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<div id="blake-et-al.-2016-re-analysis" class="section level1 tabset">
<h1>Blake et al. (2016) re-analysis</h1>
<p>Blake, K. R., Dixson, B. J. W., O’Dean, S. M., & Denson, T. F. (2016). Standardized protocols for characterizing women’s fertility: A data-driven approach. <em>Hormones and Behavior</em>, 81, 74–83. <a href="doi:%5B10.1016/j.yhbeh.2016.03.004%5D(https://dx.doi.org/10.1016/j.yhbeh.2016.03.004)" class="uri">doi:[10.1016/j.yhbeh.2016.03.004](https://dx.doi.org/10.1016/j.yhbeh.2016.03.004)</a></p>
<div id="load-data" class="section level2">
<h2>Load data</h2>
<pre class="r"><code>library(knitr)
opts_chunk$set(tidy = FALSE,cache = F, warning = F, message = F, render = formr::pander_handler)
source("0_helpers.R")</code></pre>
<pre class="r"><code>library(haven)
conc = read_sav("blake_data/BDOD Conception probability data v2.sav")
main = read_sav("blake_data/BDOD main data v3.sav")
days6 = read_sav("blake_data/BDOD Six day window data v4.sav")</code></pre>
</div>
<div id="reproduce-correlation-for-reported-backward" class="section level2">
<h2>Reproduce correlation for reported backward</h2>
<p>In paper: actual - FC: .11 actual - reported avg length BC: .35 actual - last length BC: .24 actual - last+avg length BC: .28 actual - avg all: .30</p>
<p>can only reproduce rank order, but they mentioned using some corrected correlation (because of groups)</p>
<pre class="r"><code>cor.test(conc$FCpred, conc$FCCP)</code></pre>
<table style="width:88%;">
<caption>Pearson’s product-moment correlation: <code>conc$FCpred</code> and <code>conc$FCCP</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="23%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">3.95</td>
<td align="center">1440</td>
<td align="center">0.00008179 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(conc$BCPred, conc$BCRepCP)</code></pre>
<table style="width:85%;">
<caption>Pearson’s product-moment correlation: <code>conc$BCPred</code> and <code>conc$BCRepCP</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="20%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">10.96</td>
<td align="center">1142</td>
<td align="center">1.19e-26 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(conc$BCPred, conc$BCPriorCP)</code></pre>
<table style="width:86%;">
<caption>Pearson’s product-moment correlation: <code>conc$BCPred</code> and <code>conc$BCPriorCP</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="22%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">7.753</td>
<td align="center">1006</td>
<td align="center">2.196e-14 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(conc$BCPred, conc$BCPriorRepAVCP)</code></pre>
<table style="width:86%;">
<caption>Pearson’s product-moment correlation: <code>conc$BCPred</code> and <code>conc$BCPriorRepAVCP</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="22%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">7.817</td>
<td align="center">1016</td>
<td align="center">1.349e-14 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(conc$BCPred, conc$BCAllMonCP)</code></pre>
<table style="width:86%;">
<caption>Pearson’s product-moment correlation: <code>conc$BCPred</code> and <code>conc$BCAllMonCP</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="22%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">8.18</td>
<td align="center">1016</td>
<td align="center">8.414e-16 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>lmer(FCCP ~ FCpred + (1|Subject), data = conc)</code></pre>
<pre><code>## Linear mixed model fit by REML ['merModLmerTest']
## Formula: FCCP ~ FCpred + (1 | Subject)
## Data: conc
## REML criterion at convergence: -3330
## Random effects:
## Groups Name Std.Dev.
## Subject (Intercept) 0.00202
## Residual 0.07587
## Number of obs: 1442, groups: Subject, 103
## Fixed Effects:
## (Intercept) FCpred
## 0.0565 0.1046</code></pre>
<pre class="r"><code>lmer(BCPred ~ BCRepCP + (1|Subject), data = conc)</code></pre>
<pre><code>## Linear mixed model fit by REML ['merModLmerTest']
