st">"born"</span>)
rpqa$survive1d =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age.days ><span class="st"> </span><span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">0</span>)
rpqa$survive1m =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age.days ><span class="st"> </span><span class="dv">28</span>, <span class="dv">1</span>, <span class="dv">0</span>)
rpqa$dead1d =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age.days <=<span class="st"> </span><span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">0</span>)
rpqa$dead1m =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age.days ><span class="st"> </span><span class="dv">28</span>, <span class="dv">0</span>, <span class="dv">1</span>)
rpqa$dead1y =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age ><span class="st"> </span><span class="fl">0.1</span>, <span class="dv">0</span>, <span class="dv">1</span>)
rpqa$dead5y =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age ><span class="st"> </span><span class="fl">0.5</span>, <span class="dv">0</span>, <span class="dv">1</span>)
rpqa$deadR =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age ><span class="st"> </span><span class="fl">1.5</span>, <span class="dv">0</span>, <span class="dv">1</span>)
rpqa$survive5y =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age ><span class="st"> </span><span class="fl">0.5</span>, <span class="dv">1</span>, <span class="dv">0</span>)
rpqa$survive1y =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age ><span class="st"> </span><span class="fl">0.1</span>, <span class="dv">1</span>, <span class="dv">0</span>)
rpqa$surviveR =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$age ><span class="st"> </span><span class="fl">1.5</span>, <span class="dv">1</span>, <span class="dv">0</span>)
<span class="co"># rpqa$survive1m = car::Recode(rpqa$survive1m, 'NA=0')</span>
<span class="kw">table</span>(rpqa$survive1m,<span class="dt">exclude=</span><span class="ot">NULL</span>)</code></pre></div>
<pre><code>##
## 0 1 <NA>
## 41499 198139 219953</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children'</span>, <span class="dt">wt_var =</span> <span class="st">"born"</span>)
rpqa$children.per.spouse =<span class="st"> </span>rpqa$children/rpqa$spouses
rpqa$children.per.spouse[<span class="kw">which</span>(rpqa$spouses==<span class="dv">0</span>)] =<span class="st"> </span><span class="ot">NA</span>
<span class="kw">qplot</span>(rpqa$children.per.spouse)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-1.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># well we know that people who reproduced or married usually made 15</span>
changeNAto1 =<span class="st"> </span>function(x) { <span class="kw">colwise</span>(function(x) { <span class="kw">ifelse</span>(<span class="kw">is.na</span>(x), <span class="dv">1</span>, x)})(x) }
rpqa[<span class="kw">which</span>(rpqa$children><span class="dv">0</span> |<span class="st"> </span>rpqa$spouses><span class="dv">0</span>), <span class="kw">c</span>(<span class="st">'surviveR'</span>, <span class="st">'survive1y'</span>, <span class="st">'survive1m'</span>, <span class="st">'survive1d'</span>)] =<span class="st"> </span><span class="kw">changeNAto1</span>(rpqa[<span class="kw">which</span>(rpqa$children><span class="dv">0</span> |<span class="st"> </span>rpqa$spouses><span class="dv">0</span>), <span class="kw">c</span>(<span class="st">'surviveR'</span>, <span class="st">'survive1y'</span>, <span class="st">'survive1m'</span>, <span class="st">'survive1d'</span>)])
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children.dead1d'</span>, <span class="dt">wt_var =</span> <span class="st">'dead1d'</span>)
rpqa$children.surviving1d =<span class="st"> </span>rpqa$children -<span class="st"> </span>rpqa$children.dead1d
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children.dead1m'</span>, <span class="dt">wt_var =</span> <span class="st">'dead1m'</span>)
rpqa$children.surviving1m =<span class="st"> </span>rpqa$children -<span class="st"> </span>rpqa$children.dead1m
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children.dead1y'</span>, <span class="dt">wt_var =</span> <span class="st">'dead1y'</span>)
rpqa$children.surviving1y =<span class="st"> </span>rpqa$children -<span class="st"> </span>rpqa$children.dead1y
<span class="co"># xtabs(~ rpqa$children.dead1y + rpqa$NinfantD, exclude = NULL, na.action = na.pass)</span>
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children.dead5y'</span>, <span class="dt">wt_var =</span> <span class="st">'dead5y'</span>)
rpqa$children.surviving5y =<span class="st"> </span>rpqa$children -<span class="st"> </span>rpqa$children.dead5y
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children.deadR'</span>, <span class="dt">wt_var =</span> <span class="st">'deadR'</span>)
rpqa$children.survivingR =<span class="st"> </span>rpqa$children -<span class="st"> </span>rpqa$children.deadR
changeNAto0 =<span class="st"> </span>function(x) { <span class="kw">ifelse</span>(<span class="kw">is.na</span>(x), <span class="dv">0</span>, x) }
