tag:blogger.com,1999:blog-6933659748667912562021-05-05T08:56:25.009-07:00From My SlipboxCarolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-693365974866791256.post-19168904963469366392021-05-05T08:52:00.001-07:002021-05-05T08:53:37.451-07:00Trouble that you can't fix: omitted variable bias<p><span style="font-family: inherit;"> </span></p><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><span style="font-family: inherit;"><a href="https://1.bp.blogspot.com/-2mLgWKvnaJ8/YJKz3Vmug6I/AAAAAAAAAWI/RzZe9VQuNSkNq9sX5jcVsluYOqu4t_VEQCLcBGAsYHQ/s1024/omitted-variable-bias-owl.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1024" data-original-width="683" height="320" src="https://1.bp.blogspot.com/-2mLgWKvnaJ8/YJKz3Vmug6I/AAAAAAAAAWI/RzZe9VQuNSkNq9sX5jcVsluYOqu4t_VEQCLcBGAsYHQ/s320/omitted-variable-bias-owl.jpg" /></a></span></td></tr><tr><td class="tr-caption" style="text-align: center;"><span style="font-family: inherit;"><span class="photo_usage-attribution is-block" data-v-e1c1f65a="" id="attribution"><span data-v-e1c1f65a="">credit: <a data-v-e1c1f65a="" href="https://www.flickr.com/photos/22514058@N03" rel="noopener" target="_blank">SkipsterUK</a></span> (<a class="photo_license" data-v-e1c1f65a="" href="https://creativecommons.org/licenses/by-nc-nd/2.0/?ref=ccsearch&atype=rich" rel="noopener" target="_blank">CC BY-NC-ND 2.0) </a></span></span></td></tr></tbody></table><p></p><div style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #2e3338; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><h3 style="box-sizing: border-box; text-align: left;"><span style="font-family: inherit;">Preamble</span></h3></div><div style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #2e3338; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">In the previous post in this series, I explained how to use causal diagrams to set up multivariate regressions so that statistical confounding is eliminated.</span></p></div><div style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #2e3338; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">In this post, I'll give a short and simple example of a case where statistical confounding can't be prevented, because an important variable is unavailable. This sort of thing is unfixable, and it is bound to happen sometimes in observational statistical analyses, because there are influencing variables that we just don't anticipate, and therefore don't collect. <br /></span></p></div><div style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #2e3338; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Here's the entire 'statistical confounding' series:</span></p></div><div style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #2e3338; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><ul style="box-sizing: border-box; text-align: left;"><li data-line="0" style="box-sizing: border-box;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Part 1:<span> </span><a class="external-link" href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" rel="noopener" style="background-image: linear-gradient(transparent, transparent), url("/public/images/874d8b8e340f75575caacd8d766a9659.svg"); background-position: right 4px; background-repeat: no-repeat; background-size: 13px; box-sizing: border-box; color: lightblue; outline: currentcolor none medium; padding-right: 16px;" target="_blank">Statistical confounding: why it matters</a> <br /></span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">- on the many ways that confounding affects statistical analyses. <br /></span></p></li><li data-line="2" style="box-sizing: border-box;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Part 2:<span> </span><a class="external-link" href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" rel="noopener" style="background-image: linear-gradient(transparent, transparent), url("/public/images/874d8b8e340f75575caacd8d766a9659.svg"); background-position: right 4px; background-repeat: no-repeat; background-size: 13px; box-sizing: border-box; color: lightblue; outline: currentcolor none medium; padding-right: 16px;" target="_blank">Simpson's Paradox: extreme statistical confounding</a> </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">- understanding how statistical confounding can cause you to draw exactly the wrong conclusion.</span></p></li><li data-line="4" style="box-sizing: border-box;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Part 3:<span> </span><a class="external-link" href="https://frommyslipbox.blogspot.com/2021/04/linear-regression-is-trickier-than-you.html" rel="noopener" style="background-image: linear-gradient(transparent, transparent), url("/public/images/874d8b8e340f75575caacd8d766a9659.svg"); background-position: right 4px; background-repeat: no-repeat; background-size: 13px; box-sizing: border-box; color: lightblue; outline: currentcolor none medium; padding-right: 16px;" target="_blank">Linear regression is trickier than you think</a> </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">- a discussion of multivariate linear regression models</span></p></li><li data-line="6" style="box-sizing: border-box;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Part 4:<span> </span><a class="external-link" href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" rel="noopener" style="background-image: linear-gradient(transparent, transparent), url("/public/images/874d8b8e340f75575caacd8d766a9659.svg"); background-position: right 4px; background-repeat: no-repeat; background-size: 13px; box-sizing: border-box; color: lightblue; outline: currentcolor none medium; padding-right: 16px;" target="_blank">A gentle introduction to causal diagrams</a> </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">- a causal analysis of fake data relating COVID-19 incidence to wearing protective glasses.</span></p></li><li data-line="8" style="box-sizing: border-box;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Part 5:<span> </span><a class="external-link" href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" rel="noopener" style="background-image: linear-gradient(transparent, transparent), url("/public/images/874d8b8e340f75575caacd8d766a9659.svg"); background-position: right 4px; background-repeat: no-repeat; background-size: 13px; box-sizing: border-box; color: lightblue; outline: currentcolor none medium; padding-right: 16px;" target="_blank">How to eliminate confounding in multivariate regression</a> </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">- how to do a causal analysis to eliminate confounding in your regression analyses</span></p></li><li data-line="10" style="box-sizing: border-box;"><p style="box-sizing: border-box;"><span style="font-family: inherit;">Part 6:<span> </span><a class="internal-link is-unresolved" data-href="TBD" href="https://frommyslipbox.blogspot.com/2021/05/trouble-that-you-cant-fix-omitted.html" rel="noopener" style="box-sizing: border-box; color: #5c73f2; cursor: pointer; opacity: 0.5; outline: currentcolor none medium; text-decoration: underline;" target="_blank">A simple example of omitted variable bias</a><span> </span>(this post) </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">- an example of statistical confounding that can't be fixed, using only 4 variables.</span></p><p style="box-sizing: border-box;"><span></span></p><a name='more'></a><span style="font-family: inherit;"></span><p></p><h3 style="box-sizing: border-box;"><span style="font-family: inherit;">Omitted variable bias <br /></span></h3><p style="box-sizing: border-box;"><span style="font-family: inherit;">Suppose we have a dataset whose rows consist of the following three variables:<br /><br />- $P$: the score of a parent on a general well-being measure, a continuous variable.<br />- $C$: the score of a child on a general well-being measure, a continuous variable.<br />- $T$: whether or not the parent received counseling (therapy), a binary variable.<br /><br />Presumably, if the parent receives therapy, that would increase the parent's well-being score, and through the parent would also increase the child's well-being score. This would create a positive association between therapy and the child's well-being score. The image below shows how the associated causal diagram would look. </span></p><div class="separator" style="clear: both; text-align: center;"><span style="font-family: inherit;"><a href="https://1.bp.blogspot.com/-iZxGfWmRKRw/YJK1oh0FSQI/AAAAAAAAAWQ/C0w55gC56UseGaMYJPhdK6Xk5yXHkSYVwCLcBGAsYHQ/s408/omitted-variable-1.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="271" data-original-width="408" src="https://1.bp.blogspot.com/-iZxGfWmRKRw/YJK1oh0FSQI/AAAAAAAAAWQ/C0w55gC56UseGaMYJPhdK6Xk5yXHkSYVwCLcBGAsYHQ/s320/omitted-variable-1.PNG" width="320" /></a></span></div><p style="box-sizing: border-box;"><span style="font-family: inherit;">But we can also ask whether the therapy improves the child's well-being score in a direct way, i.e., not as an indirect effect of the parent's improved well-being score. </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">We ask this question by doing a regression of the child's well-being score (as the independent variable) on the therapy variable. In order to determine whether there is a direct effect of a parent's therapy on a child's well-being, we need to condition on the parent's well-being score by including it in the regression model; this blocks the indirect effect of the parent's improved well-being on the child's well-being. <br /><br />A simple model regressing $C$ on $T$, and including $P$ as a covariate, might look like this:<br /><br />$$ <br />\begin{aligned} <br />C &\sim N(\mu, \sigma^2) \\ <br />\mu &= \alpha_{[T]}+\beta P\\ <br />\alpha_{[T]} &\sim N(\alpha_{0}, \sigma_T) \\<br />\beta &\sim N(\beta_0, \sigma_P)<br />\end{aligned} <br />$$ <br /><br />The key to understanding this model is the line: </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">$$\mu=\alpha_{[T]} + \beta P.$$ <span style="font-family: inherit;">This line says that we are modeling the mean value of the well-being score $C$ as a sum of two terms. The first is an intercept </span></span><span style="font-family: inherit;"><span style="font-family: inherit;"><span style="font-family: inherit;"><span style="font-family: inherit;">$\alpha_{[T]}$, for $T=0$ or $1$, </span>that depends on whether the parent is receiving therapy; this measures the direct effect of the therapy on $C$, and it's the term we're really interested in for this regression. The second term involves </span></span>a slope parameter $\beta$ that measures the effect on $C$ of an increase in the parent's well-being variable $P$; this is how we incorporate conditioning on $P$ into the model. The values $\alpha_0, \sigma_T, \beta_0$, and $\sigma_P$ are just constants defining the prior distributions of $\alpha_{[T=0]}, \alpha_{[T=1]}$, and $\beta$.<br /><br />Of course, it's hard to imagine that there would be a direct effect of the parent receiving therapy on the child's well-being, and that's what you'd expect such a regression to show: an insignificant difference between the posterior distributions of $\alpha_{[T=0]}$ and $\alpha_{[T=1]}$.<br /><br />However, the most likely result of the regression would be that $\alpha_{[T=0]} > \alpha_{[T=1]}$. That is, the direct influence of a parent's receiving therapy, after conditioning on the parent's well-being, would be to paradoxically <i>reduce</i> the child's well-being score!<br /><br />The reason for this odd effect is that there are likely to be lurking variables -- variables we didn't measure or include in the regression -- that impact both the parent's and the child's well-being scores. </span></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">For example, consider the influence of the family's finances on both the parent and child; having enough money for a comfortable life is highly likely to improve both the parent's and child's well-being. Call this variable $F$, for the family's annual income. The image below shows how this omitted variable affects the causal diagram: the variables inside the dotted rectangle are the only ones we have actually observed. </span></p><p style="box-sizing: border-box;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-r7i3qJDzqF8/YJK4xvofMEI/AAAAAAAAAWY/Yi5N-5fNLAs9dPHvVX8_YTRD7ESNTivvACLcBGAsYHQ/s619/omitted-variable-2.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="340" data-original-width="619" src="https://1.bp.blogspot.com/-r7i3qJDzqF8/YJK4xvofMEI/AAAAAAAAAWY/Yi5N-5fNLAs9dPHvVX8_YTRD7ESNTivvACLcBGAsYHQ/s320/omitted-variable-2.PNG" width="320" /></a></div>We cannot condition on the variable $F$ (i.e., we can't include it in the regression), because we don't know its value. But it will still cause confounding of the results. <br /><br />That's because the silent presence of $F$ has turned $P$ into a collider variable in the causal diagram. Collider variables were discussed in the previous post on this topic (<a href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" target="_blank">How to eliminate confounding in multivariate regression</a>). A collider is a variable in a causal diagram, occurring in a path between an independent variable and a dependent variable of interest, that has two arrows pointing into it from its two adjacent variables. <br /><br />In this case, the path running from $T$ through $P$ to $F$ and then to $C$ contains $P$ as a collider variable. Because $P$ is a collider in this path, including it in the regression creates a negative association between $F$ and $T$, for reasons explained below. Because the general effect of increasing finances on the child's well-being score is positive, the negative association between $F$ and $T$ creates a negative association between $C$ and $T$, and that causes the weird regression result.