## Formula: BCPred ~ BCRepCP + (1 | Subject)
## Data: conc
## REML criterion at convergence: -2736
## Random effects:
## Groups Name Std.Dev.
## Subject (Intercept) 0.0000
## Residual 0.0727
## Number of obs: 1144, groups: Subject, 103
## Fixed Effects:
## (Intercept) BCRepCP
## 0.0609 0.3128</code></pre>
</div>
<div id="reproduce-t1" class="section level2">
<h2>Reproduce T1</h2>
<p>Not quite the same corrs.</p>
<pre class="r"><code>main %>% filter(!is.na(FCDay)) %>% select(LengthRep, LengthPrior,LengthPriorRepAV, LengthallMonthsRepAV, LengthTestingCycle) %>% cor(use='na.or.complete') %>% round(2)</code></pre>
<table style="width:100%;">
<colgroup>
<col width="23%" />
<col width="10%" />
<col width="12%" />
<col width="16%" />
<col width="20%" />
<col width="17%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">LengthRep</th>
<th align="center">LengthPrior</th>
<th align="center">LengthPriorRepAV</th>
<th align="center">LengthallMonthsRepAV</th>
<th align="center">LengthTestingCycle</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>LengthRep</strong></td>
<td align="center">1</td>
<td align="center">0.52</td>
<td align="center">0.82</td>
<td align="center">0.78</td>
<td align="center">0.46</td>
</tr>
<tr class="even">
<td align="center"><strong>LengthPrior</strong></td>
<td align="center">0.52</td>
<td align="center">1</td>
<td align="center">0.91</td>
<td align="center">0.86</td>
<td align="center">0.56</td>
</tr>
<tr class="odd">
<td align="center"><strong>LengthPriorRepAV</strong></td>
<td align="center">0.82</td>
<td align="center">0.91</td>
<td align="center">1</td>
<td align="center">0.96</td>
<td align="center">0.6</td>
</tr>
<tr class="even">
<td align="center"><strong>LengthallMonthsRepAV</strong></td>
<td align="center">0.78</td>
<td align="center">0.86</td>
<td align="center">0.96</td>
<td align="center">1</td>
<td align="center">0.58</td>
</tr>
<tr class="odd">
<td align="center"><strong>LengthTestingCycle</strong></td>
<td align="center">0.46</td>
<td align="center">0.56</td>
<td align="center">0.6</td>
<td align="center">0.58</td>
<td align="center">1</td>
</tr>
</tbody>
</table>
<pre class="r"><code>main %>% filter(!is.na(FCDay)) %>% select(LengthRep, LengthPrior,LengthPriorRepAV, LengthallMonthsRepAV, LengthTestingCycle, FCDay, BCActual) %>% cor(use='na.or.complete') %>% round(2)</code></pre>
<table style="width:100%;">
<colgroup>
<col width="20%" />
<col width="8%" />
<col width="10%" />
<col width="14%" />
<col width="17%" />
<col width="15%" />
<col width="5%" />
<col width="7%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">LengthRep</th>
<th align="center">LengthPrior</th>
<th align="center">LengthPriorRepAV</th>
<th align="center">LengthallMonthsRepAV</th>
<th align="center">LengthTestingCycle</th>
<th align="center">FCDay</th>
<th align="center">BCActual</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>LengthRep</strong></td>
<td align="center">1</td>
<td align="center">0.52</td>
<td align="center">0.82</td>
<td align="center">0.78</td>
<td align="center">0.46</td>
<td align="center">0.48</td>
<td align="center">0.12</td>
</tr>
<tr class="even">
<td align="center"><strong>LengthPrior</strong></td>
<td align="center">0.52</td>
<td align="center">1</td>
<td align="center">0.91</td>
<td align="center">0.86</td>
<td align="center">0.56</td>
<td align="center">0.6</td>
<td align="center">0.13</td>
</tr>
<tr class="odd">
<td align="center"><strong>LengthPriorRepAV</strong></td>
<td align="center">0.82</td>
<td align="center">0.91</td>
<td align="center">1</td>
<td align="center">0.96</td>
<td align="center">0.6</td>
<td align="center">0.62</td>
<td align="center">0.15</td>
</tr>
<tr class="even">
<td align="center"><strong>LengthallMonthsRepAV</strong></td>
<td align="center">0.78</td>
<td align="center">0.86</td>
<td align="center">0.96</td>
<td align="center">1</td>