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children.spouses'</span>, <span class="dt">wt_var =</span> <span class="st">'spouses'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.per.spouse'</span>, <span class="dt">wt_var =</span> <span class="st">'children.per.spouse'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren'</span>,<span class="dt">wt_var=</span><span class="st">'children'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.surviving1d'</span>, <span class="dt">wt_var =</span> <span class="st">'children.surviving1d'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.surviving1m'</span>, <span class="dt">wt_var =</span> <span class="st">'children.surviving1m'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.surviving1y'</span>, <span class="dt">wt_var =</span> <span class="st">'children.surviving1y'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.surviving5y'</span>, <span class="dt">wt_var =</span> <span class="st">'children.surviving5y'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.survivingR'</span>, <span class="dt">wt_var =</span> <span class="st">'children.survivingR'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'grandchildren.dead1m'</span>, <span class="dt">wt_var =</span> <span class="st">'children.dead1m'</span>)
<span class="kw">xtabs</span>(~<span class="st"> </span>(grandchildren><span class="dv">0</span>) +(children><span class="dv">0</span>) +<span class="st"> </span>(spouses><span class="dv">0</span>) +<span class="st"> </span>surviveR,<span class="dt">data=</span>rpqa,<span class="dt">exclude=</span><span class="ot">NULL</span>, <span class="dt">na.action=</span> na.pass)</code></pre></div>
<pre><code>## , , spouses > 0 = FALSE, surviveR = 0
##
## children > 0
## grandchildren > 0 FALSE TRUE
## FALSE 137531 0
## TRUE 0 0
##
## , , spouses > 0 = TRUE, surviveR = 0
##
## children > 0
## grandchildren > 0 FALSE TRUE
## FALSE 3 2
## TRUE 0 0
##
## , , spouses > 0 = FALSE, surviveR = 1
##
## children > 0
## grandchildren > 0 FALSE TRUE
## FALSE 17753 4233
## TRUE 0 16266
##
## , , spouses > 0 = TRUE, surviveR = 1
##
## children > 0
## grandchildren > 0 FALSE TRUE
## FALSE 11499 58260
## TRUE 0 57547
##
## , , spouses > 0 = FALSE, surviveR = NA
##
## children > 0
## grandchildren > 0 FALSE TRUE
## FALSE 156497 0
## TRUE 0 0
##
## , , spouses > 0 = TRUE, surviveR = NA
##
## children > 0
## grandchildren > 0 FALSE TRUE
## FALSE 0 0
## TRUE 0 0</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">counted.parents =<span class="st"> </span><span class="kw">dcast</span>(<span class="dt">data=</span> rpqa[,<span class="kw">c</span>(<span class="st">'idParents'</span>,<span class="st">"born"</span>)],<span class="dt">formula =</span> idParents ~<span class="st"> </span>.,<span class="dt">fun.aggregate =</span> sum, <span class="dt">na.rm=</span>T, <span class="dt">value.var =</span> <span class="st">"born"</span>)
<span class="kw">names</span>(counted.parents) =<span class="st"> </span><span class="kw">c</span>(<span class="st">'idParents'</span>,<span class="st">"children"</span>)
rpqa.unions =<span class="st"> </span><span class="kw">merge</span>(rpqa.unions, counted.parents,<span class="dt">by=</span><span class="st">"idParents"</span>,<span class="dt">all.x=</span>T) <span class="co"># find childless marriages</span>
<span class="kw">table</span>(rpqa.unions$children,<span class="dt">exclude=</span><span class="ot">NULL</span>)</code></pre></div>
<pre><code>##
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
## 7252 6086 5806 5378 5093 4738 4518 4310 4193 3999 3524 2818 2076 1493 990
## 16 17 18 19 20 21 22 23 <NA>
## 623 342 205 90 45 16 4 6 9535</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa.unions =<span class="st"> </span>rpqa.unions[<span class="kw">which</span>(rpqa.unions$children ><span class="st"> </span><span class="dv">0</span>), ]
rpqa.unions =<span class="st"> </span>rpqa.unions[<span class="kw">order</span>(rpqa.unions$id_m,rpqa.unions$dat),]
rpqa.unions$fertile.marriage.order.Father =<span class="st"> </span><span class="kw">ave</span>(<span class="kw">rep</span>(<span class="ot">NA</span>, <span class="kw">nrow</span>(rpqa.unions)), rpqa.unions$id_m, <span class="dt">FUN =</span> seq_along)
rpqa.unions =<span class="st"> </span>rpqa.unions[<span class="kw">order</span>(rpqa.unions$id_f,rpqa.unions$dat),]
rpqa.unions$fertile.marriage.order.Mother =<span class="st"> </span><span class="kw">ave</span>(<span class="kw">rep</span>(<span class="ot">NA</span>, <span class="kw">nrow</span>(rpqa.unions)), rpqa.unions$id_f, <span class="dt">FUN =</span> seq_along)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, rpqa.unions[,<span class="kw">c</span>(<span class="st">'idParents'</span>,<span class="st">'fertile.marriage.order.Mother'</span>,<span class="st">'fertile.marriage.order.Father'</span>),],<span class="dt">by=</span><span class="st">"idParents"</span>,<span class="dt">all.x=</span>T)
rpqa$first.fertile.marriage =<span class="st"> </span>(rpqa$fertile.marriage.order.Mother +<span class="st"> </span>rpqa$fertile.marriage.order.Father) ==<span class="st"> </span><span class="dv">2</span>
<span class="kw">table</span>(rpqa$first.fertile.marriage,<span class="dt">exclude=</span><span class="ot">NULL</span>)</code></pre></div>
<pre><code>##
## FALSE TRUE <NA>
## 56874 357170 45547</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$children)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-2.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa[<span class="kw">which</span>(rpqa$age ><span class="st"> </span><span class="fl">1.5</span>),]$children )</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-3.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$grandchildren)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-4.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa[<span class="kw">which</span>(rpqa$age ><span class="st"> </span><span class="fl">1.5</span>),]$grandchildren )</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-5.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$children.surviving1m)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-6.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$children.dead1m)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-7.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$spouses)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-8.