<br /><br />Why does conditioning on the collider variable $P$ create a statistical association between $F$ and $T$? Because conditioning on $P$ means that you have told the statistical model what the value of $P$ is. Once you know $P$, that lets you make inferences about the value of $F$ if you already know $T$, and vice versa. <br /><br />To see how that can happen, let's suppose that you've learned that the parent's well-being score $P$ is high. If you then learn that the family is poor (low $F$), this suggests that the parent's well-being is coming from the other source in the causal diagram, therapy (i.e., it is more likely that $T=1$). Conversely, if $P$ is low, and you then learn that the family is well-off, that suggests that the parent's lower well-being score is related to the other causal variable in the causal diagram (i.e., it is more likely that $T=0$). So for any fixed and known value of $P$, $T$ is more likely to be 0 when the family finances are better, and more likely to be 1 when the family finances are worse. <p></p><p style="box-sizing: border-box;">On the other hand, if we don't know the value of $P$, then there is no relationship between $T$ and $F$. We say that $T$ and $F$ are <i>marginally independent</i>, and <i>conditionally dependent given $P$</i>. <br /><br />In general, we know that both therapy and good finances are likely to positively impact a parent's well-being score. Suppose $P$ takes on values from 1 (lowest well-being) to 4 (highest well-being). Then we expect that for a fixed income $F$, $P$ will be higher on average for people receiving therapy. Similarly, for a fixed value 0 or 1 of $T$, $P$ will be higher on average if $F$ is higher. This results in a graph like the one below, where level sets of $P$ for values of $F$ and $T$ are shown as lines with a negative slope. Conditioning on $P$ means restricting the values of $F$ and $T$ to one of those level set lines, producing the negative association between $F$ and $T$.<br /><span style="font-family: inherit;"></span></p><p style="box-sizing: border-box;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-W87JRNJhnxQ/YJK6LyJRmAI/AAAAAAAAAWg/HMJ5mwiMFhcxsU2QhOuTMkoNonPFdHBXACLcBGAsYHQ/s479/omitted-variable-3.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="245" data-original-width="479" src="https://1.bp.blogspot.com/-W87JRNJhnxQ/YJK6LyJRmAI/AAAAAAAAAWg/HMJ5mwiMFhcxsU2QhOuTMkoNonPFdHBXACLcBGAsYHQ/s320/omitted-variable-3.PNG" width="320" /></a></div><br /><span style="font-family: inherit;">The negative association between $F$ and $T$ that is set up when we condition on $P$ may not be strong, but it doesn't take much to produce a result that shows a weird negative association between a parent's therapy and a child's well-being. But it would be wrong to conclude that the relationship is causal. <br /><br />This is a situation in which the statistical confounding can't be fixed. If we don't condition on $P$, then we will be measuring the positive association between therapy and a child's well-being caused by the parent's well-being. If we do condition on $P$, then because we do not know the value of $F$, we'll be measuring the non-causal negative association between $T$ and $F$, which translates to a negative association between $T$ and $C$. Either way, we aren't measuring the true direct impact of the parent's therapy on the child's well-being. </span><p></p><p style="box-sizing: border-box;"><span style="font-family: inherit;">This is why randomized controlled experiments are the gold standard for making causal inferences; they break up the influence of omitted variables on the measured variables, thereby solving the omitted variable problem. <br /></span></p></li></ul></div>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-23690692695713653302021-04-30T09:32:00.009-07:002021-05-05T08:54:34.424-07:00How to eliminate confounding in multivariate regression<p> </p><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-6-CHHaaRwu0/YItQi0jpLOI/AAAAAAAAAU8/ebRvmT6YxAA08spH16YrC0LJjAcXlbcJgCLcBGAsYHQ/s1024/great-grey-owl.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="796" data-original-width="1024" src="https://1.bp.blogspot.com/-6-CHHaaRwu0/YItQi0jpLOI/AAAAAAAAAU8/ebRvmT6YxAA08spH16YrC0LJjAcXlbcJgCLcBGAsYHQ/s320/great-grey-owl.jpg" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Great grey owl (Creative Commons).<br /></td></tr></tbody></table><p></p><h3 style="text-align: left;">Preamble</h3><p><br />For my previous post on causal diagrams, I made up a fake dataset relating the incidence of COVID-19 to the wearing of protective goggles for hypothetical individuals. The dataset included several related covariates, such as whether the person in question was worried about COVID-19. </p><p></p><p>The goal of the exercise was to (hypothetically!) determine whether protective glasses was an effective intervention for COVID-19, and to see how accidental associations due to other variables could mess up the analysis. <br /><br />I faked the data so that COVID-19 incidence was independent of whether the person wore protective goggles. But then I demonstrated, using multivariate regressions, that it is easy to incorrectly conclude that protective glasses <i>are </i>significantly effective for reducing the risk of COVID-19. I also showed how a causal diagram relating the variables can be used to determine which variables to include and exclude from the analysis.<br /><br />In this article, I'll explain how to recognize the patterns in causal diagrams that lead to statistical confounding, and show how to do a causal analysis yourself. <br /></p><p>Here's the entire 'statistical confounding' series:</p><p>- Part 1: <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical confounding: why it matters:</a> on the many ways that confounding affects statistical analyses </p><p>- Part 2: <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">Simpson's Paradox: extreme statistical confounding</a>: understanding how statistical confounding can cause you to draw exactly the wrong conclusion</p><p>- Part 3: <a href="https://frommyslipbox.blogspot.com/2021/04/linear-regression-is-trickier-than-you.html" target="_blank">Linear regression is trickier than you think</a>: a discussion of multivariate linear regression models <br /></p><p>- Part 4: <a href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" target="_blank">A gentle introduction to causal diagrams</a>: a causal analysis of fake data relating COVID-19 incidence to wearing protective goggles</p><p>- Part 5: <a href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" target="_blank">How to eliminate confounding in multivariate regression</a> (this post): how to do a causal analysis to eliminate confounding in your regression analyses </p><p style="box-sizing: border-box;">-Part 6: <span style="font-family: inherit;"><a class="internal-link is-unresolved" data-href="TBD" href="https://frommyslipbox.blogspot.com/2021/05/trouble-that-you-cant-fix-omitted.html" rel="noopener" style="box-sizing: border-box; color: #5c73f2; cursor: pointer; opacity: 0.5; outline: currentcolor none medium; text-decoration: underline;" target="_blank">A simple example of omitted variable bias</a>: an example of statistical confounding that can't be fixed, using only 4 variables.</span></p><p> </p><h3 style="text-align: left;">Introduction</h3><p style="text-align: left;">In <a href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" target="_blank">A gentle introduction to causal diagrams</a>, I introduced a fake dataset in which rows represented individuals, containing the following information:<br /><br />- $C$: does the person test positive for COVID-19?<br />- $G$: does the person wear protective glasses in public?<br />- $W$: is the person worried about COVID-19?<br />- $S$: does the person avoid social contact?<br />- $V$: is the person vaccinated? <br /><br /><br />I then did some multivariate logistic regressions to answer the following question: does wearing protective goggles help reduce the likelihood of catching COVID-19? </p><p style="text-align: left;">In generating the dataset, I made the following assumptions: <br /><br />- protective glasses have no direct effect on COVID-19 incidence;<br />- avoiding social contact has a significant negative effect on COVID-19 incidence; <br />- getting vaccinated has a very significant negative effect on COVID-19 incidence; <br />- being worried about COVID makes a person much more likely to get vaccinated, avoid social contact, and wear protective glasses;<br />- being vaccinated makes a person less likely to avoid social contact. <br /></p><p style="text-align: left;">The causal diagram associated with these variables and assumptions is shown below. An arrow from one variable to another indicates that the value of the 'to' variable depends on the 'from' variable. </p><p style="text-align: left;">The exercise in the article was to determine which variables to include in a multivariate regression, in order to analyze whether protective glasses reduce the risk of catching COVID-19. The colored nodes are the ones that were ultimately included; only the $W$ (worried about COVID-19) variable was used as a covariate, in addition to the dependent and independent variables $G$ and $C$. <br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-AANBBcNzkyI/YItS9zqi_CI/AAAAAAAAAVE/fNa0ENxfW10nlEZhffB-ubLA3o-QIBEMgCLcBGAsYHQ/s807/mask-wearing-covid-causal-diagram-6.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="409" data-original-width="807" src="https://1.bp.blogspot.com/-AANBBcNzkyI/YItS9zqi_CI/AAAAAAAAAVE/fNa0ENxfW10nlEZhffB-ubLA3o-QIBEMgCLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-6.PNG" width="320" /></a></div><p><br /> </p><h3 style="text-align: left;">Backdoor paths</h3><p><br />In the diagram above, the causal relationship we want to assess (between $G$ and $C$) is represented by the gray dashed arrow. But there are a lot of other connections with intermediate variables, in the form of paths in the graph between $G$ and $C$, that can accidentally generate statistical associations between $G$ and $C$.<br /><br />The first such path is shown below: it passes from $G$ to $W$ to $S$ to $C$. This is called a 'backdoor path' because arrow 1 points into $G$, rather than emitting from $G$. This path can be described in words as follows: if the person is worried about COVID-19, this makes her more likely to both wear protective glasses and socially distance. Since social distancing is an effective intervention against COVID-19, this sets up a negative correlation between wearing glasses and catching COVID-19; but the dataset was constructed so that protective glasses had no impact on COVID-19, so the effect is only due to correlation, not causation.<br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-UF98lAM5jKM/YItTK05F5bI/AAAAAAAAAVI/fOWN7hp_xLwJ7u0V6BbskiCAneAXU-6MQCLcBGAsYHQ/s788/back-door-path-1.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="422" data-original-width="788" src="https://1.bp.blogspot.com/-UF98lAM5jKM/YItTK05F5bI/AAAAAAAAAVI/fOWN7hp_xLwJ7u0V6BbskiCAneAXU-6MQCLcBGAsYHQ/s320/back-door-path-1.PNG" width="320" /></a></div><br /><p>A second path is shown below: it passes from $G$ through $W$ to $V$ and then to $C$. In words: If a person is worried about COVID-19, he is more likely to both wear protective glasses and to get vaccinated. Since vaccination is an effective intervention against COVID-19, this again sets up a negative correlation between wearing glasses and catching COVID-19.<br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-5WwKO6zyQJM/YItTac-gxpI/AAAAAAAAAVU/CO7C4Uw4xGMSzOXa6rhIEUrZ7AoqV2i-wCLcBGAsYHQ/s788/back-door-path-2.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="425" data-original-width="788" src="https://1.bp.blogspot.com/-5WwKO6zyQJM/YItTac-gxpI/AAAAAAAAAVU/CO7C4Uw4xGMSzOXa6rhIEUrZ7AoqV2i-wCLcBGAsYHQ/s320/back-door-path-2.PNG" width="320" /></a></div><br /><p>A third path is shown below: it passes from $G$ through $W$ to $V$, then to $S$ and finally $C$. In words: if a person is worried about COVID-19, she is more likely to get vaccinated, after which she may be less likely to socially distance. This is a problem in our analysis if we do not know the person's vaccination status, since the presence of a lot of people who do not socially distance, and yet do not catch COVID-19, will obscure the effectiveness of social distancing as an intervention. In the presence of enough vaccine-positive people, it might even appear that people who do not socially distance are *less* likely to get COVID-19 if we don't know people's vaccination status!