<td align="center">0.58</td>
<td align="center">0.62</td>
<td align="center">0.13</td>
</tr>
<tr class="odd">
<td align="center"><strong>LengthTestingCycle</strong></td>
<td align="center">0.46</td>
<td align="center">0.56</td>
<td align="center">0.6</td>
<td align="center">0.58</td>
<td align="center">1</td>
<td align="center">0.56</td>
<td align="center">0.67</td>
</tr>
<tr class="even">
<td align="center"><strong>FCDay</strong></td>
<td align="center">0.48</td>
<td align="center">0.6</td>
<td align="center">0.62</td>
<td align="center">0.62</td>
<td align="center">0.56</td>
<td align="center">1</td>
<td align="center">-0.23</td>
</tr>
<tr class="odd">
<td align="center"><strong>BCActual</strong></td>
<td align="center">0.12</td>
<td align="center">0.13</td>
<td align="center">0.15</td>
<td align="center">0.13</td>
<td align="center">0.67</td>
<td align="center">-0.23</td>
<td align="center">1</td>
</tr>
</tbody>
</table>
</div>
<div id="descriptives-of-bcfc-ovulation-day" class="section level2">
<h2>Descriptives of BC/FC ovulation day</h2>
<pre class="r"><code>qplot(main$BCActual) + ggtitle("Which day was the surge day relative to next menstrual onset?")</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-5-1.png" width="672" /></p>
<pre class="r"><code>mean(main$BCActual, na.rm = T)</code></pre>
<p><em>14.26</em></p>
<pre class="r"><code>sd(main$BCActual, na.rm = T)</code></pre>
<p><em>3.813</em></p>
<pre class="r"><code>mean(main$BCActual, na.rm = T, trim = 0.1)</code></pre>
<p><em>14.21</em></p>
<pre class="r"><code>mad(main$BCActual, na.rm = T)</code></pre>
<p><em>2.965</em></p>
<pre class="r"><code>qplot(main$FCDay)</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-5-2.png" width="672" /></p>
<pre class="r"><code>mean(main$FCDay, na.rm = T)</code></pre>
<p><em>16.8</em></p>
<pre class="r"><code>sd(main$FCDay, na.rm = T)</code></pre>
<p><em>3.163</em></p>
<pre class="r"><code>mad(main$FCDay, na.rm = T)</code></pre>
<p><em>2.965</em></p>
</div>
<div id="when-does-ovulation-occur-by-cycle-length" class="section level2">
<h2>When does ovulation occur by cycle length?</h2>
<pre class="r"><code>main = main %>% filter(LengthTestingCycle<50)
xtabs(~ I(BCActual + FCDay - 1) == LengthTestingCycle, data = main)</code></pre>
<table style="width:8%;">
<colgroup>
<col width="8%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">TRUE</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">94</td>
</tr>
</tbody>
</table>
<pre class="r"><code>ggplot(main, aes(FCDay, BCActual)) + geom_jitter() + ggtitle("Pre-/post-surge, follicular v. luteal", subtitle = "The lengths of pre- and post-ovulation \nhalf are uncorrelated")</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-6-1.png" width="672" /></p>
<pre class="r"><code>ggplot(main, aes(LengthTestingCycle, BCActual)) + geom_jitter()+ ggtitle("Length of cycle and post-surge time", subtitle = "The longer the cycle, the earlier the ovulation") + geom_smooth(method = 'lm')</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-6-2.png" width="672" /></p>
<pre class="r"><code>ggplot(main, aes(LengthTestingCycle/1.7 - 3.5, BCActual)) + geom_jitter()+ ggtitle("Length of cycle and post-surge time", subtitle = "Ovulation tends to be in the cycle middle") + geom_smooth(method = 'lm') + geom_abline(slope = 1) + coord_fixed()</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-6-3.png" width="672" /></p>
<pre class="r"><code>lm(BCActual ~ LengthTestingCycle, data = main)</code></pre>
<table style="width:96%;">
<caption>Fitting linear model: BCActual ~ LengthTestingCycle</caption>
<colgroup>
<col width="34%" />
<col width="15%" />
<col width="18%" />
<col width="13%" />
<col width="13%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>LengthTestingCycle</strong></td>
<td align="center">0.5668</td>
<td align="center">0.06455</td>
<td align="center">8.781</td>