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(children,children.surviving1m, <span class="dt">data=</span>rpqa,<span class="dt">geom=</span><span class="st">"jitter"</span>,<span class="dt">alpha=</span><span class="kw">I</span>(<span class="fl">0.02</span>))</code></pre></div>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-9.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(children.surviving1d, children.surviving1m, <span class="dt">data=</span>rpqa,<span class="dt">geom=</span><span class="st">"jitter"</span>,<span class="dt">alpha=</span><span class="kw">I</span>(<span class="fl">0.2</span>))</code></pre></div>
<p><img src="0_rpqa_massage_files/figure-html/kids.and.spouses-10.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa =<span class="st"> </span>rpqa[<span class="kw">order</span>(rpqa$idParents),]
rpqa$paternalage.mean =<span class="st"> </span><span class="kw">ave</span>(rpqa$paternalage ,rpqa$idParents,<span class="dt">FUN=</span> function(x) { <span class="kw">mean</span>(x,<span class="dt">na.rm=</span>T) } )
rpqa$paternalage.diff =<span class="st"> </span>rpqa$paternalage -<span class="st"> </span>rpqa$paternalage.mean
rpqa$maternalage.mean =<span class="st"> </span><span class="kw">ave</span>(rpqa$maternalage,rpqa$idMere,<span class="dt">FUN=</span> function(x) { <span class="kw">mean</span>(x,<span class="dt">na.rm=</span>T) } )
rpqa$maternalage.diff =<span class="st"> </span>rpqa$maternalage -<span class="st"> </span>rpqa$maternalage.mean
rpqa$urban =<span class="st"> </span><span class="kw">factor</span>(rpqa$codeLieuNaiss %in%<span class="st"> </span><span class="kw">c</span>(<span class="dv">3901</span>, <span class="dv">4501</span>),<span class="kw">c</span>(<span class="st">"FALSE"</span>,<span class="st">"TRUE"</span>),<span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>))
<span class="kw">table</span>(rpqa$urban)</code></pre></div>
<pre><code>##
## 0 1
## 400287 59304</code></pre>
</div>
<div id="calculate-predictors" class="section level2">
<h2>calculate predictors</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa =<span class="st"> </span>rpqa[<span class="kw">order</span>(rpqa$idParents,rpqa$bdate), ]
rpqa <-<span class="st"> </span><span class="kw">transform</span>(rpqa, <span class="dt">siblings =</span> <span class="kw">ave</span>(<span class="kw">rep</span>(<span class="ot">NA</span>, <span class="kw">nrow</span>(rpqa)), rpqa$idParents, <span class="dt">FUN =</span> length)-<span class="dv">1</span>) <span class="co"># sibling count</span>
rpqa <-<span class="st"> </span><span class="kw">transform</span>(rpqa, <span class="dt">birthorder =</span> <span class="kw">ave</span>(<span class="kw">rep</span>(<span class="ot">NA</span>, <span class="kw">nrow</span>(rpqa)), rpqa$idParents, <span class="dt">FUN =</span> seq_along)) <span class="co"># old trick to get birth order, don't know what this does to those with missings for father though</span>
<span class="kw">qplot</span>(rpqa$birthorder)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-1.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$younger_siblings =<span class="st"> </span>rpqa$siblings +<span class="st"> </span><span class="dv">1</span> -<span class="st"> </span>rpqa$birthorder
<span class="kw">table</span>(rpqa$younger_siblings)</code></pre></div>
<pre><code>##
## 0 1 2 3 4 5 6 7 8 9 10 11
## 74394 57339 50743 44738 39259 34103 29321 24777 20447 16242 12237 8710
## 12 13 14 15 16 17 18 19 20 21 22
## 5891 3815 2321 1331 708 366 161 71 26 10 6</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">table</span>( rpqa$qualiteDateNaiss ==<span class="st"> </span><span class="dv">3</span> ) <span class="co"># born dead or died before baptism</span></code></pre></div>
<pre><code>##
## FALSE TRUE
## 450756 8835</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$age[rpqa$qualiteDateNaiss ==<span class="st"> </span><span class="dv">3</span>] *<span class="dv">10</span>)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-2.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$age[rpqa$qualiteDateNaiss !=<span class="st"> </span><span class="dv">3</span>] *<span class="dv">10</span>) +<span class="st"> </span><span class="kw">xlim</span>(<span class="dv">0</span>,<span class="dv">1</span>)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-3.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$age.years =<span class="st"> </span>rpqa$dyear-<span class="st"> </span>rpqa$byear
rpqa =<span class="st"> </span>rpqa[<span class="kw">order</span>(rpqa$idParents,rpqa$birthorder), ]
rpqa$nr.siblings =<span class="st"> </span><span class="kw">ave</span>(rpqa$born,rpqa$idParents, <span class="dt">FUN =</span> function(x) { <span class="kw">sum</span>(x,<span class="dt">na.rm=</span>T) } ) -<span class="dv">1</span> <span class="co"># dont count self</span>
<span class="kw">qplot</span>(rpqa$nr.siblings,<span class="dt">binwidth=</span><span class="dv">1</span>)</code></pre></div>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-4.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$nr.dead.siblings1m =<span class="st"> </span><span class="kw">ave</span>(rpqa$dead1m,rpqa$idParents,<span class="dt">FUN=</span> function(x) { <span class="kw">sum</span>(x,<span class="dt">na.rm=</span>T) } ) -<span class="st"> </span>rpqa$dead1m
<span class="kw">qplot</span>(rpqa$nr.dead.siblings1m,<span class="dt">binwidth=</span><span class="dv">1</span>)</code></pre></div>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-5.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$infant.death.cluster =<span class="st"> </span>rpqa$nr.dead.siblings1m/rpqa$nr.siblings <span class="co"># dont count self</span>