</p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-8lYCv7gAjUY/YItTmFEGCHI/AAAAAAAAAVY/ikrEqR_xsvca2FMs3xfUsP0FegJXd7JMwCLcBGAsYHQ/s793/back-door-path-3.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="425" data-original-width="793" src="https://1.bp.blogspot.com/-8lYCv7gAjUY/YItTmFEGCHI/AAAAAAAAAVY/ikrEqR_xsvca2FMs3xfUsP0FegJXd7JMwCLcBGAsYHQ/s320/back-door-path-3.PNG" width="320" /></a></div><br /><p>There is another type of backdoor path to consider, shown below. Backdoor path 4 passes from $G$ to $W$, through $S$ and $V$, to $C$. Backdoor path 4 will not cause confounding <i>unless</i> we make the mistake of conditioning on variable $S$. The variable $S$ is called a collider variable, because it has two arrows in the path pointing into it. We have to be careful not to condition on a collider variable, i.e., not to include it in the multivariable regression. <br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-3agNF7fwsJI/YItTwybHYWI/AAAAAAAAAVg/1BAk22dpCAcBgJpYmYtbiv-qvEXo3FUVgCLcBGAsYHQ/s809/back-door-path-4.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="425" data-original-width="809" height="168" src="https://1.bp.blogspot.com/-3agNF7fwsJI/YItTwybHYWI/AAAAAAAAAVg/1BAk22dpCAcBgJpYmYtbiv-qvEXo3FUVgCLcBGAsYHQ/w320-h168/back-door-path-4.PNG" width="320" /></a></div><br /><h3 style="text-align: left;">Patterns of confounding</h3><p>Each of the backdoor paths in any causal diagram can be broken down into a series of connections among three variables in the path. There are 3 relationships that can occur among these 3 variables: the 'fork' pattern, the 'pipe' pattern, and the 'collider' pattern.<br /> </p><p><b>Fork pattern </b><br /><br />The image below shows the 'fork' pattern, which occurs in our example among the variables $G, W$, and $S$. The fork occurs when a single variable affects two 'child' variables; in this case, being worried makes a person both more likely to socially distance, and more likely to wear protective glasses.<br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-lmuLorqLw6k/YItUDZ5dkOI/AAAAAAAAAVs/pF2rM7kORKsduVNvJXAGN0Tc5Jdn8p4FACLcBGAsYHQ/s478/fork-pattern.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="362" data-original-width="478" height="242" src="https://1.bp.blogspot.com/-lmuLorqLw6k/YItUDZ5dkOI/AAAAAAAAAVs/pF2rM7kORKsduVNvJXAGN0Tc5Jdn8p4FACLcBGAsYHQ/w320-h242/fork-pattern.PNG" width="320" /></a></div><br /><p style="text-align: left;">If three variables are related by the fork pattern, then the two child variables will be marginally statistically dependent, but will be independent if we condition on the parent variable. Mathematically, the fork pattern says that:<br /><br />$$p(G, W, S) = p(G|W)p(S|W)p(W).$$<br /><br />Since $p(G,S)=\int p(G|V)p(S|V)p(V) dV$, it follows that $p(G,S)\ne p(G)\cdot p(S)$ in general. However, $p(G,S|V)=p(G|V)\cdot p(S|V)$; in this graph of 3 variables, $W$ and $S$ are conditionally independent given $V$. <br /><br />In words, this says that if I know whether a person is worried about COVID-19, then knowing whether a person socially distances tells me nothing additional about whether they are likely to wear glasses. <br /></p><p style="text-align: left;"><b>Pipe pattern</b></p><p style="text-align: left;">The image below shows the 'pipe' pattern, which occurs in our example among the variables $W, S$, and $C$. The pipe occurs when a variable is causally 'in-between' two other variables. In this case, being worried causes a person to socially distance, which in turn reduces their chance of getting COVID-19. </p><p style="text-align: left;"><b> <br /></b></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-ylhmzWZ8b8w/YItcejJN-HI/AAAAAAAAAV0/LX8scav58bgHVMLhu20AytoYe8_CNYWYgCLcBGAsYHQ/s408/pipe-pattern.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="315" data-original-width="408" src="https://1.bp.blogspot.com/-ylhmzWZ8b8w/YItcejJN-HI/AAAAAAAAAV0/LX8scav58bgHVMLhu20AytoYe8_CNYWYgCLcBGAsYHQ/s320/pipe-pattern.PNG" width="320" /></a></div>If three variables are related by the pipe pattern, then the two outer variables will be marginally statistically dependent, but will be independent if we condition on the inner variable. Mathematically, $p(W,C)\ne p(W)\cdot p(C)$ in general, but $p(W,C|S)=p(W|S)p(C|S)$. The fork and pipe patterns are alike in this regard.<br /><br />In words, this says that if I know whether a person is avoiding social contact, then knowing whether the person is worried about COVID-19 tells me nothing additional about whether they might have caught it. <br /><br /><b>Collider pattern</b><br /><br />The collider pattern occurs when a single variable is dependent on two unrelated parent variables. There aren't any simple collider pattern examples in our example causal diagram -- for example, social distancing $S$ is dependent both on $V$ and $W$, but these two variables are also directly related to each other. So I've added an extra random variable in the diagram below: $N$, which is 1 if the person is nearsighted, and 0 otherwise. Clearly, being nearsighted is another reason why someone might wear glasses. <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-Qo2mysTIU54/YItcw1M1swI/AAAAAAAAAV8/FiJH2X3neDMhJc-vsDh3QkgmSgT-uP9VwCLcBGAsYHQ/s466/collider-pattern.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="321" data-original-width="466" src="https://1.bp.blogspot.com/-Qo2mysTIU54/YItcw1M1swI/AAAAAAAAAV8/FiJH2X3neDMhJc-vsDh3QkgmSgT-uP9VwCLcBGAsYHQ/s320/collider-pattern.PNG" width="320" /></a></div><br /><p style="text-align: left;">The collider pattern is different from the fork and pipe patterns. In the collider pattern, the two parents of the common child are marginally independent of each other. Mathematically, we have $p(N,W) = p(N)p(W)$ (it follows from the definition of the joint distribution, $p(N,W,G)=p(G|N,W)p(N)p(W)$), but $p(N,W|G)\ne p(N|G)\cdot p(W|G)$ in general. In other words, conditioning the regression on the 'collider variable' $G$ causes the parent variables $N,W$ to <i>become associated</i>. But the association is purely statistical; the two parent variables are still causally unrelated. <br /><br />To see why this happens, imagine that you know nothing about whether a person wears glasses or not. Then knowing in addition that the person is nearsighted gives you no additional information about whether they are worried about COVID-19. <br /><br />But suppose that you now know that the person is wearing glasses (i.e., you are conditioning on $G=1$). If you know in addition that the person is not nearsighted, then the odds are higher that they are wearing glasses because they are worried about COVID-19; and if you know that they are not worried about COVID-19, the odds increase that they are wearing glasses because they are nearsighted. So the parent variables become related. Collider bias is sometimes called 'explaining away'; knowing that a person is nearsighted 'explains away' their reason for wearing glasses. <br /> </p><p style="text-align: left;"><b>Putting it together<br /></b><br />This tells you everything you need to know in order to construct an unconfounded multivariate regression analysis, in order to determine whether one variable has a causal impact on another. The game is to 'block all the backdoor paths', to prevent them from causing accidental correlations between the dependent and independent variables. <br /><br />For example, consider 'backdoor path 1' at the beginning of the article. This path contains a fork pattern (the variable $W$, pointing to $G$ and $S$) and a pipe pattern (the variable $S$, which is pointed to by $W$, and which points to $C$). If we don't condition on $W$ or $S$, then these variables will set up associations between $G$ and $S$, and between $W$ and $C$; the unbroken line of associations sets up a relationship between $G$ and $C$ that is only a correlation, not causal. <br /><br />In order to prevent this from happening, we need to condition on either $W$ or $S$. We must choose one of them; conditioning on either one of them will break that chain of association. This is called 'blocking the backdoor path'. But blocking one backdoor path isn't enough; we must block all of them. <br /><br />Consider backdoor path 2 from $G$ to $C$; it contains a fork variable, $W$, and a pipe variable, $V$. Conditioning on either $V$ or $W$ will block backdoor path 2. Note that conditioning on $W$ will block both backdoor paths 1 and 2, but conditioning on $V$ or $S$ will leave one of the paths unblocked.<br /><br />Now consider backdoor path 3. Backdoor path 3 contains a fork variable, $W$; a pipe variable, $V$; and another pipe variable, $S$. Conditioning on any of these will block this backdoor path, so again, $W$ will work for this path.<br /><br />Finally, looking at backdoor path 4, we see that $S$ is a collider variable in this path. Looking at this path in isolation, $W$ and $V$ will be marginally independent of each other. But if we condition on the variable $S$, that will set up an association between $W$ and $V$, which will connect all the variables in backdoor path 4, and cause confounding. <br /><br />The following shows how the association between $W$ and $V$ can occur, as a result of knowing the value of $S$. Suppose we know for sure that a person is not avoiding social contact (i.e., we have conditioned on $S$). Suppose we also know that this person is worried about COVID-19; then this makes it highly likely that the person is vaccinated, since they would otherwise be avoiding people. Conversely, if we know that a person is not avoiding social contact, and we also know that the person is not vaccinated, then it is highly likely that they just aren't worried about COVID-19. <br /><br />The fact that $S$ is a collider in this path means that we have to avoid conditioning on $S$ (including it in the regression). Conditioning on it will open backdoor path 4, which would otherwise be blocked. <br /><br />To summarize, there are 5 total backdoor paths in this diagram -- the four we have discussed, and one other that also contains the variable $S$ as a collider (see if you can find it). Conditioning on $W$ will block the first 3 backdoor paths, and will not accidentally unblock the two paths that contain $S$ as a collider variable. Therefore, a multivariate regression that contains only $W$ as a covariate, $G$ as the independent variable, and $C$ as the dependent variable, will correctly show that wearing glasses has no effect on COVID-19 incidence. <br /></p><p style="text-align: left;"><b> </b><br /></p>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-75346580698519471112021-04-22T14:41:00.008-07:002021-05-05T08:55:20.251-07:00A gentle introduction to causal diagrams<p> <br /></p><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-dOS2OimKkKY/YIHr2QVTPNI/AAAAAAAAAU0/mwk3nC6l2GA8SD--Eh7IK_5tBRmHEolfwCLcBGAsYHQ/s1024/gentle-intro-dags-brown-owl.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1024" data-original-width="723" height="320" src="https://1.bp.blogspot.com/-dOS2OimKkKY/YIHr2QVTPNI/AAAAAAAAAU0/mwk3nC6l2GA8SD--Eh7IK_5tBRmHEolfwCLcBGAsYHQ/s320/gentle-intro-dags-brown-owl.jpg" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Cute burrowing owl. (creative commons)<br /></td></tr></tbody></table><br /><p></p><p> In a recent blog post, <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical confounding: why it matters</a>, I touched a bit on the topic of causal diagrams, and defined statistical confounding as occurring when the association between two variables is influenced by a third variable, leading (potentially) to incorrect conclusions about the causal relationship between them. </p><p>In this blog post, I'll work through an example of a simple (and totally hypothetical! but nevertheless kind of plausible!) causal diagram, and show how it can be used to select variables for multiple regressions so that causality can be inferred. Please note that this is a completely made-up example using data that I generated. I've just made up a story around COVID-19 because it is an important statistical problem to which most people can intensely relate!</p><p>Imagine that we've collected data for a huge observational study, in an attempt to determine whether wearing protective glasses affects the likelihood of catching COVID-19. Our dataset consists of many thousands of rows of data; each row represents an individual. The dataset has two columns: $G$, a boolean variable indicating whether the person wears protective glasses, and $C$, a boolean variable indicating whether the person has tested positive for covid. The causal relationship we want to test can be diagrammed like this:</p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-inzfFBUzEjM/YIHpWCzcsBI/AAAAAAAAAUE/EI88MAYMBQ0YZY5cE0UQbynJQGPlSRivwCLcBGAsYHQ/s695/mask-wearing-covid-causal-diagram-1.