<td align="center">8.356e-14</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">-2.772</td>
<td align="center">1.934</td>
<td align="center">-1.434</td>
<td align="center">0.155</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(main$LengthTestingCycle, main$BCActual)</code></pre>
<table style="width:86%;">
<caption>Pearson’s product-moment correlation: <code>main$LengthTestingCycle</code> and <code>main$BCActual</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="22%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">8.781</td>
<td align="center">92</td>
<td align="center">8.356e-14 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(main$LengthTestingCycle, main$FCDay)</code></pre>
<table style="width:93%;">
<caption>Pearson’s product-moment correlation: <code>main$LengthTestingCycle</code> and <code>main$FCDay</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="29%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">6.711</td>
<td align="center">92</td>
<td align="center">0.000000001556 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>lm(BCActual ~ I(LengthTestingCycle/2), data = main)</code></pre>
<table>
<caption>Fitting linear model: BCActual ~ I(LengthTestingCycle/2)</caption>
<colgroup>
<col width="40%" />
<col width="14%" />
<col width="17%" />
<col width="13%" />
<col width="13%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>I(LengthTestingCycle/2)</strong></td>
<td align="center">1.134</td>
<td align="center">0.1291</td>
<td align="center">8.781</td>
<td align="center">8.356e-14</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">-2.772</td>
<td align="center">1.934</td>
<td align="center">-1.434</td>
<td align="center">0.155</td>
</tr>
</tbody>
</table>
<pre class="r"><code>lm(BCActual ~ LengthTestingCycle, data = main %>% filter(LengthTestingCycle < 40))</code></pre>
<table style="width:96%;">
<caption>Fitting linear model: BCActual ~ LengthTestingCycle</caption>
<colgroup>
<col width="34%" />
<col width="15%" />
<col width="18%" />
<col width="13%" />
<col width="13%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>LengthTestingCycle</strong></td>
<td align="center">0.5892</td>
<td align="center">0.07078</td>
<td align="center">8.324</td>
<td align="center">8.123e-13</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">-3.415</td>
<td align="center">2.106</td>
<td align="center">-1.621</td>
<td align="center">0.1084</td>
</tr>
</tbody>
</table>
<pre class="r"><code>lm(BCActual ~ I(LengthTestingCycle/2), data = main %>% filter(LengthTestingCycle < 40))</code></pre>
<table>
<caption>Fitting linear model: BCActual ~ I(LengthTestingCycle/2)</caption>
<colgroup>
<col width="40%" />
<col width="14%" />
<col width="17%" />
<col width="13%" />
<col width="13%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>I(LengthTestingCycle/2)</strong></td>
<td align="center">1.178</td>
<td align="center">0.1416</td>
<td align="center">8.324</td>
<td align="center">8.123e-13</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">-3.415</td>
<td align="center">2.106</td>
<td align="center">-1.621</td>
<td align="center">0.1084</td>
</tr>
</tbody>
</table>
<pre class="r"><code>lm(BCActual ~ I(LengthTestingCycle/2 - 3), data = main %>% filter(LengthTestingCycle < 40))</code></pre>
<table>
<caption>Fitting linear model: BCActual ~ I(LengthTestingCycle/2 - 3)</caption>
<colgroup>
<col width="39%" />
<col width="15%" />
<col width="17%" />
<col width="13%" />
<col width="13%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>I(LengthTestingCycle/2 - 3)</strong></td>
<td align="center">1.178</td>
<td align="center">0.1416</td>
<td align="center">8.324</td>
<td align="center">8.123e-13</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">0.1205</td>
<td align="center">1.685</td>
<td align="center">0.07152</td>
<td align="center">0.9431</td>
</tr>