<span class="kw">qplot</span>(rpqa$infant.death.cluster)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-6.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa[<span class="kw">which</span>(rpqa$nr.siblings><span class="dv">1</span>),]$infant.death.cluster)</code></pre></div>
<pre><code>## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.</code></pre>
<p><img src="0_rpqa_massage_files/figure-html/add.some.indicators-7.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">lag<span class="fl">.0</span> =<span class="st"> </span>function(x) {
if(<span class="kw">length</span>(x)==<span class="dv">1</span>) <span class="dv">0</span>
else <span class="kw">c</span>(<span class="dv">0</span>,x[ <span class="dv">1</span>:(<span class="kw">length</span>(x)-<span class="dv">1</span>)])
}
inv.lag<span class="fl">.0</span> =<span class="st"> </span>function(x) {
if(<span class="kw">length</span>(x)==<span class="dv">1</span>) <span class="dv">0</span>
else <span class="kw">c</span>(x[ <span class="dv">2</span>:<span class="kw">length</span>(x)],<span class="dv">0</span>)
}
rpqa =<span class="st"> </span><span class="kw">transform</span>(rpqa, <span class="dt">older.sib.made.15y =</span> <span class="kw">ave</span>(surviveR, idPere, <span class="dt">FUN =</span> lag<span class="fl">.0</span>))
rpqa =<span class="st"> </span><span class="kw">transform</span>(rpqa, <span class="dt">younger.sib.made.15y =</span> <span class="kw">ave</span>(surviveR, idPere, <span class="dt">FUN =</span> inv.lag<span class="fl">.0</span>))
rpqa$older_siblings =<span class="st"> </span><span class="kw">factor</span>(<span class="kw">ifelse</span>((rpqa$birthorder -<span class="st"> </span><span class="dv">1</span>) ><span class="st"> </span><span class="dv">4</span>,<span class="st">"5+"</span>, rpqa$birthorder -<span class="st"> </span><span class="dv">1</span>))
rpqa$last_born =<span class="st"> </span><span class="kw">ifelse</span>(rpqa$birthorder ==<span class="st"> </span>rpqa$nr.siblings, <span class="dv">1</span>, <span class="dv">0</span>)</code></pre></div>
</div>
<div id="get-grandparents" class="section level2">
<h2>Get grandparents</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">grandparents =<span class="st"> </span>rpqa[, <span class="kw">c</span>(<span class="st">'idIndividu'</span>,<span class="st">'idPere'</span>,<span class="st">'idMere'</span>, <span class="st">'paternalage'</span>, <span class="st">'maternalage'</span>)]
<span class="kw">names</span>(grandparents) =<span class="st"> </span><span class="kw">c</span>(<span class="st">'idMere'</span>, <span class="st">'idMaternalGrandfather'</span>, <span class="st">'idMaternalGrandmother'</span>, <span class="st">'maternal.grandpaternalage'</span>, <span class="st">'maternal.grandmaternalage'</span>)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, grandparents, <span class="dt">by =</span> <span class="st">"idMere"</span>, <span class="dt">all.x =</span>T)
<span class="kw">names</span>(grandparents) =<span class="st"> </span><span class="kw">c</span>(<span class="st">'idPere'</span>, <span class="st">'idPaternalGrandfather'</span>, <span class="st">'idPaternalGrandmother'</span>, <span class="st">'paternal.grandpaternalage'</span>, <span class="st">'paternal.grandmaternalage'</span>)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, grandparents, <span class="dt">by =</span> <span class="st">"idPere"</span>, <span class="dt">all.x =</span>T)
rpqa$idPaternalGrandparents =<span class="st"> </span><span class="kw">paste</span>(rpqa$idPaternalGrandfather, rpqa$idPaternalGrandmother)
rpqa$idMaternalGrandparents =<span class="st"> </span><span class="kw">paste</span>(rpqa$idMaternalGrandfather, rpqa$idMaternalGrandmother)
grandparent =<span class="st"> </span>rpqa[, <span class="kw">c</span>(<span class="st">'idIndividu'</span>, <span class="st">'ddate'</span>, <span class="st">'bdate'</span>)]
<span class="kw">names</span>(grandparent) =<span class="st"> </span><span class="kw">c</span>(<span class="st">"idPaternalGrandfather"</span>, <span class="st">"ddate.paternalGrandfather"</span>, <span class="st">"bdate.paternalGrandfather"</span>)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, grandparent, <span class="dt">by =</span> <span class="st">"idPaternalGrandfather"</span>, <span class="dt">all.x =</span> T)
<span class="kw">names</span>(grandparent) =<span class="st"> </span><span class="kw">c</span>(<span class="st">"idMaternalGrandfather"</span>, <span class="st">"ddate.maternalGrandfather"</span>, <span class="st">"bdate.maternalGrandfather"</span>)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, grandparent, <span class="dt">by =</span> <span class="st">"idMaternalGrandfather"</span>, <span class="dt">all.x =</span> T)
<span class="kw">names</span>(grandparent) =<span class="st"> </span><span class="kw">c</span>(<span class="st">"idPaternalGrandmother"</span>, <span class="st">"ddate.paternalGrandmother"</span>, <span class="st">"bdate.paternalGrandmother"</span>)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, grandparent, <span class="dt">by =</span> <span class="st">"idPaternalGrandmother"</span>, <span class="dt">all.x =</span> T)
<span class="kw">names</span>(grandparent) =<span class="st"> </span><span class="kw">c</span>(<span class="st">"idMaternalGrandmother"</span>, <span class="st">"ddate.maternalGrandmother"</span>, <span class="st">"bdate.maternalGrandmother"</span>)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, grandparent, <span class="dt">by =</span> <span class="st">"idMaternalGrandmother"</span>, <span class="dt">all.x =</span> T)
<span class="kw">library</span>(lubridate)