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="147" data-original-width="695" src="https://1.bp.blogspot.com/-inzfFBUzEjM/YIHpWCzcsBI/AAAAAAAAAUE/EI88MAYMBQ0YZY5cE0UQbynJQGPlSRivwCLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-1.PNG" width="320" /></a></div><p> </p><p> where an arrow from $G$ to $C$ indicates that glasses-wearing has a causal effect on catching COVID-19. </p><p>I've generated some data representing the results of such an observational study. Because I faked the data, I know for certain that there is no direct causal impact of $G$ on $C$ in it; $C$ is generated from an expression that doesn't include $G$. The generated data includes $G$ and $C$ and several other boolean variables, including $W$ (is the person concerned about COVID-19?) and $S$ (is the person avoiding social contact?). <br /><br />The diagram below shows the true causal relationships among these 4 random variables. There is no directed arrow between $G$ and $C$, indicating that wearing protective glasses neither prevents nor causes a person to catch COVID-19. There are arrows from $W$ to both $G$ and $S$, indicating that concern about COVID-19 drives people to both wear protective glasses, and to socially distance. There is an arrow from $S$ to $C$, indicating that avoiding social contact actually does prevent catching COVID-19. <br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-2L4aLlQaF4A/YIHpWTAgUEI/AAAAAAAAAUI/sOgDAgafjNgpg9YdLgYVa8IYlZ6q2_swgCLcBGAsYHQ/s642/mask-wearing-covid-causal-diagram-2.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="350" data-original-width="642" src="https://1.bp.blogspot.com/-2L4aLlQaF4A/YIHpWTAgUEI/AAAAAAAAAUI/sOgDAgafjNgpg9YdLgYVa8IYlZ6q2_swgCLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-2.PNG" width="320" /></a></div><p></p><p> But let's suppose we don't know anything about the data. In order to investigate the question of whether glasses-wearing helps prevent COVID-19, we do a Bayesian logistic regression using the following model:<br /><br />$$ <br />\begin{aligned} <br />C_i &\sim\text{Bernoulli}(p) \\ <br />\text{logit}(p) &= \alpha_0 + \alpha_{[G_i]}\\ <br />\alpha_0 & \sim N(\mu=0, \sigma=1.5) \\<br />\alpha_{[G_i]} & \sim N(\mu=0, \sigma=3) <br />\end{aligned} <br />$$<br /><br />where $G_i$ is either 0 or 1. The line $\text{logit}(p)=\alpha_0+\alpha_{[G_i]}$ indicates that we are modeling the probability of catching COVID-19 as a function only of $G$ (wearing protective glasses); we aren't including any other covariates. <br /><br />We fit this model, and find that the differences between the values of the model's posterior parameters $\alpha_{[G==0]}$ and $\alpha_{[G==1]}$ are large, indicating that protective glasses make a difference. The graph below shows the histogram of the differences between the fitted values of $\alpha_{[G==0]}$ and $\alpha_{[G==1]}$; more than 95% of the histogram's mass lies between the red lines, to the right of 0. <br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-qWAN1aniCos/YIHpV3fxATI/AAAAAAAAAUA/p6AyF4nBAbokTKQaOtCNIWOankaS5BqvQCLcBGAsYHQ/s787/gentle-intro-dags-1.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="480" data-original-width="787" src="https://1.bp.blogspot.com/-qWAN1aniCos/YIHpV3fxATI/AAAAAAAAAUA/p6AyF4nBAbokTKQaOtCNIWOankaS5BqvQCLcBGAsYHQ/s320/gentle-intro-dags-1.PNG" width="320" /></a></div><p></p><p>In fact, the mean fitted (posterior) probability of catching COVID-19 is 0.02 for the group that does not wear protective glasses, and 0.005 for the group that does wear protective glasses. Can we conclude that wearing protective glasses reduces the risk of catching covid by a factor of about 4?<br /><br />Well, no. But this set of causal relationships can nevertheless produce values of $G$ and $C$ that make it look like wearing protective glasses is highly effective for preventing COVID-19. This is because we've messed up by using a model that depends only on $G$ and $C$.<br /><br />In the diagram below, the causal relationship we want to assess is represented by the gray arrow between $G$ and $C$ (these are in red, indicating that they were included in the regression model). But there is a second path in the graph from $G$ to $C$ that can generate an association between $G$ and $C$, the one from $G$ to $W$ to $S$ to $C$. Unlike the one we want to test, it is a 'back-door' path from $G$ to $C$, meaning that it starts with a causal arrow that points *into* $G$ rather than away from $G$. <br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-1xeQj-aWRK0/YIHpWzJCEWI/AAAAAAAAAUM/npVdY3hWVxkHde4L3MwAE-r4xQxg0-lsACLcBGAsYHQ/s637/mask-wearing-covid-causal-diagram-3.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="344" data-original-width="637" src="https://1.bp.blogspot.com/-1xeQj-aWRK0/YIHpWzJCEWI/AAAAAAAAAUM/npVdY3hWVxkHde4L3MwAE-r4xQxg0-lsACLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-3.PNG" width="320" /></a></div><p></p><p>Here's what's going on: the factor $W$ is driving both glasses-wearing $G$ (an ineffective intervention) and social distancing $S$ (the effective intervention). This creates an association between $G$ and $S$: if a person is wearing protective glasses, they are highly likely to also be social distancing, and vice-versa. Therefore, a person wearing protective glasses is probably also social distancing, and therefore is less likely to catch COVID-19. And so, if all you're using in your model are the variables $G$ and $C$, it looks like wearing protective glasses is effective against COVID-19. <br /><br />But if you then pass a law that everyone has to wear protective glasses, it will have no effect on the COVID-19 rate, and you'll have spent a lot of political capital getting an ineffective resolution passed, and people won't listen to your advice anymore. This is a bad outcome. <br /><br />How can we fix this statistical problem? <br /><br />If the above causal diagram is the true one (a big if!), then we can fix it. We need to have collected not only the values of $G$ and $C$, but also those of $S$. What we are going to do is to 'block the back-door path' from $G$ to $C$ by conditioning on $S$, which (in the regression context) means we are going to include $S$ as a variable in the regression model. We write the new model as:<br /><br />$$ <br />\begin{aligned} <br />C_i &\sim\text{Bernoulli}(p) \\ <br />\text{logit}(p) &= \alpha_0+\alpha_{[G_i]} +\alpha_{[S_i]}\\<br />\alpha_0 &\sim N(0, 1.5) \\<br />\alpha_{[G_i]} & \sim N(0, 3) \\<br />\alpha_{[S_i]} & \sim N(0, 3)<br />\end{aligned} <br />$$<br /><br />where now we have added new terms to the model that depend on whether the person is social distancing. The new causal diagram model looks like the one below; in which we are conditioning on $S$.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-T86cR7I2YTo/YIHpXSiVdNI/AAAAAAAAAUQ/JODlv6WnQEkPLmSn1LUZvATE2oDoaVfuwCLcBGAsYHQ/s660/mask-wearing-covid-causal-diagram-4.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="373" data-original-width="660" src="https://1.bp.blogspot.com/-T86cR7I2YTo/YIHpXSiVdNI/AAAAAAAAAUQ/JODlv6WnQEkPLmSn1LUZvATE2oDoaVfuwCLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-4.PNG" width="320" /></a></div><p></p><p>We fit this model, but we find that the differences between the values of the model's posterior parameters $\alpha_{[G==0]}$ and $\alpha_{[G==1]}$ are still large. The graph below shows the histogram of the differences between the fitted values of $\alpha_{[G==0]}$ and $\alpha_{[G==1]}$ for this second model; once again, more than 95% of the histogram's mass lies to the right of 0. If we were convinced that our previous causal diagram was correct, then we would again conclude erroneously that protective glasses help prevent COVID-19. <br /></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-aFMJkE8bXT0/YIHpVlqCWGI/AAAAAAAAAT8/QyA-2J2uytIEDMIGi1BLHE2gUvhYB12RACLcBGAsYHQ/s788/gentle-intro-dags-2.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="488" data-original-width="788" src="https://1.bp.blogspot.com/-aFMJkE8bXT0/YIHpVlqCWGI/AAAAAAAAAT8/QyA-2J2uytIEDMIGi1BLHE2gUvhYB12RACLcBGAsYHQ/s320/gentle-intro-dags-2.PNG" width="320" /></a></div><br /><p></p><p>The problem this time (and this is the last problem, I promise) is that we've omitted an important variable from the causal diagram: $V$, whether the person is vaccinated. The (real!) true causal diagram that generated the data, including $V$, is shown below.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-VvjJDR8ylPE/YIHpXyUGIII/AAAAAAAAAUU/4eCYPpQdEKw7CV175PqDIhemklS_IfRcQCLcBGAsYHQ/s801/mask-wearing-covid-causal-diagram-5.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="402" data-original-width="801" src="https://1.bp.blogspot.com/-VvjJDR8ylPE/YIHpXyUGIII/AAAAAAAAAUU/4eCYPpQdEKw7CV175PqDIhemklS_IfRcQCLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-5.PNG" width="320" /></a></div><p></p><p>Adding $V$ adds some new and interesting connections to the causal diagram. There is an arrow from $W$ to $V$, because if a person is concerned about COVID-19, they're more likely to get the vaccine. There is an arrow from $V$ to $S$, because if a person is vaccinated, they're likely to be less careful about social distancing. And clearly, whether a person is vaccinated directly impacts their risk of catching COVID-19. <br /><br />Because of $V$, our new, true causal diagram still has an unblocked back-door path in it from $G$ to $C$: the one from $G$ through $W$, to $V$ and then to $C$. Also because of $V$, the back-door path from $G$ to $W$ through $S$ to $C$ that we thought was blocked is actually unblocked. These unblocked back-door paths from $G$ to $C$ are still producing confounding that makes it look as though wearing protective glasses helps with COVID-19. <br /><br />How can we fix the problem with $V$? Well, analyzing the causal diagram shows that including $V$ in the model with $G$ and $S$ would block all of the back-door paths from $G$ to $C$. But what if we don't have $V$ in the data we collected, because we never thought to collect it? <br /><br />In some situations, we might be unable to fix confounding. Unobserved variables like $V$ are often present in statistical studies, and you may not even suspect they are there, but they can still cause confounding. The best we can do in statistical analyses of causality is to try to collect all the variables that might influence the problem, and think about possible causal diagrams for the variables.<br /><br />In this example, even if we didn't collect vaccination information, we can still fix the problem by conditioning on $W$ instead of $S$, as shown in the diagram below. Since all of the backdoor paths from $G$ to $C$ lead through the variable $W$, conditioning on $W$ blocks them all at once. So, in order to get an unconfounded model, the only information we need to add to the model is whether the person is Concerned About COVID-19.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-URhy4ner1ps/YIHpYKEoBLI/AAAAAAAAAUY/Q-08cuFBegEAP7PgvyWktVSqMfLaicX3ACLcBGAsYHQ/s807/mask-wearing-covid-causal-diagram-6.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="409" data-original-width="807" src="https://1.bp.blogspot.com/-URhy4ner1ps/YIHpYKEoBLI/AAAAAAAAAUY/Q-08cuFBegEAP7PgvyWktVSqMfLaicX3ACLcBGAsYHQ/s320/mask-wearing-covid-causal-diagram-6.PNG" width="320" /></a></div><p> </p><p> Our final and good model would look like this:<br /><br />$$ <br />\begin{aligned} <br />C_i &\sim\text{Bernoulli}(p) \\ <br />\text{logit}(p) &= \alpha_0+\alpha_{[G_i]} +\alpha_{[W_i]}\\<br />\alpha_0 &\sim N(0, 1.5) \\<br />\alpha_{[G_i]} & \sim N(0, 3) \\<br />\alpha_{[W_i]} & \sim N(0, 3)<br />\end{aligned} <br />$$<br /><br />After fitting this model, we find that the histogram of the differences between $\alpha_{[G==0]}$ and $\alpha_{[G==1]}$ for this final model straddles 0 as shown below, indicating that the variable $G$ is not significant for modeling the rate at which people catch COVID-19. </p><p><br /></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-7ZXw9paJqqw/YIHpV3tZTcI/AAAAAAAAAT4/IQmzul52RhQ2NpyTp21pXKR7DTBoc2BpACLcBGAsYHQ/s783/gentle-intro-dags-3.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="489" data-original-width="783" src="https://1.bp.blogspot.com/-7ZXw9paJqqw/YIHpV3tZTcI/AAAAAAAAAT4/IQmzul52RhQ2NpyTp21pXKR7DTBoc2BpACLcBGAsYHQ/s320/gentle-intro-dags-3.PNG" width="320" /></a></div><br /><p></p><p> In my next post, I'll explain how you can analyze causal diagrams yourself, find back-door paths, and block them by conditioning on specific variables (and not conditioning on others!), in order to prevent statistical confounding in statistical analyses. </p><p>--- <br /></p><p>Here's the entire 'statistical confounding' series:</p><p>- Part 1: <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical confounding: why it matters:</a> on the many ways that confounding affects statistical analyses </p><p>- Part 2: <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">Simpson's Paradox: extreme statistical confounding</a>: understanding how statistical confounding can cause you to draw exactly the wrong conclusion</p><p>- Part 3: <a href="https://frommyslipbox.blogspot.com/2021/04/linear-regression-is-trickier-than-you.html" target="_blank">Linear regression is trickier than you think</a>: a discussion of multivariate linear regression models <br /></p><p>- Part 4: <a href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" target="_blank">A gentle introduction to causal diagrams</a> (this post): a causal analysis of fake data relating COVID-19 incidence to wearing protective goggles</p><p>- Part 5: <a href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" target="_blank">How to eliminate confounding in multivariate regression</a>: how to do a causal analysis to eliminate confounding in your regression analyses </p><p>-Part 6: <span style="font-family: inherit;"><a class="internal-link is-unresolved" data-href="TBD" href="https://frommyslipbox.blogspot.com/2021/05/trouble-that-you-cant-fix-omitted.html" rel="noopener" style="box-sizing: border-box; color: #5c73f2; cursor: pointer; opacity: 0.5; outline: currentcolor none medium; text-decoration: underline;" target="_blank">A simple example of omitted variable bias</a>: an example of statistical confounding that can't be fixed, using only 4 variables.