</tbody>
</table>
<pre class="r"><code>ggplot(main, aes(LengthTestingCycle/2, FCDay)) + geom_jitter()+ ggtitle("Length of cycle and pre-surge time", subtitle = "Ovulation tends to be in the cycle middle") + geom_smooth(method = 'lm')</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-6-4.png" width="672" /></p>
<pre class="r"><code>lm(FCDay ~ I(LengthTestingCycle/2 + 5), data = main %>% filter(LengthTestingCycle < 40))</code></pre>
<table>
<caption>Fitting linear model: FCDay ~ I(LengthTestingCycle/2 + 5)</caption>
<colgroup>
<col width="38%" />
<col width="14%" />
<col width="17%" />
<col width="13%" />
<col width="17%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>I(LengthTestingCycle/2 + 5)</strong></td>
<td align="center">0.8216</td>
<td align="center">0.1416</td>
<td align="center">5.804</td>
<td align="center">0.00000009353</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">0.3069</td>
<td align="center">2.81</td>
<td align="center">0.1092</td>
<td align="center">0.9133</td>
</tr>
</tbody>
</table>
<pre class="r"><code>ggplot(main, aes(LengthRep/2, FCDay)) + geom_jitter()+ ggtitle("Average reported cycle length and pre-surge time", subtitle = "Ovulation tends to be in the cycle middle") + geom_smooth(method = 'lm') + geom_abline(slope = 1) + coord_fixed()</code></pre>
<p><img src="1_blake_data_files/figure-html/unnamed-chunk-6-5.png" width="672" /></p>
<pre class="r"><code>lm(FCDay ~ I(LengthRep/2), data = main %>% filter(LengthTestingCycle < 40))</code></pre>
<table style="width:92%;">
<caption>Fitting linear model: FCDay ~ I(LengthRep/2)</caption>
<colgroup>
<col width="29%" />
<col width="15%" />
<col width="18%" />
<col width="13%" />
<col width="15%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>I(LengthRep/2)</strong></td>
<td align="center">1.116</td>
<td align="center">0.2175</td>
<td align="center">5.13</td>
<td align="center">0.000001624</td>
</tr>
<tr class="even">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">0.1557</td>
<td align="center">3.206</td>
<td align="center">0.04857</td>
<td align="center">0.9614</td>
</tr>
</tbody>
</table>
<pre class="r"><code>cor.test(main$LengthRep, main$FCDay)</code></pre>
<table style="width:90%;">
<caption>Pearson’s product-moment correlation: <code>main$LengthRep</code> and <code>main$FCDay</code></caption>
<colgroup>
<col width="23%" />
<col width="6%" />
<col width="26%" />
<col width="33%" />
</colgroup>
<thead>
<tr class="header">
<th align="center">Test statistic</th>
<th align="center">df</th>
<th align="center">P value</th>
<th align="center">Alternative hypothesis</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">5.285</td>
<td align="center">92</td>
<td align="center">0.0000008396 * * *</td>
<td align="center">two.sided</td>
</tr>
</tbody>
</table>
<pre class="r"><code>summary(lm(BCActual ~ LengthTestingCycle + LengthRep, data = main))</code></pre>
<table style="width:96%;">
<colgroup>
<col width="34%" />
<col width="15%" />
<col width="18%" />
<col width="13%" />
<col width="13%" />
</colgroup>
<thead>
<tr class="header">
<th align="center"> </th>
<th align="center">Estimate</th>
<th align="center">Std. Error</th>
<th align="center">t value</th>
<th align="center">Pr(>|t|)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><strong>LengthTestingCycle</strong></td>
<td align="center">0.664</td>
<td align="center">0.07028</td>
<td align="center">9.449</td>
<td align="center">3.629e-15</td>
</tr>
<tr class="even">
<td align="center"><strong>LengthRep</strong></td>
<td align="center">-0.3349</td>
<td align="center">0.1139</td>
<td align="center">-2.941</td>
<td align="center">0.004146</td>
</tr>
<tr class="odd">
<td align="center"><strong>(Intercept)</strong></td>
<td align="center">4.192</td>
<td align="center">3.01</td>
<td align="center">1.393</td>
<td align="center">0.1671</td>
</tr>
</tbody>
</table>