rpqa$maternalgrandfatherloss =<span class="st"> </span><span class="kw">factor</span>(rpqa$bdate +<span class="st"> </span><span class="kw">years</span>(<span class="dv">5</span>) ><span class="st"> </span>rpqa$ddate.maternalGrandfather,<span class="dt">exclude =</span> <span class="ot">NULL</span>)
rpqa$paternalgrandfatherloss =<span class="st"> </span><span class="kw">factor</span>(rpqa$bdate +<span class="st"> </span><span class="kw">years</span>(<span class="dv">5</span>) ><span class="st"> </span>rpqa$ddate.paternalGrandfather,<span class="dt">exclude =</span> <span class="ot">NULL</span>)
rpqa$maternalgrandmotherloss =<span class="st"> </span><span class="kw">factor</span>(rpqa$bdate +<span class="st"> </span><span class="kw">years</span>(<span class="dv">5</span>) ><span class="st"> </span>rpqa$ddate.maternalGrandmother,<span class="dt">exclude =</span> <span class="ot">NULL</span>)
rpqa$paternalgrandmotherloss =<span class="st"> </span><span class="kw">factor</span>(rpqa$bdate +<span class="st"> </span><span class="kw">years</span>(<span class="dv">5</span>) ><span class="st"> </span>rpqa$ddate.paternalGrandmother,<span class="dt">exclude =</span> <span class="ot">NULL</span>)</code></pre></div>
</div>
<div id="compute-high-level-predictors" class="section level2">
<h2>compute high-level predictors</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$born =<span class="st"> </span><span class="ot">NULL</span> <span class="co"># was just an aid</span>
rpqa$byear.years =<span class="st"> </span><span class="kw">year</span>(rpqa$bdate)
rpqa$dyear.years =<span class="st"> </span><span class="kw">year</span>(rpqa$ddate)
rpqa =<span class="st"> </span>rpqa %>%
<span class="st"> </span><span class="kw">group_by</span>(idParents) %>%
<span class="st"> </span><span class="kw">mutate</span>(
<span class="dt">younger_sibs_ad_5y =</span> <span class="kw">younger_sibs_alive_and_dependent</span>(<span class="dt">survive5y=</span>survive5y, <span class="dt">byear=</span>byear.years, <span class="dt">dyear=</span>dyear.years) ,
<span class="dt">older_sibs_ad_5y =</span> <span class="kw">older_sibs_alive_and_dependent</span>(<span class="dt">survive5y=</span>survive5y, <span class="dt">byear=</span>byear.years, <span class="dt">dyear=</span>dyear.years),
<span class="dt">dependent_sibs_f5y =</span> <span class="kw">dependent_sibs_f5y</span>(<span class="dt">survive1y=</span>survive1y, <span class="dt">byear=</span>byear, <span class="dt">dyear=</span>dyear)
) %>%<span class="st"> </span><span class="kw">data.table</span>()</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">min_na =<span class="st"> </span>function(x) { <span class="kw">ifelse</span>(<span class="kw">all</span>(<span class="kw">is.na</span>(x)), <span class="ot">NA</span>, <span class="kw">min</span>(x, <span class="dt">na.rm=</span>T) ) }
max_na =<span class="st"> </span>function(x) { <span class="kw">ifelse</span>(<span class="kw">all</span>(<span class="kw">is.na</span>(x)), <span class="ot">NA</span>, <span class="kw">max</span>(x, <span class="dt">na.rm=</span>T) ) }
rpqa[, paternalage_at_1st_sib :<span class="er">=</span><span class="st"> </span><span class="kw">ave</span>(paternalage, idPere, <span class="dt">FUN =</span> min_na)]
rpqa[, paternalage_at_last_sib :<span class="er">=</span><span class="st"> </span><span class="kw">ave</span>(paternalage, idPere, <span class="dt">FUN =</span> max_na)]
rpqa[, maternalage_at_1st_sib :<span class="er">=</span><span class="st"> </span><span class="kw">ave</span>(maternalage, idMere, <span class="dt">FUN =</span> min_na)]
rpqa[, maternalage_at_last_sib :<span class="er">=</span><span class="st"> </span><span class="kw">ave</span>(maternalage, idMere, <span class="dt">FUN =</span> max_na)]
fathers =<span class="st"> </span>rpqa[!<span class="kw">duplicated</span>(idPere), <span class="kw">list</span>(idPere, paternalage_at_1st_sib, paternalage_at_last_sib)]
<span class="kw">names</span>(fathers) =<span class="st"> </span><span class="kw">c</span>(<span class="st">"idIndividu"</span>,<span class="st">"age_at_1st_child"</span>, <span class="st">"age_at_last_child"</span>)
mothers =<span class="st"> </span>rpqa[!<span class="kw">duplicated</span>(idMere), <span class="kw">list</span>(idMere, maternalage_at_1st_sib, maternalage_at_last_sib)]
<span class="kw">names</span>(mothers) =<span class="st"> </span><span class="kw">c</span>(<span class="st">"idIndividu"</span>,<span class="st">"age_at_1st_child"</span>, <span class="st">"age_at_last_child"</span>)
parents =<span class="st"> </span><span class="kw">rbind</span>(fathers, mothers)
rpqa =<span class="st"> </span><span class="kw">merge</span>(rpqa, parents, <span class="dt">by =</span> <span class="st">"idIndividu"</span>, <span class="dt">all.x =</span> T)
rpqa$maternalage_c =<span class="st"> </span>QuantPsyc::<span class="kw">meanCenter</span>(rpqa$maternalage)
rpqa$paternalage_c =<span class="st"> </span>QuantPsyc::<span class="kw">meanCenter</span>(rpqa$paternalage)
rpqa$nr.siblings =<span class="st"> </span>rpqa$siblings
rpqa %>%<span class="st"> </span>
<span class="kw">mutate</span>(<span class="dt">maternal_loss_age =</span> dyear.Mother -<span class="st"> </span>byear
,<span class="dt">maternal_loss_age =</span> <span class="kw">as.numeric</span>(<span class="kw">ifelse</span>(maternal_loss_age >=<span class="st"> </span>-<span class="dv">1</span> &<span class="st"> </span>maternal_loss_age <<span class="st"> </span><span class="dv">0</span>, <span class="dv">0</span>, maternal_loss_age))