</span></p>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-90244534350723524432021-04-15T20:18:00.004-07:002021-05-05T08:55:38.754-07:00Linear regression is trickier than you think<h3 style="text-align: left;"><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-Er4mOPrLBdw/YHj_LaqNPqI/AAAAAAAAATc/QnSjmkXteUkYTz1xZf1qzEshaOiPoSQNACLcBGAsYHQ/s1024/miffed-looking-owl.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="683" data-original-width="1024" src="https://1.bp.blogspot.com/-Er4mOPrLBdw/YHj_LaqNPqI/AAAAAAAAATc/QnSjmkXteUkYTz1xZf1qzEshaOiPoSQNACLcBGAsYHQ/s320/miffed-looking-owl.jpg" width="320" /></a></div> Preamble</h3><div style="text-align: left;">In my last two posts, I talked about statistical confounding: <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">why it matters</a> in statistics, and what it looks like when it gets really extreme <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">(Simpson's Paradox)</a>. <br /></div><p>In my next few blog posts, I want to talk about some tricks for controlling statistical confounding in the context of multivariate linear regression, which is about the simplest kind of model that can be used to relate more than 2 variables. Although I've taken a full load of statistics classes including a whole course on multivariate linear regression alone, I never learned how to choose the right variables to include for a desired analysis until I came across it in <a href="https://xcelab.net/rm/statistical-rethinking/" target="_blank">Richard McElreath's book 'Statistical Rethinking'. </a></p><p>In short, it's likely to be something that most machine learning and data science practitioners wouldn't ordinarily pick up in a class on regression, and it's useful and kind of fun. <br /></p><p>Controlling confounding requires drawing hypothetical diagrams of how your variables might relate causally to each other, doing some checks to determine whether the data conflict with the hypotheses, and then using the diagrams to derive sets of variables to exclude and include. It's a nice interplay between high level thinking about causality, and mechanical variable selection. <br /></p><p>This week's post is an introduction where I'll set the stage a bit. </p><p>---<br /></p><p>Here's the entire 'statistical confounding' series:</p><p>- Part 1: <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical confounding: why it matters:</a> on the many ways that confounding affects statistical analyses </p><p>- Part 2: <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">Simpson's Paradox: extreme statistical confounding</a>: understanding how statistical confounding can cause you to draw exactly the wrong conclusion</p><p>- Part 3: <a href="https://frommyslipbox.blogspot.com/2021/04/linear-regression-is-trickier-than-you.html" target="_blank">Linear regression is trickier than you think </a>(this post): a discussion of multivariate linear regression models <br /></p><p>- Part 4: <a href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" target="_blank">A gentle introduction to causal diagrams</a>: a causal analysis of fake data relating COVID-19 incidence to wearing protective goggles</p><p>- Part 5: <a href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" target="_blank">How to eliminate confounding in multivariate regression</a>: how to do a causal analysis to eliminate confounding in your regression analyses </p><p>-Part 6: <span style="font-family: inherit;"><a class="internal-link is-unresolved" data-href="TBD" href="https://frommyslipbox.blogspot.com/2021/05/trouble-that-you-cant-fix-omitted.html" rel="noopener" style="box-sizing: border-box; color: #5c73f2; cursor: pointer; opacity: 0.5; outline: currentcolor none medium; text-decoration: underline;" target="_blank">A simple example of omitted variable bias</a>: an example of statistical confounding that can't be fixed, using only 4 variables.</span> <br /></p><p> </p><h3 style="text-align: left;">Multivariate linear regression<br /></h3><p>Multivariate linear regressions are the first type of frequentist models you encounter as a statistician. They are used to relate an outcome variable $Y$ in a data set to any number of covariates $X_i$ which accompany it. For example, the height that a tree grows this year, $H$, might be associated with several continuous covariates, such as the number of hours of sunlight it receives per day $S$, the amount of water it receives per day $W$, and the iron content of the soil around it, $I$. These variables in turn may be associated with each other; for example, if the tree is not artificially watered, then $S$ and $W$ may be negatively correlated, since the sun doesn't usually shine when it's raining. <br /><br />The model specification below is for a Bayesian linear regression model with $n$ covariates, and no higher-order terms. The distribution of $Y$ is normal, with a mean that linearly depends on the covariates $X_i$, and a variance parameter. All the parameters have priors, which the model specifies. Models like this are usually fitted using methods that sample the posterior distribution of the parameters given the observed data. The results of Bayesian model fitting are usually very similar to frequentist model fitting results when there is sufficient data for analysis. <br /><br />$<br />\begin{aligned}<br />Y &\sim N(\mu, \sigma^2) \\<br />\mu &= \alpha + \beta_1X_1 + ... + \beta_nX_n \\<br />\alpha &\sim N(1, 0.5) \\<br />\beta_j &\sim N(0, 0.2) \text{ for } j=1,...,n \\<br />\sigma & \sim \text{exp}(1)<br />\end{aligned}<br />$<br /><br />The fact that the scale of the modeled parameter $\mu$ is the same as that of $Y$, and the absence of higher-order terms (such as $x_1x_3$), make it easy to interpret the meaning of each slope parameter: $\beta_j$ is the expected change in the value of the outcome variable when the covariate $X_j$ changes by one unit. The assumption that this expected change is always the same, independent of the values of the $n$ covariates, is built right into this model.<br /><br />This model is about as simple a statistical model as you can have for modeling data sets with a lot of variables. But when I was studying multivariate regression, the covariates used for modeling were often chosen without much explanation. Sometimes we would use all the variables available, and sometimes we would only use a subset of them. It wasn't until later that I learned how to choose which variables to include in a multivariate regression model. The choice depends on what you're trying to study, and on the causal relationships among all the variables. <br /><br />And, of course, you don't know the causal relationships among the variables -- often, this is what you're trying to figure out by doing linear regression -- so you need to consider several possible diagrams of causal relationships.<br /><br />The ultimate goal is to get statistical models that clearly answer your questions, and don't 'lie'. Actually, statistical models never lie, but they can mislead. Statistical confounding occurs when the apparent relationship between the value of a covariate $X$ and the outcome variable $Y$, as measured by a model, differs from the true causal effect of $X$ on $Y$. The effects of confounding can be so extreme that they result in <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">Simpson's Paradox reversals</a>, where the apparent association between variables is the opposite of the causal association. <br /></p><p>It takes some know-how to eliminate confounding. Sometimes you have to be sure to include a variable in a multivariate regression in order to get an unconfounded model; sometimes including a variable will *cause* confounding. </p><p>Sometimes, nothing you can do will prevent confounding, because of an unobserved variable. But here is what you can do:<br /><br />1. You can hypothesize one or more causal diagrams that relate the variables under study. You can consider some that include variables you may not have measured, in order to anticipate problems.<br />2. You might be able to discard some of these hypotheses, if the implied condiional independence relationships between the variables aren't supported by the data. <br />3. You can learn how to choose what variables to include and exclude, on the basis of the remaining hypothetical causal diagrams, to get multivariate regressions that aren't confounded.<br />4. You can also determine when confounding can't be prevented, because you would need to include a variable that isn't available. </p><p>In succeeding posts, I'll show you how to go about doing this yourself. <br /><br /></p>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-56876595457665846512021-04-12T08:04:00.001-07:002021-04-12T08:04:50.121-07:00A new productivity trick <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://lh3.googleusercontent.com/-0PH55g0Tsos/YHRcRU3ADTI/AAAAAAAAATU/gVBwnNJxjnkDwy5ZWvFoIEpcaGB7l13aACLcBGAsYHQ/owl_in_flight.jpg" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="625" data-original-width="1024" height="195" src="https://lh3.googleusercontent.com/-0PH55g0Tsos/YHRcRU3ADTI/AAAAAAAAATU/gVBwnNJxjnkDwy5ZWvFoIEpcaGB7l13aACLcBGAsYHQ/owl_in_flight.jpg" width="320" /></a></div><br /><br /><p></p><p>This past week, instead of posting an article from my Zettelkasten, <a href="https://www.linkedin.com/pulse/managing-myself-help-split-personalities-carolyn-johnston/" target="_blank">I wrote an article for LinkedIn on a new self-management trick I've been using</a>. I've found that dissociating my 'worker' persona from my 'manager' persona -- literally, pretending that they are different people -- has been a useful aid for me to getting work planned and done. <br /></p><p>I certainly don't want to give the impression that I'm any master of productivity and time management. I'm still looking for the perfect regimen that I can stick to. I've tried quite a few of them, and kept a couple of them; I'm a fan of <a href="https://gettingthingsdone.com/what-is-gtd/" target="_blank">Getting Things Done</a> and <a href="https://todoist.com/productivity-methods/time-blocking" target="_blank">Time Blocking</a>, and I use both of those approaches when the mood to get my ducks in a row comes upon me. I've concluded that the best I can do is to have an arsenal of productivity tricks that I can deploy when I'm feeling uninspired (including the 'split-personality' trick), and to establish firm habits around scheduled work times. I can be found with my butt in my seat at my desk at the usual hours during every work day. That is the only trick I've ever found that really works consistently. <br /></p><p><br /></p>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-86364099287687563322021-04-01T12:34:00.007-07:002021-05-05T08:55:56.732-07:00Simpson's Paradox: extreme statistical confounding<h3 style="text-align: left;"><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-dL8jZ7jVXjU/YGYNat7RCXI/AAAAAAAAARo/X-NHoqv8dWU_bWPpWYfD0qu0mxVx23qbQCLcBGAsYHQ/s1024/202104%2Bconfusion%2B--%2BSimpsons%2Bparadox.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="681" data-original-width="1024" src="https://1.bp.blogspot.com/-dL8jZ7jVXjU/YGYNat7RCXI/AAAAAAAAARo/X-NHoqv8dWU_bWPpWYfD0qu0mxVx23qbQCLcBGAsYHQ/s320/202104%2Bconfusion%2B--%2BSimpsons%2Bparadox.jpg" width="320" /></a></div> </h3><h3 style="text-align: left;">Preamble</h3><h3 style="text-align: left;"> </h3><div style="text-align: left;">Simpson's Paradox is an extreme example of the effects of statistical confounding, which I discussed in last week's blog post, "<a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical Confounding: why it matters</a>".<br /><br />Simpson's Paradox can occur when an apparent association between two variables $X$ and $Y$ is affected by the presence of a confounding variable, $Z$. In Simpson's Paradox, the confounding is so extreme that the association between $X$ and $Y$ actually disappears or reverses itself after conditioning on the confounder $Z$. </div><div style="text-align: left;"><br /></div><div style="text-align: left;">Simpson's paradox can occur in count data or in continuous data. In this post, I'll talk about how to visualize Simpson's paradox for count data, and how to understand it as an example of statistical confounding.