Calling BS Read-Along Week 8: Publication Bias

Welcome to the Calling Bullshit Read-Along based on the course of the same name from Carl Bergstorm and Jevin West  at the University of Washington. Each week we’ll be talking about the readings and topics they laid out in their syllabus. If you missed my intro and want the full series index, click here or if you want to go back to Week 7 click here.

Well hello Week 8! How’s everyone doing this week? A quick programming note before we get going: the videos for the lectures for the Calling Bullshit class are starting to be posted on the website here. Check them out!

This week we’re taking a look at publication bias, and all the problems that can cause. And what is publication bias? As one of the readings so succinctly puts it, publication bias  “arises when the probability that a scientific study is published is not independent of its results.” This is a problem because it not only skews our view of what the science actually says, but also is troubling because most of us have no way of gauging how extensive an issue it is.  How do you go about figuring out what you’re not seeing?

Well, you can start with the first reading, the 2005 John Ioannidis paper “Why Most Published Research Findings are False“.  This  provocatively titled yet stats heavy paper does a deep dive in to the math behind publication and why our current research practices/statistical analysis methods may lead to lots of false positives reported in the literature. I find this paper so fascinating/important I actually did a seven part deep dive in to it a few months ago, because there’s a lot of statistical meat in there that I think is important. If that’s TL;DR for you though, here’s the recap: the statistical methods we use to control for false positives and false negatives (alpha and beta) are insufficient to capture all the factors that might make a paper more or less likely to reach an erroneous conclusion.  Ioannidis lays out quite a few factors we should be looking at more closely such as:

  1. Prior probability of a positive result
  2. Sample size
  3. Effect size
  4. “Hotness” of field
  5. Bias

Ioannidis also flips the typical calculation of “false positive rate” or “false negative rate” to one that’s more useful for those of us reading a study: positive predictive value. This is the chance that any given study with a “positive” finding (as in a study that reports a correlation/significant difference, not necessarily a “positive” result in the happy sense) is actually correct. He adds all of the factors above (except hotness of field) in to the typical p-value calculation, and gives an example table of results. (1-beta is study power which includes sample size and effect size, R is his symbol for probability of a positive result, u is bias factor):

Not included is the “hotness” factor, where he points out that multiple research teams working on the same question will inevitably produce more false positives than just one team will. This is likely true even if you only consider volume of work, before you even get to corner cutting due to competition.

Ultimately, Ioannidis argues that we need bigger sample sizes, more accountability aimed at reducing bias (such as telling others your research methods up front or trial pre-registration), and to stop rewarding researchers only for being the first to find something (this is aimed at both the public and at journal editors). He also makes a good case that fields should be setting their own “pre-study odds” numbers and that researchers should have to factor in how often they should be getting null results.

It’s a short paper that packs a punch, and I recommend it.

Taking the issues a step further is a real life investigation contained in the next reading “Selective Publication of Antidepressant Trials and Its Influence on Apparent Efficacy” from Turner et al in the New England Journal of Medicine. They reviewed all the industry sponsored antidepressant trials that had pre-registered with the FDA, and then reviewed journals to see which ones got published. Since the FDA gets the results regardless of publication, this was a chance to see what was made it to press and what didn’t. The results were disappointing, but probably not surprising:

Positive results that showed the drugs worked were almost always published, negative results that showed no difference from placebo  often went unpublished. Now the study authors did note they don’t know why this is, they couldn’t differentiate between the “file drawer” effect (where researchers put negative findings in their drawer and don’t publish them) and journals that rejected papers with null results. It seems likely both may be a problem. The study authors also found that the positive papers were presented as very positive, whereas some of the negative papers had “bundled” their results.

In defense of the anti-depressants and their makers, the study authors did find that a meta-analysis of all the results generally showed the drugs were superior to a placebo. Their concern was the magnitude of the effect may have been overstated. By not having many negative results to look it, the positive results are never balanced out and it appears the drugs are much more effective than they actually are.

The last reading is “Publication bias and the canonization of false facts.“by Nissen et al, a pretty in depth look at the effects of publication bias on our ability to distinguish between true and false facts. They set out to create a model of how we move an idea between theory and “established fact” through scientific investigation and  publication, and then test what publication bias would do to that process. A quick caveat from the end of the paper I want to give up front: this model is supposed to represent the trajectory of investigations in to “modest” facts, not highly political or big/sticky problems. Those beasts have their own trajectory, much of which has little to do with publication issues. What we’re talking about here is the type of fact that would get included in a textbook with no footnote/caveat after 12 or so supportive papers.

They start out by looking at the overwhelming bias towards publishing “positive” findings. Those papers that find a correlation, reject the null hypothesis, or find statistically significant differences are all considered “positive” findings. Almost 80% of all published papers are “positive” findings, and in some fields this is as high as 90%. While hypothetically this could mean that researchers just pick really good questions, the Turner et al paper and the Ioannidis analysis suggest that this is probably not the full story. “Negative” findings (those that fail to reject the null or find no correlation or difference) just aren’t published as often as positive ones. Now again, it’s hard to tell if this is the journals not publishing or researchers not submitting, or a vicious circle where everyone blames everyone else, but here we are.

The paper goes on to develop a model to test how often this type of bias may lead to the canonization of false facts. If negative studies are rarely published and almost no one knows how many might be out there, it stands to reason that at least some “established facts” are merely those theories whose counter-evidence is sitting in a file drawer. The authors base their model on the idea that every positive publication will increase belief, and negative ones will decrease it, but they ALSO assume we are all Bayesians about these things and constantly updating our priors. In other words, our chances of believing in a particular fact as more studies get published probably look a bit like that line in red:

This is probably a good time to mention that the initial model was designed only to look at publication bias, they get to other biases later. They assumed that the outcomes of studies that reach erroneous conclusions are all due to random chance, and that the beliefs in question were based only on the published literature.