,<span class="dt">maternal_loss =</span> <span class="kw">as.character</span>(<span class="kw">cut</span>(maternal_loss_age, <span class="dt">breaks =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>,<span class="dv">5</span>,<span class="dv">10</span>,<span class="dv">15</span>,<span class="dv">20</span>,<span class="dv">25</span>,<span class="dv">30</span>,<span class="dv">35</span>,<span class="dv">40</span>,<span class="dv">45</span>), <span class="dt">include.lowest =</span> T ))
,<span class="dt">maternal_loss =</span> <span class="kw">ifelse</span>( maternal_loss_age >=<span class="st"> </span><span class="dv">45</span>, <span class="st">"later"</span>, maternal_loss)
,<span class="dt">maternal_loss =</span> <span class="kw">ifelse</span>(<span class="kw">is.na</span>(maternal_loss_age) |<span class="st"> </span>maternal_loss_age <<span class="st"> </span><span class="dv">0</span>, <span class="st">"unclear"</span>, maternal_loss)
,<span class="dt">maternal_loss =</span> <span class="kw">factor</span>(maternal_loss, <span class="dt">levels =</span> <span class="kw">c</span>(<span class="st">"later"</span>,<span class="st">"[0,1]"</span>, <span class="st">"(1,5]"</span>, <span class="st">"(5,10]"</span>, <span class="st">"(10,15]"</span>, <span class="st">"(15,20]"</span>, <span class="st">"(20,25]"</span>, <span class="st">"(25,30]"</span>, <span class="st">"(30,35]"</span>, <span class="st">"(35,40]"</span>, <span class="st">"(40,45]"</span>, <span class="st">"unclear"</span>))
,<span class="dt">paternal_loss_age =</span> dyear.Father -<span class="st"> </span>byear
,<span class="dt">paternal_loss_age =</span> <span class="kw">as.numeric</span>(<span class="kw">ifelse</span>(paternal_loss_age >=<span class="st"> </span>-<span class="dv">1</span> &<span class="st"> </span>paternal_loss_age <<span class="st"> </span><span class="dv">0</span>, <span class="dv">0</span>, paternal_loss_age))
,<span class="dt">paternal_loss =</span> <span class="kw">as.character</span>(<span class="kw">cut</span>(paternal_loss_age, <span class="dt">breaks =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>,<span class="dv">5</span>,<span class="dv">10</span>,<span class="dv">15</span>,<span class="dv">20</span>,<span class="dv">25</span>,<span class="dv">30</span>,<span class="dv">35</span>,<span class="dv">40</span>,<span class="dv">45</span>), <span class="dt">include.lowest =</span> T ))
,<span class="dt">paternal_loss =</span> <span class="kw">ifelse</span>( paternal_loss_age >=<span class="st"> </span><span class="dv">45</span>, <span class="st">"later"</span>, paternal_loss)
,<span class="dt">paternal_loss =</span> <span class="kw">ifelse</span>(<span class="kw">is.na</span>(paternal_loss_age) |<span class="st"> </span>paternal_loss_age <<span class="st"> </span><span class="dv">0</span>, <span class="st">"unclear"</span>, paternal_loss)
,<span class="dt">paternal_loss =</span> <span class="kw">factor</span>(paternal_loss, <span class="dt">levels =</span> <span class="kw">c</span>(<span class="st">"later"</span>,<span class="st">"[0,1]"</span>, <span class="st">"(1,5]"</span>, <span class="st">"(5,10]"</span>, <span class="st">"(10,15]"</span>, <span class="st">"(15,20]"</span>, <span class="st">"(20,25]"</span>, <span class="st">"(25,30]"</span>, <span class="st">"(30,35]"</span>, <span class="st">"(35,40]"</span>, <span class="st">"(40,45]"</span>, <span class="st">"unclear"</span>))
) %>%
<span class="st"> </span><span class="kw">data.table</span>() ->
<span class="st"> </span>rpqa
<span class="kw">table</span>(rpqa$maternal_loss, <span class="dt">exclude =</span> <span class="ot">NULL</span>)</code></pre></div>
<pre><code>##
## later [0,1] (1,5] (5,10] (10,15] (15,20] (20,25] (25,30] (30,35]
## 96785 8922 17870 19592 18031 18390 21247 25498 29276
## (35,40] (40,45] unclear <NA>
## 32748 27878 143354 0</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">table</span>(rpqa$paternal_loss, <span class="dt">exclude =</span> <span class="ot">NULL</span>)</code></pre></div>
<pre><code>##
## later [0,1] (1,5] (5,10] (10,15] (15,20] (20,25] (25,30] (30,35]
## 67685 5903 12520 17507 21294 26344 32911 36337 37820
## (35,40] (40,45] unclear <NA>
## 37750 28036 135484 0</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">recenter_all =<span class="st"> </span>function(x) { <span class="kw">recenter.pat</span>( <span class="kw">recenter.pat</span>( x, <span class="dt">among_who=</span><span class="st">"idParents"</span>), <span class="dt">what =</span> <span class="st">"maternalage"</span>, <span class="dt">among_who =</span> <span class="st">"idParents"</span>) }
rpqa[, ever_married :<span class="er">=</span><span class="st"> </span><span class="kw">ifelse</span>(spouses ><span class="st"> </span><span class="dv">0</span>,<span class="dv">1</span>,<span class="dv">0</span>) ]
rpqa[, birth.cohort :<span class="er">=</span><span class="st"> </span><span class="kw">year_bins</span>(byear)]
rpqa[byear <<span class="st"> </span><span class="dv">1635</span>, birth.cohort :<span class="er">=</span><span class="st"> "1630-1635"</span>]
<span class="kw">crosstabs</span>(rpqa$birth.cohort)</code></pre></div>
<pre><code>## rpqa$birth.cohort
## 1630-1635 1635-1640 1640-1645 1645-1650 1650-1655 1655-1660 1660-1665
## 1348 735 954 921 805 866 1235
## 1665-1670 1670-1675 1675-1680 1680-1685 1685-1690 1690-1695 1695-1700
## 1705 2527 2651 2694 2835 3457 4488
## 1700-1705 1705-1710 1710-1715 1715-1720 1720-1725 1725-1730 1730-1735
## 5373 5713 6449 7220 8550 10247 12112
## 1735-1740 1740-1745 1745-1750 1750-1755 1755-1760 1760-1765 1765-1770
## 12810 14107 15585 18836 20213 22616 26447
## 1770-1775 1775-1780 1780-1785 1785-1790 1790-1795 1795-1800 <NA>
## 27417 30140 32575 36765 40126 47163 31906</code></pre>
</div>
<div id="subset-and-save" class="section level2">
<h2>Subset and save</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa =<span class="st"> </span><span class="kw">recenter_all</span>(rpqa)
