This lecture's going to be about some basic principles for building analytic graphics. The basic goal is to provide some general rules that one can follow when we're building analytic graphics from data, and we're trying to tell a story about what's happening in the data. I find these rules to be quite useful when thinking through building data graphics and they apply to many different situations. so, I've kind of cribbed these rules from, a book by Edward Tuffey. I'll give the reference at the end of the lecture. This is from his book, Beautiful Evidence, where he, where he kind of goes through a number of principles, and so, I'm going to talk through some of these ideas and kind, and kind of show them, in, in context. So, the first principle, that Tufty talks about, is to show comparisons. And this is a very basic idea in all of science. And the basic idea is that evidence for a hyp, for a hypothesis or an idea about the world, is always going to be relative to another hypothesis, right? So evidence is always relative. And so, if you're comparing Hypothesis A, there has to be some alternative hypothesis that you're going to compare it to. And so, so whenever you hear a statement or hear a a summary of evidence, based on data you should always be asking a question compared to what? Alright, so here's a quick example. The basic idea is that we have a, a boxplot which looks at the effect of an air cleaner on the asthma symptoms of children who in a certain, in a set of homes. So the idea is that an air cleaner was introduced into a child's home, to reduce indoor air pollution levels. And we want to see if their asthma symptoms are improving. So the outcome is, it's what's called symptom-free days. So a higher number is better. And here we can see that the group of children that got the air cleaner in their home had an increase in their symptom-free days. About, on the median increase was about one symptom-free day over 2 weeks. So that's a positive outcome, and we might be inclined to think that of course that the air cleaner works. But of course, the real question is compared to what? So what do we compare the air cleaner to? And so the, the what we compare them to in this case, is nothing. So our, our control setting where the air, or the control set of houses are have no air cleaner, and just kind of live their daily lives. So this was a randomized control trial that looked at installing an air cleaner in a child's home. And, and, and installing nothing in the child's home. And you can see now that in the control homes, the average change in the symptom free case was about 0. So there's really no change. And then the average change in the air cleaner homes was about 1 symptom free day for, 2 weeks. And so, just now you can say okay, well relative to doing nothing, the air cleaner is actually a little bit better at showing an improvement in the child's symptoms. So it's always important to show a comparison in a plot. So that you can, you can have a basis to, to compare what you're showing and, c, so you can compare the evidence to, between 2 different hypothesis. The 2nd basic principle, is to show causality or mechanism or, to, to make an explanation and to s, to kind of show what's going on, show some systematic structure. So I mean, the, the use of the word causality here is not supposed to be formal. But rather, is just to show kind of what you believe, and how you believe the world works, right. So you need to be able to show what, how you believe the system is kind of operating, so to speak. And so so what's the causal framework for thinking about the question that you're kind of interested in? And so if I might extend the example from the previous slide, previously we saw that if you install an air cleaner in a child's home, that on average, they're going to experience a one symptom-free day increase, so a better outcome in their asthma symptoms. Now, we might ask, okay, well why does that occur? Why is it that installing an air cleaner in a child's home, improves their symptoms? Well, of course, we hypothesize that the air cleaner is cleaning the air. It's removing particulate matter from the air, and so this particulate matter that's not, that's being removed, is no longer going in the child's lungs, and no longer triggering their asthma symptoms. So that's kind of how we believe things work. And so we can show a plot, that might corroborate that evidence. And so we can show another plot, which has the symptom free days on the left hand side, and then the particulate matter, on the right hand side. So now we can see what was the effect of the air cleaner on the, on the particulate matter levels inside the child's home? And you can see that for the control group, there was basically no change in the particulate matter levels. Maybe in the slight increase, in the, in the levels. But there was a pretty, substantial decrease in particulate matter levels. For the group of homes that got the air cleaner. So now we can see that not only did a child's symptom free days increase when they got the air cleaner, that they're that they're indoor air particulate matter levels decreased, also when they got the air cleaner on average. So, we can think about, you know, what is the explanation for, you know, why the the air cleaner seems to improve symptoms in children. And we can, and we can show, using the data that we observed, that it does seem to decrease their particulate matter levels. Now, of course, to really confirm that this hypothesis that the air cleaner operates through, by reducing PM, we'd have to do a lot, a little bit more investigation and perhaps more experimentation. But this graphic kind of suggests a possible explanation. The third principle that that [INAUDIBLE] talks about is to show multivariate data. And the basic this rule can be boiled down to show as much data on a single plot as you can. And the reason is because, data are, the world is inherently multivariate, there's lots of things going on all the time. And if you just plot 2 variables, or maybe even 3 variables. It's not going to show the real picture of what's happening in the world. So if you can, you can integrate, if you put a lot of data on a plot, then you'll be able to tell a much richer story. So here is an example of a plot which is another air pollution example, but now we're, this a, a, if data comes from outdoor air pollution. So on the X axis we have, particulate matter less than 10 microns in aerodynamic diameter, the concentrations of those, from day to day. So, every circle on this plot represents a daily concentration. And on the y axis, we have the daily mortality in New York City. This is for the time period 1987 to, 2000. And you can see that