</div><div style="text-align: left;"><br /></div><div style="text-align: left;">It isn't actually a paradox; it makes complete sense, once you understand what's going on. It's just that it's not what our intuition tells us should happen. And whether it's 'wrong' depends on what goal you're shooting for. In the example below, if you want to make a choice for yourself based on understanding the relative effectiveness of the two treatments, you'd be best off choosing Treatment A. But if your goal is prediction -- who is likely to do better, a random patient who gets Treatment A or Treatment B? -- you're best off with Treatment B.</div><div style="text-align: left;"> </div><div style="text-align: left;">If that confuses you, keep reading. </div><div style="text-align: left;"> </div><div style="text-align: left;">---</div><div style="text-align: left;"> </div><div style="text-align: left;"><p>Here's the entire 'statistical confounding' series:</p><p>- Part 1: <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical confounding: why it matters:</a> on the many ways that confounding affects statistical analyses </p><p>- Part 2: <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">Simpson's Paradox: extreme statistical confounding</a> (this post): understanding how statistical confounding can cause you to draw exactly the wrong conclusion</p><p>- Part 3: <a href="https://frommyslipbox.blogspot.com/2021/04/linear-regression-is-trickier-than-you.html" target="_blank">Linear regression is trickier than you think</a>: a discussion of multivariate linear regression models <br /></p><p>- Part 4: <a href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" target="_blank">A gentle introduction to causal diagrams</a>: a causal analysis of fake data relating COVID-19 incidence to wearing protective goggles</p>- Part 5: <a href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" target="_blank">How to eliminate confounding in multivariate regression</a>: how to do a causal analysis to eliminate confounding in your regression analyses </div><div style="text-align: left;"><br /></div><div style="text-align: left;">-Part 6: <span style="font-family: inherit;"><a class="internal-link is-unresolved" data-href="TBD" href="https://frommyslipbox.blogspot.com/2021/05/trouble-that-you-cant-fix-omitted.html" rel="noopener" style="box-sizing: border-box; color: #5c73f2; cursor: pointer; opacity: 0.5; outline: currentcolor none medium; text-decoration: underline;" target="_blank">A simple example of omitted variable bias</a>: an example of statistical confounding that can't be fixed, using only 4 variables.</span></div><div style="text-align: left;"> <br /></div><h3 style="text-align: left;">A famous example: kidney stone treatments<br /></h3><p>Here is a famous example of Simpson's Paradox occurring in nature, in a medical study comparing the efficacy of kidney stone treatments (here's a link to the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1339981/" target="_blank">original study</a>).<br /><br />In this example, we are comparing two treatments for kidney stones. The data show that, over all patients, Treatment B is successful in 83% of cases, and Treatment A is successful in only 78% of cases. <br /><br />However, if we consider only patients with large kidney stones, then Treatment A is successful in 73% of cases, whereas Treatment B is successful in only 69% of cases. <br /><br />And if we consider only patients with small kidney stones, the Treatment A is successful in 93% of cases, where Treatment B is successful in only 87% of cases.<br /><br />Suppose you're a kidney stone patient. Which treatment would <i>you </i>prefer? Since I'd presumably have either a small kidney stone or a large one, and Treatment A works better for either one, I'd prefer Treatment A. But looking at all patients overall, this result says Treatment B is better. Does this mean that if I don't know what size kidney stone I have, I should prefer Treatment B? (No). Why is this happening?<br /><br />This is happening because the small-vs-large-kidney stone factor is a confounding variable, as discussed in this <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">post on statistical confounding from last week</a>. </p><p>The diagram below shows the causal relationships among three variables applying to every kidney stone patient. Either Treatment A or B is selected for the patient. Either the treatment is either considered successful, or it isn't. And the confounding variable is in red: either the patient has a large kidney stone, or they do not. </p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-SYlFHlzfpfU/YGYN-aVWHgI/AAAAAAAAARs/rNqvn9o3R9IfDRDqIM4NMvRABTALuFDlwCLcBGAsYHQ/s628/kidney-stones-simpsons-paradox.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="320" data-original-width="628" height="326" src="https://1.bp.blogspot.com/-SYlFHlzfpfU/YGYN-aVWHgI/AAAAAAAAARs/rNqvn9o3R9IfDRDqIM4NMvRABTALuFDlwCLcBGAsYHQ/w640-h326/kidney-stones-simpsons-paradox.PNG" width="640" /></a><br /></div><p>The size of the kidney stone, reasonably, has an impact on how successful the treatment is; similarly, we're assuming the treatment choice affects the success of the treatment. </p><p>But here's the confounding factor: the stone size, in red, also affects the choice of treatment for the patient. Treatment A is more invasive (it's surgical), and so it's more likely than Treatment B to be applied to severe cases with larger kidney stones. Conversely, Treatment B is more likely to be applied to smaller kidney stone cases, which are lower risk to begin with. Since the size of the kidney stone is influencing the choice of Treatments A vs. B, the causal diagram has an arrow from the size variable to the Treatment variable. And this is the 'back door', from the stone size variable into the Treatment choice variable, that is causing the confounding.<br /><br />To see what is actually happening, look at the total numbers of patients in each of the four kidney stone subgroups:</p><p></p><ul style="text-align: left;"><li>Treatment A, large stones: 263</li><li>Treatment A, small stones: 87</li><li>Treatment B, large stones: 80</li><li>Treatment B, small stones: 270<br /></li></ul><p>Clearly the size of the stone is impacting the treatment choice. </p><p>But stone size is also a huge predictor for treatment success: the larger the stone size, the harder it is for <i>any</i> treatment to succeed. So a higher proportion of small stone, Treatment B cases succeed than of large stone, Treatment A cases. And that's what's causing Simpson's Paradox. <br /></p><h3 style="text-align: left;">Visualizing Simpson's Paradox for count data</h3><div style="text-align: left;"> </div><div style="text-align: left;">Suppose we're running an experiment to assess the effect of a variable $x$ on a 'coin flip' variable $Y$. Each time we flip the coin, we'll call that a trial T. Each time $Y$ comes up heads, we'll call that a success S. The graph above has T on the x axis, and S on the y axis. Many experiments are modeled this way. In the kidney stone example, the variable $x$ refers to the choice of treatment, and the variable $Y$ refers to whether it had a successful outcome. <br /><br />During data analysis, we'll break down the total sample of kidney stone patients into subgroups by whether they got Treatment A or B. We can break it down further in any way we choose; for example, we can subset the data by age, by gender, or by both at once. Or we can further subset the patients based on whether they had a large kidney stone. This subsetting will result in groups which we'll denote by $g$. <br /><br />We can visualize subgroup $g$'s experimental results by placing it in the graph as a vector $\vec{g}$ from the origin to the point $(S_g,T_g)$, where $T_g$ is the number of patients in the group, and $S_g$ is the number of patients in the group with successful outcomes. </div><div style="text-align: left;"> </div><div style="text-align: left;">The slope of $\vec{g}$ is $S_g/T_g$, so the slopes of the vectors therefore indicate the success rate within each subgroup (note that the slopes of these vectors can never be larger than 1, since you can't have more successes than trials). When you compare the success rates between groups in an experiment, you only need to look at the slopes of these vectors -- the sizes of the subgroups are not visible to you. But it's the disparities in subgroup sizes that cause Simpson's paradox to occur. </div><div style="text-align: left;"> </div><div style="text-align: left;">The lengths of the vectors are a rough indicator of how many patients there were within each subgroup; the larger the number of patients in the group, $T_g$, the longer $\vec{g}$ will be.</div><div style="text-align: left;"><br /></div><div style="text-align: left;"></div><div style="text-align: left;"></div><div style="text-align: left;"></div><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-LaBHvyW1R64/YGYTsJdVgaI/AAAAAAAAAR4/fwIEy8OZErcYD9WQ93qbeMHyA-M77kT-wCLcBGAsYHQ/s1156/kidney%2Bstone%2Bsimpsons%2Bvisualization.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="613" data-original-width="1156" height="339" src="https://1.bp.blogspot.com/-LaBHvyW1R64/YGYTsJdVgaI/AAAAAAAAAR4/fwIEy8OZErcYD9WQ93qbeMHyA-M77kT-wCLcBGAsYHQ/w640-h339/kidney%2Bstone%2Bsimpsons%2Bvisualization.PNG" width="640" /></a></div><p></p><p>In the diagram above, we see that the subgroups Treatment A for small stones, and Treatment B for large stones, were much smaller in length than the other two (because there were fewer trials in those subgroups). But their lengths do not matter when considering the per-group success rates $S_g/T_g$; all that matters is their slopes. Treatment A's slope for small stones is higher than Treatment B's slope for small stones; the same holds the large stone groups. So within each subgroup, Treatment A is more successful.</p><p>But if we restrict our attention to the two longest vectors in the middle, we can see that the Treatment B, small stones vector has a higher slope than the Treatment A, large stones vector. This is mainly due to the fact that people with large kidney stones generally have worse outcomes, regardless of how they are treated. <br /></p><div style="text-align: left;"></div><div style="text-align: left;"></div><div style="text-align: left;"></div><div style="text-align: left;">In the diagram below, we are looking at the resulting vectors when all the Treatment A and B patients are grouped together, regardless of stone size. </div><div style="text-align: left;"><br />We get the vector corresponding to the combined group in Treatment A by summing the two green Treatment A vectors. Similarly, we sum the two black Treatment B vectors to get the aggregated Treatment B vector. When we do this, we can see that the Treatment B vector has the higher slope. </div><div style="text-align: left;"><br /></div><div style="text-align: center;"><a href="https://1.bp.blogspot.com/-OMsHT12SU8A/YGYVE80_Q2I/AAAAAAAAASA/6ZD7YI9-UUcpHv5Io5kTgsFkaTgbU_SAQCLcBGAsYHQ/s795/sum-vectors-simpsons-paradox.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="431" data-original-width="795" height="346" src="https://1.bp.blogspot.com/-OMsHT12SU8A/YGYVE80_Q2I/AAAAAAAAASA/6ZD7YI9-UUcpHv5Io5kTgsFkaTgbU_SAQCLcBGAsYHQ/w640-h346/sum-vectors-simpsons-paradox.PNG" width="640" /></a><br /></div><div style="text-align: left;"> </div><div style="text-align: left;">This happens because, when we add the green vectors together to get the total Treatment A vector, the result is only slightly different from the much longer Treatment A, small stones group vector. Similarly, the summed vector for Treatment B is only slightly different from the much longer Treatment B, large stones group vector. </div><div style="text-align: left;"> </div><div style="text-align: left;">As a result, the combined Treatment A vector has a lower slope than the combined Treatment B vector, making it look less effective overall. This is Simpson's Paradox in visual form. </div><div style="text-align: left;"></div><div style="text-align: left;"></div><div style="text-align: left;"><br />Simpson's Paradox reversals don't occur often in nature, though there are a few examples (like this one). But subtler forms of statistical confounding definitely do occur, all the time, in settings where they affect the conclusions of observational studies.<br /></div>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-66220489257795581502021-03-26T08:25:00.008-07:002021-05-05T08:56:16.283-07:00Statistical confounding: why it matters<p><b>Preamble </b></p><p>This article is a brief introduction to statistical confounding. My hope is that, having read it, you'll be more on the lookout for it, and interested in learning a bit more about it. <br /></p><p>Statistical confounding, leading to errors in data-based decision-making, is a problem that has important consequences for public policy-making. This is always true, but it seems especially true in 2020-2021. Consider these questions:</p><p>1. Is lockdown the best policy to reduce COVID death rates, or would universal masking work just as well? <br /></p><p>2. Would outlawing assault rifles lower death rates due to violence in the US? </p><p>3. Would outlawing hate speech reduce the incidence of crime against minorities in the US? </p><p>4. What effect would shutting down Trump's access to social media have on his more extreme supporters?