rpqa =<span class="st"> </span><span class="kw">recenter.pat</span>(rpqa, <span class="dt">what =</span> <span class="st">"paternal.grandpaternalage"</span>, <span class="dt">among_who =</span> <span class="st">"idPaternalGrandparents"</span>)
rpqa =<span class="st"> </span><span class="kw">recenter.pat</span>(rpqa, <span class="dt">what =</span> <span class="st">"maternal.grandpaternalage"</span>, <span class="dt">among_who =</span> <span class="st">"idMaternalGrandparents"</span>)
rpqa[, any_surviving_children :<span class="er">=</span><span class="st"> </span><span class="kw">ifelse</span>(children.survivingR ><span class="st"> </span><span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">0</span>)]
rpqa[, children.wddate :<span class="er">=</span><span class="st"> </span>children.dead1y +<span class="st"> </span>children.surviving1y]
rpqa[, maternalage.factor :<span class="er">=</span><span class="st"> </span><span class="kw">cut</span>((<span class="dv">10</span>*maternalage), <span class="dt">breaks =</span> <span class="kw">c</span>(<span class="dv">14</span>, <span class="dv">20</span>, <span class="dv">35</span>, <span class="dv">50</span>))]
rpqa$maternalage.factor =<span class="st"> </span><span class="kw">relevel</span>(rpqa$maternalage.factor, <span class="dt">ref =</span> <span class="st">"(20,35]"</span>)
<span class="kw">crosstabs</span>(~<span class="st"> </span><span class="kw">is.na</span>(codeLieuNaiss) +<span class="st"> </span>(codeLieuNaiss <<span class="st"> </span><span class="dv">10000</span>), <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## codeLieuNaiss < 10000
## is.na(codeLieuNaiss) FALSE TRUE <NA>
## FALSE 10814 416629 0
## TRUE 0 0 32148</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$known_to_be_born_in_quebec =<span class="st"> </span>!<span class="kw">is.na</span>(rpqa$codeLieuNaiss) &<span class="st"> </span>rpqa$codeLieuNaiss <<span class="st"> </span><span class="dv">10000</span>
<span class="kw">crosstabs</span>(rpqa$known_to_be_born_in_quebec)</code></pre></div>
<pre><code>## rpqa$known_to_be_born_in_quebec
## FALSE TRUE
## 42962 416629</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$known_to_have_died_in_quebec =<span class="st"> </span>!<span class="kw">is.na</span>(rpqa$codeLieuDeces) &<span class="st"> </span>rpqa$codeLieuDeces <<span class="st"> </span><span class="dv">10000</span>
<span class="kw">crosstabs</span>(~<span class="st"> </span><span class="kw">is.na</span>(rpqa$codeLieuDeces) +<span class="st"> </span><span class="kw">is.na</span>(dyear), <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## is.na(dyear)
## is.na(rpqa$codeLieuDeces) FALSE TRUE
## FALSE 244806 667
## TRUE 8 214110</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$might_have_died_in_quebec =<span class="st"> </span><span class="kw">is.na</span>(rpqa$codeLieuDeces) |<span class="st"> </span>rpqa$codeLieuDeces <<span class="st"> </span><span class="dv">10000</span>
<span class="kw">crosstabs</span>(~<span class="st"> </span>might_have_died_in_quebec +<span class="st"> </span>known_to_have_died_in_quebec, <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## known_to_have_died_in_quebec
## might_have_died_in_quebec FALSE TRUE
## FALSE 39 0
## TRUE 214118 245434</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">crosstabs</span>(rpqa$might_have_died_in_quebec)</code></pre></div>
<pre><code>## rpqa$might_have_died_in_quebec
## FALSE TRUE
## 39 459552</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$parents_known_to_have_married_in_quebec =<span class="st"> </span>!<span class="kw">is.na</span>(rpqa$codeLieuM.Parents) &<span class="st"> </span>rpqa$codeLieuM.Parents <<span class="st"> </span><span class="dv">10000</span>
rpqa$parents_might_have_married_in_quebec =<span class="st"> </span><span class="kw">is.na</span>(rpqa$codeLieuM.Parents) |<span class="st"> </span>rpqa$codeLieuM.Parents <<span class="st"> </span><span class="dv">10000</span>
<span class="kw">crosstabs</span>(~<span class="st"> </span><span class="kw">is.na</span>(codeLieuM.Parents) +<span class="st"> </span>(codeLieuM.Parents <<span class="st"> </span><span class="dv">10000</span>), <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## codeLieuM.Parents < 10000
## is.na(codeLieuM.Parents) FALSE TRUE <NA>
## FALSE 302 409187 0
## TRUE 0 0 50102</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">crosstabs</span>(~<span class="st"> </span>parents_known_to_have_married_in_quebec +<span class="st"> </span>might_have_died_in_quebec +<span class="st"> </span>known_to_be_born_in_quebec, <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## , , known_to_be_born_in_quebec = FALSE
##
## might_have_died_in_quebec
## parents_known_to_have_married_in_quebec FALSE TRUE
## FALSE 19 34990
## TRUE 0 7953
##
## , , known_to_be_born_in_quebec = TRUE
##
## might_have_died_in_quebec
## parents_known_to_have_married_in_quebec FALSE TRUE
## FALSE 8 15387
## TRUE 12 401222</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">crosstabs</span>(~<span class="st"> </span>parents_might_have_married_in_quebec +<span class="st"> </span>might_have_died_in_quebec +<span class="st"> </span>known_to_be_born_in_quebec, <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## , , known_to_be_born_in_quebec = FALSE
##
## might_have_died_in_quebec
## parents_might_have_married_in_quebec FALSE TRUE
## FALSE 0 106
## TRUE 19 42837
##
## , , known_to_be_born_in_quebec = TRUE
##
## might_have_died_in_quebec
## parents_might_have_married_in_quebec FALSE TRUE
## FALSE 0 196
## TRUE 20 416413</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa =<span class="st"> </span><span class="kw">data.frame</span>(rpqa)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children_born_in_quebec'</span>,<span class="dt">wt_var =</span> <span class="st">'known_to_be_born_in_quebec'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children_died_in_quebec'</span>,<span class="dt">wt_var =</span> <span class="st">'known_to_have_died_in_quebec'</span>)
rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'children_probably_died_in_quebec'</span>,<span class="dt">wt_var =</span> <span class="st">'might_have_died_in_quebec'</span>)