overall, when, there seems to be a night-, a slightly negative association between PM 10 levels and mortality. Cause you can see that the regression line that I put through there, is slightly downwards sloping. So that seems interesting, cause you might, one might hypothesis that higher air pollution levels might be associated with higher mortality, not lower mortality. So but you can look at other variables. So there's not just air pollution and mortality that is kind of, kind of, that is of interest here. There are other variables that may be of interest. And may kind of be part of the system, and may confound this relationship. So, one of the things that we can look at is see, well, how does this relationship change across different seasons. So if you look at, you know, particulate matter and mor-, and mortality in winter, spring, summer, and fall, what does that look like? So, we can make a, a different plot to show that relationship. And this is the plot that we can make. So this plot shows the relationship between pm10 and mortality. So, it's the same plot as we saw as we showed on the previous slide, but it's split across the different seasons. So we see it separately for winter, spring, summer, and fall. And we can see that in each plot, the relationship is actually now slightly positive. So within each season, the relationship between PM and mortality is positive, but if you look overall, the relationship appears to be negative. So this is an example of Simpson's Paradox. If you may have heard it. But the basic idea is that the season in which we look at the relationship, is confounding the relationship between PM 10 and mortality. And so when we look across with with the [INAUDIBLE] we look at the relationship within each season it changes. So it's important to show as many variables as is reasonable at a given time, so that you can sh, get a clear picture of the relationships in your data. So the fourth principle is to integrate. The evidence that you have. And, and the basic idea here is that you want to use as, as many different modes of evidence, or as, or displaying evidence as you can. And so there's no reason to say if you're just, if you have a tool that makes a plot, to only show a plot. Or if you only have the ability to make a table, to only show a table. You should be able to combine different modes of evidence into a single presentation, to, to make edit, to make your graphic or whatever display that you're making as information rich as possible. And so, the idea is not, is not to let the tools that you use to drive the kinds of plot that you make. You should make a plot that you want to make, and not just let the tools do the thinking. And so what, that's one of the nice advantages of a system like R, because the, the tools are very flexible in R, and you can make all kinds of customized plots to show the data and to kind of integrate different modes of evidence. So this is just one very quick example from a published paper. In the Journal of the American Medical Association, looking at the relationship between coarse particulate matter and hospitalizations in the elderly. And the basic idea is the details of this plot are not particularly important, but I just wanted to show that they're, there are kind of point estimates here, which are in the solid circles, and then there's confidence intervals indicated by the lines going through the confident, through the solid circles. But then on the right hand side here you see this label called posterior probability that the relative risk is created in 0. And so this is a measure of the strength of the evidence that the, the kind of the association between coarse particulate matter, and, and hospitalizations is, is, in fact, different from 0. And so, so here, we integrate, the, the, kind of, the point estimates as, as dots and lines. Then we also have texts on the right which also, it shows another piece of evidence, which is kind of the strength of that evidence, as encoded by the posterior probability. So you can use these kinds of tools to put lots of information on your plots. And now, I have to resort to putting diff-, putting information in different places where they may be difficult to track down. The fifth principle is to det-, to describe and document the evidence that you present, with using labels and sources and, and whatever, and, and, and in particular, if you're going to be making a plot with, a system like R, it's important to preserve the computer code that made the plot. So the idea is that you want to lend some credibility to the evidence that you present. So, sources of where the data came from that's very important and how you made the plot is also important. So that's a very basic principle and it's important for your credibility. The very last principle of course is that, content is king, so if you don't have an interesting story to tell, then there's no amount of presentation that will make it interesting. So when, when you're making plots, when you're making figures, and you're making graphs, the first thing about what's the content that you're trying to present? What's the story you're trying to tell? What's the data that you have? And then think about well what's the best way to present that? How am I going to present it? And what is it going to look like? Because if you don't have very good content, then there's really not much you're going to be able to do beyond that. So just to quickly summarize the, the 6 basic principles are, first show comparisons. Always show something relative to something else. Show causality or mechanism, or explain at least try to explain how the system is working. How the world is working, at least according to your ideas. The third is to show multivariate data. So always try to show more than 2 variables, because the world is complex and involve many variables. Principle number 4 is integrate multiple modes of evidence. So that you can use things like tables and plots and texts all together. You don't have to keep them separate, if you don't want to. Describe and document your evidence. Always have sources and, and source code. And, and, to lend credibility to your plots. And finally, always remember that the story that you tell and the data that you use are the most important elements of any graphic. So just the, the P reference that I would use for this presentation is, Edward Tufte's book, Beautiful Evidence. And you can, you can read about it at his website which I point to here. It's an excellent book, I highly recommend it. So, so that's some, these are some basic principles about building analytic graphics, and then we're, and, in, and in future lectures we'll talk about how to do that using the various plotting systems in R.