</p>If you're making data-based decisions (or deciding whether to support them), it's important to be aware that confounding happens. For people practicing statistics, including scientists and analysts, it's important to understand how to prevent confounding from influencing your inferences, if possible. <p>Identifying and preventing confounding is a topic that I haven't seen covered in most places -- not even in my multivariate linear regression classes. It's explained beautifully in <a href="https://www.amazon.com/Statistical-Rethinking-Bayesian-Examples-Chapman-dp-036713991X/dp/036713991X/">Chapter 5 of Richard McElreath's book "Statistical Rethinking"</a>, which I highly recommend if you're up for a major investment of time and thought. </p><p>This topic is the first in a cluster about statistical inference from my slipbox (<a href="https://www.blogger.com/u/1/blog/post/edit/preview/693365974866791256/4685863230191610018">what's a slipbox?</a>).</p><p>Important note: I use the 'masking' example below as a case where confounding might hypothetically occur. I am not suggesting for a moment that masks don't fight COVID transmission. I am a huge fan of masking! Even though I wear glasses and am constantly fogged up.</p><p>---</p><p>Here's the entire 'statistical confounding' series:</p><p>- Part 1: <a href="https://frommyslipbox.blogspot.com/2021/03/statistical-confounding-why-it-matters.html" target="_blank">Statistical confounding: why it matters</a> (this post): on the many ways that confounding affects statistical analyses </p><p>- Part 2: <a href="https://frommyslipbox.blogspot.com/2021/04/simpsons-paradox-extreme-statistical.html" target="_blank">Simpson's Paradox: extreme statistical confounding</a>: understanding how statistical confounding can cause you to draw exactly the wrong conclusion</p><p>- Part 3: <a href="https://frommyslipbox.blogspot.com/2021/04/linear-regression-is-trickier-than-you.html" target="_blank">Linear regression is trickier than you think</a>: a discussion of multivariate linear regression models <br /></p><p>- Part 4: <a href="https://frommyslipbox.blogspot.com/2021/04/a-gentle-introduction-to-causal-diagrams.html" target="_blank">A gentle introduction to causal diagrams</a>: a causal analysis of fake data relating COVID-19 incidence to wearing protective goggles</p><p>- Part 5: <a href="https://frommyslipbox.blogspot.com/2021/04/how-to-eliminate-confounding-in.html" target="_blank">How to eliminate confounding in multivariate regression</a>: how to do a causal analysis to eliminate confounding in your regression analyses </p><p>-Part 6: <span style="font-family: inherit;"><a class="internal-link is-unresolved" data-href="TBD" href="https://frommyslipbox.blogspot.com/2021/05/trouble-that-you-cant-fix-omitted.html" rel="noopener" style="box-sizing: border-box; color: #5c73f2; cursor: pointer; opacity: 0.5; outline: currentcolor none medium; text-decoration: underline;" target="_blank">A simple example of omitted variable bias</a>: an example of statistical confounding that can't be fixed, using only 4 variables.</span> <br /></p><p><b>Statistical Confounding</b><br /></p>Suppose you've got an outcome you desire: for example, you want covid cases per capita in your state to go down. Give COVID cases per capita a name: call it $Y$. <p>You've also got another variable, $X$, that you believe has an effect on $Y$. Perhaps $X$ is the fraction of people utilizing masks whenever they go out in public. $X=0$ means no one is wearing masks: $X=1$ means everyone is. </p><p>You believe, based on numbers collected in a lot of other locations, that the higher the value of $X$ is, the lower the value of $Y$ is. After a political fight, you might be able to require everyone to mask up by passing a strict public mask ordinance: in this case, you would be forcing $X$ to have the value 1. <br /><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-ojl2O8B2tVk/YF4GG18bfQI/AAAAAAAAARI/oG2l_Nnj-1wmzOdEj6EW2imNGsB-2BZVgCLcBGAsYHQ/s431/association-between-mask-wearing-and-covid-rate-diagram.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="279" data-original-width="431" src="https://1.bp.blogspot.com/-ojl2O8B2tVk/YF4GG18bfQI/AAAAAAAAARI/oG2l_Nnj-1wmzOdEj6EW2imNGsB-2BZVgCLcBGAsYHQ/s320/association-between-mask-wearing-and-covid-rate-diagram.PNG" width="320" /></a></div><br /><p></p><p>In order to determine whether to do this, you set up an experiment, a clinical trial for masks. You start with a representative group of people, and set half of them at random to wear masks whenever they go out, and the other half to not wear masks. The 'at-random' piece is important here, as it is in clinical trials. Setting $X$ forcibly to a specific value, chosen at random, can be thought of as applying an operator to $X$: call it the "do-operator". </p><p>The do-operator is routinely applied in experimental science. For example, in a vaccine clinical trial, people aren't allow to choose whether they get the placebo or vaccine: one of these possibilities is chosen at random. This lets you assess the true causal effect of $X$ on $Y$.</p><p>If your experiment shows that mask-wearing is effective at lowering the per capita COVID case rate, you can then support a mask-wearing ordinance, with confidence that the ordinance will have the desired effect 'in the wild'. </p><p>Statistical confounding occurs when the apparent relationship $p(Y|X)$ between the value of $X$ and the value of $Y$, observed in the wild rather than under experiment, differs from the true causal effect of $X$ on $Y$, $p(Y|do(X)$.</p><p>To put this in the context of masking, suppose we've observed in the wild that people who wear their masks when they go outside the house have lower COVID case rates per capita than people who don't. If we enforce a mask ordinance on the basis of this observation, it's possible that we might find that the law has no effect on the COVID case rate. </p><p>This might happen because of the presence of other variables which affect the outcome variable, called confounder variables. In the case of the masking question, it may be that an important confounder is whether a person is concerned about catching COVID. If a person is concerned, it may be that in addition to wearing masks when they go out, they are also avoiding close contact with people outside their household. And perhaps that is the true cause of the reduction in the COVID rate among people who wear masks.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://1.bp.blogspot.com/-OK2pRY8HS6c/YFtzJtI9B4I/AAAAAAAAAQs/IGDdDd091_gcHUxFgJgYympIXj5o45NfQCLcBGAsYHQ/s589/explanation%2Bfor%2Bassociation%2Bbetween%2Bmask%2Bwearing%2Band%2Bcovid%2Brate%2Bdiagram.PNG" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="343" data-original-width="589" height="213" src="https://1.bp.blogspot.com/-OK2pRY8HS6c/YFtzJtI9B4I/AAAAAAAAAQs/IGDdDd091_gcHUxFgJgYympIXj5o45NfQCLcBGAsYHQ/w366-h213/explanation%2Bfor%2Bassociation%2Bbetween%2Bmask%2Bwearing%2Band%2Bcovid%2Brate%2Bdiagram.PNG" width="366" /></a></div><br /><p></p><p>If it is the case that avoiding in-person meetings is the real cause of the lowered case rates, rather than wearing masks, then enforcing a masking law will not have the desired effect of reducing the case rate. And you definitely want to avoid passing an ineffective ordinance, for obvious reasons.<br /></p><p>Next week, I'll talk about Simpson's Paradox<i>, </i>an extreme example of statistical confounding. <br /></p>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com2tag:blogger.com,1999:blog-693365974866791256.post-84025414511750051982021-03-19T09:54:00.001-07:002021-04-30T10:04:15.515-07:00COVID vaccine efficacy<h4 style="text-align: left;">Preamble</h4><div style="text-align: left;"> This note started out as a reminder to myself about the definition of relative risk and vaccine efficacy, and morphed into a perusal of the FDA briefs on the Pfizer, Moderna, and J&J vaccines (links to all 3 briefs are at the bottom of the article).<br /></div><div style="text-align: left;"> </div><div style="text-align: left;"> It's really worth looking at the actual numbers of COVID cases among people in the studies -- they are surprisingly low. In some cases, they are so low that they make inference about vaccine efficacy hard. </div><div style="text-align: left;"> </div><div style="text-align: left;"> This is my first close look at the outcome of a clinical study. You have to make a lot of semi-arbitrary decisions, it seems, in order to design a clinical study. Even something as simple as a difference of 5 years in your cutoff for the 'older' age group can have an effect on inference. The 3 teams made all sorts of different decisions that make it hard to compare their outcomes head-to-head.<br /></div><div style="text-align: left;"><br /></div><div style="text-align: left;"> Above all, while writing this note, I wished many times that I could have gotten my hands on the actual data. I guess the current age of copious open data has spoiled me. </div><div style="text-align: left;"><br /></div><div style="text-align: left;"> Disclaimer: I do not have medical training, and nothing written here should be taken as medical advice. </div><h4 style="text-align: left;"> </h4><h4 style="text-align: left;">Definition of efficacy</h4><div style="text-align: left;"> </div><div style="text-align: left;"> Vaccine efficacy is defined as:<br /><br />$$1-\text{relative risk} = 1-\frac{\text{Prob(outcome|treatment)}}{\text{Prob(outcome|no treatment)}}.$$<br /><br />If the experiment has roughly equal treatment and control groups (as all the vaccine clinical trials did), then the probabilities can be replaced by counts:<br /><br />$$1-\text{relative risk} \approx 1-\frac{\text{Count(outcome|treatment)}}{\text{Count(outcome|no treatment)}}.$$<br /><br />So 95% effectiveness means that <br /><br />$$\frac{\text{Count(outcome|treatment)}}{\text{Count(outcome|no treatment)}}\approx 1 - 0.95 = \frac{1}{20};$$<br /><br />that is, for every 1 event in the vaccinated group, there were 20 in the unvaccinated group. </div><div style="text-align: left;"><br /></div><div style="text-align: left;"> <h4 style="text-align: left;"> What was the measured event (aka Primary Endpoint) used to measure vaccine efficacy? <br /> </h4> <div style="text-align: left;"><b> </b></div> <div style="text-align: left;"> <b>TL;DR</b>: Patients needed to have more symptoms in order to satisfy the J&J or Moderna primary endpoints than to satisfy the Pfizer primary endpoint. All confirmed cases in all 3 clinical trials required positive PCR tests. <br /><br />For Moderna: First Occurrence of confirmed COVID-19 (as defined by an adjudicated committee using a formal protocol) starting 14 Days after the Second Dose. Confirmed COVID-19 is defined on page 13 of the FDA brief, and requires at least 2 moderate COVID symptoms (i.e., fever, sore throat, cough, loss of taste or smell) or at least 1 severe respiratory symptom, as well as a positive PCR test. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;" > <tbody> <tr> <td style="text-align: center;"> <a href="https://lh3.googleusercontent.com/-63nG_rm0I-w/YFPQINpx5FI/AAAAAAAAAPs/x_V23dRJdaYqUPTLFDlC99MAPgunuwOMQCLcBGAsYHQ/Moderna_endpoint.PNG" style="margin-left: auto; margin-right: auto;" ><img alt="" data-original-height="313" data-original-width="831" height="121" src="https://lh3.googleusercontent.com/-63nG_rm0I-w/YFPQINpx5FI/AAAAAAAAAPs/x_V23dRJdaYqUPTLFDlC99MAPgunuwOMQCLcBGAsYHQ/Moderna_endpoint.PNG" width="320" /></a> </td> </tr> <tr> <td class="tr-caption" style="text-align: center;"> Moderna primary endpoint results. </td> <td class="tr-caption" style="text-align: center;"><br /></td> <td class="tr-caption" style="text-align: center;"><br /></td> </tr> </tbody> </table> <br />For Pfizer: Confirmed COVID-19 beginning 7 days after the second dose. Confirmed cases had at least one symptom from the usual list of COVID symptoms, and a positive PCR test for COVID within 4 days of the symptom. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;" > <tbody> <tr> <td style="text-align: center;"> <a href="https://lh3.googleusercontent.com/-5l8NJSb1nKc/YFPQUhLhAoI/AAAAAAAAAPw/t0k3Qb--CdQcTWku2Fc6L6s2c7rgbD7vgCLcBGAsYHQ/Pfizer_endpoint.PNG" style="margin-left: auto; margin-right: auto;" ><img alt="" data-original-height="442" data-original-width="833" height="170" src="https://lh3.googleusercontent.com/-5l8NJSb1nKc/YFPQUhLhAoI/AAAAAAAAAPw/t0k3Qb--CdQcTWku2Fc6L6s2c7rgbD7vgCLcBGAsYHQ/Pfizer_endpoint.PNG" width="320" /></a> </td> </tr> <tr> <td class="tr-caption" style="text-align: center;"> Pfizer primary endpoint results.<br /> </td> </tr> </tbody> </table> <br />for J&J: 'Molecularly confirmed' (by a PCR test) moderate-to-severe/critical COVID infection, measured at least 14 and at least 28 days post-vaccination. They also studied the rates of severe/critical COVID, which required signs of at least one of severe respiratory illness, organ failure, respiratory failure, shock, ICU admission, or death. Definitions of the COVID illness levels are on page 15 of the FDA brief, and are similar to the Moderna definition of Confirmed COVID-19. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <div class="separator" style="clear: both; text-align: center;"> <a href="https://lh3.googleusercontent.com/-s_HWKknCr1E/YFPQtDMC_RI/AAAAAAAAAP8/f2HG4f-KZhA0iqJBkjw6G1QsHhI1EbRYwCLcBGAsYHQ/JnJ_endpoint.PNG" style="margin-left: 1em; margin-right: 1em;" ><img alt="" data-original-height="589" data-original-width="845" height="223" src="https://lh3.googleusercontent.com/-s_HWKknCr1E/YFPQtDMC_RI/AAAAAAAAAP8/f2HG4f-KZhA0iqJBkjw6G1QsHhI1EbRYwCLcBGAsYHQ/JnJ_endpoint.PNG" width="320" /></a> </div> <br /> <h4 style="text-align: left;"> </h4> <h4 style="text-align: left;">Thoughts about the results</h4> <div style="text-align: left;"> </div> <div style="text-align: left;"> Moderna and Pfizer both reported very high efficacies of about 95%. These were point estimates, i.e., single values summarizing the measured efficacy. <br /><br />But the confidence interval (CI) is the thing to look at for each result, not the point estimate. The CI gives you information about not only the point estimate for efficacy, but about the certainty of the efficacy measurement. The CI for efficacy always contains its point estimate, but the wider the CI, the less confidence you can have in the point estimate. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <b><u> </u></b> </div> <div style="text-align: left;"> <b><u>Moderna</u></b> </div> <div style="text-align: left;"> </div> <div style="text-align: left;"> </div> <div style="text-align: left;"> The vaccine was tested with roughly equal control and vaccine arms. There were about 21,600 participants in each arm.<br /><br />The 95% CI for people aged 18-65 is (90.6%, 97.9%), which is very high. <br /><br />The point estimate of efficacy for people aged 65 and up was a bit lower, at 86.4%. The 95% confidence interval was (61.4%, 95.5%). The reason the confidence interval is wider is that only about 7000 people over 65 were enrolled in the clinical trial, and there were only 33 covid cases among that group (as opposed to 163 in the younger group). This caused the CI to be wider, reflecting increased uncertainty as to the true efficacy of the vaccine.<br /><br />If the cutoff for the older age group were lower, there would have been more cases in that group, and more confidence in the result. It would have been nice to have access to the raw clinical trial data. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <b><u> </u></b> </div> <div style="text-align: left;"> <b><u>Pfizer</u></b> </div> <div style="text-align: left;"> <b><u> </u></b> </div> <div style="text-align: left;"> <b><u> </u></b> </div> <div style="text-align: left;"> The vaccine was tested with roughly equal control and vaccine arms. There were about 18200 people in each arm.<br /><br />The division along age lines in this table occurs at age 55 years, rather than 65 years. This made the age groups a bit more balanced and resulted in more cases in the 55+ age group. Thus the 95% CI for the older age group is narrower than Moderna's, at (80.6%, 98.8%). The results for the younger group are even better. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <u><b> </b></u> </div> <div style="text-align: left;"> <u><b>Johnson & Johnson</b></u> </div> <div style="text-align: left;"> </div> <div style="text-align: left;"> </div> <div style="text-align: left;"> J&J had two endpoints, one corresponding to moderate illness, and one to severe and critical illness. J&J has emphasized the efficacy of their vaccine against their endpoint of severe or critical COVID-19, so that's where I focused my attention. <br /><br />The J&J study had some issues in its design that make it hard to draw conclusions. Because severe COVID is rarer, there were fewer cases of it in the final analysis, which means increased uncertainty for the conclusions. They also ran studies across several countries with wildly different base rates of covid, and with different dominant COVID<br />-19 strains. This makes me think nervously about aggregation confounding (Simpson's paradox) when all the results are thrown into one bucket. Again, access to the raw data would have been nice.<br /><br />J&J's point estimate of 85% efficacy in the US against severe covid, which you hear about all the time, is of questionable value, because the 95% CI was (-9,% 99.7%)! That's because there were only 8 severe COVID cases in the US arm of the trial -- 7 in the placebo group and one in the vaccine group. That's not enough to base any conclusions on. The same problem with a low total case count was found in Brazil.<br /><br />Probably the best estimate of J&J efficacy against severe covid came from the South African arm of the study, where the number of severe cases was largest (26 severe cases in both arms of the study after 28 days post-vaccination -- 22 in the placebo group and 4 in the vaccinated group). The point estimate there was 81.7%, and the 95% CI was (46.2%, 95.4%). Remember that the tough South African COVID variant was spreading during this study, so that's pretty good news as to J&J's efficacy against that variant.<br /><br />If you throw all the people in those 3 locations into one bucket, you get this table describing the aggregate result for severe covid:<br /><br /> </div> <div style="text-align: left;"> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;" > <tbody> <tr> <td style="text-align: center;"> <a href="https://lh3.googleusercontent.com/-_V6rFkALy7Y/YFPSjN5Wy_I/AAAAAAAAAQE/anggNmhcDOUU0jm2XvBK5B1XGcnjaDrmgCLcBGAsYHQ/J%2526J_severe_cases.PNG" style="margin-left: auto; margin-right: auto;" ><img alt="" data-original-height="353" data-original-width="876" height="129" src="https://lh3.googleusercontent.com/-_V6rFkALy7Y/YFPSjN5Wy_I/AAAAAAAAAQE/anggNmhcDOUU0jm2XvBK5B1XGcnjaDrmgCLcBGAsYHQ/J%2526J_severe_cases.PNG" width="320" /></a> </td> </tr> <tr> <td class="tr-caption" style="text-align: center;"> J&J aggregate results across all sites for severe COVID<br /> </td> </tr> </tbody> </table> </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> I have two thoughts about this; one is that I'm suspicious of aggregation effects, due to the fact that the studies in the 3 countries were so different. The second is that the evidence for the effectiveness of J&J's vaccine is significantly stronger for onset 28 days post-vaccination than for 14 days post-vaccination; the jump in efficacy against severe COVID in the younger age group is more than 10 percentage points. <br /><br />So, although I've read that you can consider yourself officially "J&J-immunized" after 14 days post-vaccination -- I intend to wait another 2 weeks after that, till the 28-day mark, before really relaxing the rules. </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <u><b> </b></u> </div> <div style="text-align: left;"> <u><b>References</b></u> </div> <div style="text-align: left;"> <u><b> </b></u> </div> <div style="text-align: left;"> <u ><b></b ><a href="https://www.fda.gov/media/146217/download" >J&J FDA review brief</a > </u > </div> <div style="text-align: left;"><u> </u></div> <div style="text-align: left;"></div> <div style="text-align: left;"></div> <div style="text-align: left;"> <a href="https://www.fda.gov/media/144434/download" >Moderna FDA review brief</a > </div> <div style="text-align: left;"><br /></div> <div style="text-align: left;"> <a href="https://www.fda.gov/media/144245/download" >Pfizer FDA review brief</a ><br /> </div> </div></div>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0tag:blogger.com,1999:blog-693365974866791256.post-46858632301916100182021-03-19T09:42:00.000-07:002021-03-19T09:42:33.357-07:00Launching "From my Slipbox"<p> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://lh3.googleusercontent.com/-NxtIM11YbaM/YFOieetayZI/AAAAAAAAAPk/LFNon7onIlQcFeTAYzasPT27geH6s_9mQCLcBGAsYHQ/luhmann-zettelkasten.jpg" style="margin-left: auto; margin-right: auto;"><img alt="" data-original-height="357" data-original-width="635" height="180" src="https://lh3.googleusercontent.com/-NxtIM11YbaM/YFOieetayZI/AAAAAAAAAPk/LFNon7onIlQcFeTAYzasPT27geH6s_9mQCLcBGAsYHQ/luhmann-zettelkasten.jpg" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Niklas Luhmann's original Zettelkasten<br /></td></tr></tbody></table><br /></p><p>This post is the first in a series I'm launching on statistics, machine learning, productivity, and related interests: "From my slipbox".</p><p>A slipbox ("Zettelkasten" in German, translating to card-box) is a personal written record of ideas that you've gotten from things you've read, seen, or heard. Each Zettel is a card containing a writeup of a single concept that you've thoroughly digested and translated into your own words. The cards are also annotated with the addresses of other, related ideas captured in your slip-box, allowing you to follow the threads of ideas. </p><p>The Zettelkasten idea is credited to mid-20th-century German sociologist Niklas Luhmann, who spent decades building a physical slip-box in order to flesh out his ideas on a theory of society. It was constructed like a library card catalog, with ordered unique IDs for every card/idea (see the photo above -- it actually was housed in a library card catalog, apparently). </p><p> These days, a slip-box is more likely than not to be digital, and there is specialized software to support it. <a href="https://zettelkasten.de/the-archive/">The Archive</a> seems to be especially popular among ZK aficionados, but I just noticed that it is only supported on MacOS. My own choice of tool is <a href="https://obsidian.md/">Obsidian.md</a>, which is supported on all architectures (including Linux!), and supports math markdown. Both tools use local markdown files so that your data is not stored in a proprietary format (links to both tools are below). I store my ZK in a private Github repository for safety and versioning support.</p><p>There are plenty of people who build their ZK using physical cards and boxes, just as Luhmann did, just for the pleasure of it. I understand that pleasure -- I think by writing longhand -- but there are huge benefits to hyperlinking and digital backups. <br /></p><p>I took up Zetteling very recently, in January 2021. I've always written copious longhand notes about technical things I've read and digested, some of which have become the 'writeups' I've posted in the past on topics like Kalman filters, the backpropagation algorithm, and design of experiments. But my longhand notes sometimes get lost or accidentally thrown out, and the effort required to get from my handwritten notes to material worth publishing is sometimes a deterrent. </p><p>I got excited about making a Zettelkasten for the following reasons:</p><p>1. It encourages my writing habit<br /></p><p>2. It lets me put my thoughts into semi-formal writing immediately, rather than waiting until I have a large writing job to do</p><p>3. It fights the brain leakage problem, wherein I quickly forget the details of what I've learned</p><p>4. Luhmann claimed that new ideas emerged spontaneously from his Zettelkasten, simply because of its massive size and interconnectedness -- sort of like a huge neural network developing consciousness (I'd like to see that happen!)<br /></p><p>5. The promise of more easily generating quality written content from existing Zettels is appealing</p><p>6. The idea is for you to spend time 'curating' your slip-box -- rereading your ideas, making new connections, etc. -- which aids my memory, appeals to my love of organization, and makes me feel productive even when I'm too tired to actually write.<br /></p><p>A little over a month after getting started, I've written around 150 Zettels on topics such as neural nets, productivity, project planning, variational calculus, causality, statistical modeling, and on Zetteling itself. Each one is a sort of soundbite of some story or idea I found interesting. <br /></p><p>Every Friday, I'll be posting a Zettel from my Zettelkasten -- often technical, but sometimes relating to consulting, productivity, or other topics. <br /></p><p>I am hoping that this series results in conversations, and occasional 'super-Zetteling' -- making new connections to interesting content from minds beyond my own. </p><p><em>Some Zettelkasten resources:</em></p><ul><li><a href="https://zettelkasten.de/posts/overview/" rel="nofollow noopener" target="_blank">Zettelkasten.de forum: how to get started</a></li><li><a href="https://obsidian.md/" rel="nofollow noopener" target="_blank">Obsidian.md (Free all-platform software for ZK: local markdown file based, supports MathML)</a></li><li><a href="https://zettelkasten.de/the-archive/">The Archive (MacOS software for ZK)</a> </li><li><a href="https://www.youtube.com/watch?v=BG1tfC7tSYw" target="_blank">Introductory video for ZK that I found inspiring</a></li><li><a href="https://www.youtube.com/watch?v=U2hxygqjx2k" target="_blank">Another introductory video that I enjoyed</a></li></ul>Carolynhttp://www.blogger.com/profile/05723628019672417161noreply@blogger.com0