rpqa$all_kids_born_and_died_in_quebec =<span class="st"> </span>rpqa$children_born_in_quebec ==<span class="st"> </span>rpqa$children_died_in_quebec &<span class="st"> </span>rpqa$children_born_in_quebec ==<span class="st"> </span>rpqa$children
rpqa$all_kids_born_and_probably_died_in_quebec =<span class="st"> </span>rpqa$children_born_in_quebec ==<span class="st"> </span>rpqa$children_probably_died_in_quebec &<span class="st"> </span>rpqa$children_born_in_quebec ==<span class="st"> </span>rpqa$children
<span class="kw">crosstabs</span>(~<span class="st"> </span>all_kids_born_and_died_in_quebec +<span class="st"> </span>all_kids_born_and_probably_died_in_quebec, <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## all_kids_born_and_probably_died_in_quebec
## all_kids_born_and_died_in_quebec FALSE TRUE
## FALSE 29204 89926
## TRUE 0 340461</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">crosstabs</span>(~<span class="st"> </span>all_kids_born_and_probably_died_in_quebec +<span class="st"> </span>parents_known_to_have_married_in_quebec, <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## parents_known_to_have_married_in_quebec
## all_kids_born_and_probably_died_in_quebec FALSE TRUE
## FALSE 18659 10545
## TRUE 31745 398642</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">crosstabs</span>(rpqa$all_kids_born_and_died_in_quebec &<span class="st"> </span>rpqa$parents_known_to_have_married_in_quebec)</code></pre></div>
<pre><code>## rpqa$all_kids_born_and_died_in_quebec & rpqa$parents_known_to_have_married_in_quebec
## FALSE TRUE
## 140295 319296</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">crosstabs</span>(rpqa$all_kids_born_and_probably_died_in_quebec &<span class="st"> </span>rpqa$parents_known_to_have_married_in_quebec)</code></pre></div>
<pre><code>## rpqa$all_kids_born_and_probably_died_in_quebec & rpqa$parents_known_to_have_married_in_quebec
## FALSE TRUE
## 60949 398642</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$sibs_born_in_quebec =<span class="st"> </span><span class="kw">ave</span>(rpqa$known_to_be_born_in_quebec, rpqa$idParents, <span class="dt">FUN =</span> function(x) { <span class="kw">sum</span>(x, <span class="dt">na.rm =</span> T) })
rpqa$sibs_died_in_quebec =<span class="st"> </span><span class="kw">ave</span>(rpqa$might_have_died_in_quebec, rpqa$idParents, <span class="dt">FUN =</span> function(x) { <span class="kw">sum</span>(x, <span class="dt">na.rm =</span> T) })
<span class="kw">crosstabs</span>(<span class="kw">I</span>(rpqa$sibs_born_in_quebec -<span class="st"> </span>rpqa$sibs_died_in_quebec))</code></pre></div>
<pre><code>## I(rpqa$sibs_born_in_quebec - rpqa$sibs_died_in_quebec)
## -9 -8 -7 -6 -5 -4 -3 -2 -1 0
## 12 11 88 245 445 1029 2867 10092 74394 370282
## 1
## 126</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(rpqa$sibs_born_in_quebec -<span class="st"> </span>rpqa$sibs_died_in_quebec, <span class="dt">binwidth =</span> <span class="dv">1</span>)</code></pre></div>
<p><img src="0_rpqa_massage_files/figure-html/sbset-1.png" width="1440px" height="900px" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa =<span class="st"> </span><span class="kw">count_and_merge</span>(rpqa, <span class="st">'all_sibs_born_and_died_in_quebec'</span>,<span class="dt">wt_var =</span> <span class="st">'all_kids_born_and_died_in_quebec'</span>)
<span class="kw">crosstabs</span>(~<span class="st"> </span>all_sibs_born_and_died_in_quebec +<span class="st"> </span>parents_known_to_have_married_in_quebec, <span class="dt">data =</span> rpqa)</code></pre></div>
<pre><code>## parents_known_to_have_married_in_quebec
## all_sibs_born_and_died_in_quebec FALSE TRUE
## 0 29424 308036
## 1 9947 10995
## 2 2196 10535
## 3 1707 10675
## 4 1486 10456
## 5 1235 10169
## 6 1169 9289
## 7 913 8413
## 8 702 7475
## 9 519 6310
## 10 394 4895
## 11 254 4018
## 12 174 2794
## 13 81 1878
## 14 83 1287
## 15 39 847
## 16 29 479
## 17 21 314
## 18 11 151
## 19 8 72
## 20 6 42
## 21 2 27
## 22 2 19
## 23 1 3
## 24 0 3
## 25 0 2
## 27 1 2
## 29 0 1</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$probably_complete_records =<span class="st"> </span>rpqa$all_kids_born_and_probably_died_in_quebec &<span class="st"> </span>rpqa$parents_might_have_married_in_quebec
<span class="kw">table</span>(rpqa$probably_complete_records)</code></pre></div>
<pre><code>##
## FALSE TRUE
## 29493 430098</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">rpqa$birth_cohort =<span class="st"> </span><span class="kw">factor</span>(rpqa$birth.cohort)
rpqa$male =<span class="st"> </span><span class="kw">factor</span>(rpqa$male)
rpqa$last_born =<span class="st"> </span><span class="kw">factor</span>(rpqa$last_born)
rpqa<span class="fl">.1</span> =<span class="st"> </span>rpqa %>%<span class="st"> </span><span class="kw">filter</span>(byear <<span class="st"> </span><span class="dv">1740</span> &<span class="st"> </span>byear >=<span class="st"> </span><span class="dv">1670</span> &<span class="st"> </span>probably_complete_records)
<span class="kw">save</span>(rpqa, rpqa<span class="fl">.1</span>,<span class="dt">file =</span> <span class="st">"rpqa.rdata"</span>)</code></pre></div>
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