The building of the model was pretty interesting, so you should definitely check that out if you like that sort of thing. Overall though, it is the conclusions that I want to focus on. A few things they found:

  1. True findings were almost always canonized
  2. False findings were canonized more often if the “negative” publication rate was low
  3. High standards for evidence and well designed experiments are not enough to overcome publication bias/reporting negative results

That last point is particularly interesting to me. We often ask for “better studies” to establish certain facts, but this model suggests that even great studies are misleading if we’re seeing a non-random sample. Indeed, their model showed that if we have a negative publication rate of under 20%, false facts would be canonized despite high evidence standards. This is particularly alarming since the antidepressant study found around a 10% negative publication rate.

To depress us even further, the authors then decided to add researcher bias in to the mix and put some p-hacking in to play. Below is their graph of the likelihood of canonizing a false fact vs the actual false positive rate (alpha). The lightest line is what happens wehn alpha = .05 (a common cut off), and each darker line shows what happens if people are monkeying around to get more positive results than they should:

Figure 8 from “Research: Publication bias and the canonization of false facts”

Well that’s not good.

On the plus side, the paper ends by throwing yet another interesting parameter in to the mix. What happens if people start publishing contradictory evidence when a fact is close to being canonized? While it would be ideal if negative results were published in large numbers up front, does last minute pushback work? According to the model, yes, though not perfectly. This is a ray of hope because it seems like in at least some fields, this is what happens. Negative results that may have been put in the file drawer or considered uninteresting when a theory was new can suddenly become quite interesting if they contradict the current wisdom.

After presenting all sorts of evidence that publishing more negative findings is a good thing, the discussion section of the paper goes in to some of the counterarguments. These are:

  1. Negative findings may lead to more true facts being rejected
  2. Publishing too many papers may make the scientific evidence really hard to wade through
  3. Time spent writing up negative results may take researchers away from other work

The model created here predicts that #1 is not true, and #2 and #3 are still fairly speculative. On the plus side, the researchers do point to some good news about our current publication practices that may make the situation better than the model predicts:

  1. Not all results are binary positive/negative They point out that if results are continuous, you could get “positive” findings that contradict each other. For example, if a correlation was positive in one paper and negative in another paper, it would be easy to conclude later that there was no real effect even without any “negative” findings to balance things out.
  2. Researchers drop theories on their own Even if there is publication bias and p-hacking, most researchers are going to figure out that they are spending a lot more time getting some positive results than others, and may drop lines of inquiry on their own.
  3. Symmetry may not be necessary The model assumes that we need equal certainty to reject or accept a claim, but this may not be true. If we reject facts more easily than we accept them, the model may look different.
  4. Results are interconnected The model here assumes that each “fact” is independent and only reliant on studies that specifically address it. In reality, many facts have related/supporting facts, and if one of those supporting facts gets disproved it may cast doubt on everything around it.

Okay, so what else can we do? Well, first recognize the importance of “negative” findings. While “we found nothing” is not exciting, it is important data. They call on journal editors to consider the possible damage of considering such papers uninteresting. Next, they point to new journals springing up dedicated just to “negative results” as a good trend. They also suggest that perhaps some negative findings should be published as pre-prints without peer review. This wouldn’t help settle questions, but it would give people a sense of what else might be out there, and it would settle some of the time commitment problems.

Finally a caveat which I mentioned at the beginning but is worth repeating: this model was created with “modest” facts in mind, not huge sticky social/public health problems. When a problem has a huge public interest/impact (like say smoking and lung cancer links) people on both sides come out of the woodwork to publish papers and duke it out. Those issues probably operate under very different conditions than less glamorous topics.

Okay, over 2000 words later, we’re done for this week! Next week we’ll look at an even darker side of this topic: predatory publishing and researcher misconduct. Stay tuned!

5 Things You Should Know About the “Backfire Effect”

I’ve been ruminating a lot on truth and errors this week, so it was perhaps well timed that someone sent me this article on the “backfire effect” a few days ago. The backfire effect is a name given to a psychological phenomena in which attempting to correct someone’s facts actually increases their belief in their original error. Rather than admit they are wrong when presented with evidence they narrative goes, people double down. Given the current state of politics in the US, this has become a popular thing to talk about. It’s popped up in my Facebook feed and is commonly cited as the cause of the “post-fact” era.

So what’s up with this? Is it true that no one cares about facts any more? Should I give up on this whole facts thing and find something better to do with my time?

Well, as with most things, it turns out it’s a bit more complicated than that. Here’s a few things you should know about the state of this research:

  1. The most highly cited paper focused heavily on the Iraq War The first paper that made headlines was from Nyhan and Reifler back in 2010, and was performed on college students at a Midwest Catholic University. They presented some students with stories including political misperceptions, and some with stories that also had corrections. They found that the students that got corrections were more likely to believe the original misperception. The biggest issue this showed up with was whether or not WMDs were found in Iraq. They also tested facts/corrections around the tax code and stem cell research bans, but it was the WMD findings that grabbed all the headlines. What’s notable is that the research was performed in 2005 and 2006, when the Iraq War was heavily in the news.
  2. The sample size was fairly small and composed entirely of college students One of the primary weaknesses of the first papers (as stated by the authors themselves) is that 130 college students are not really a representative sample. The sample was half liberal and 25% conservative. It’s worth noting that they believe that was a representative sample for their campus, meaning all of the conservatives were in an environment where they were the minority. Given that one of the conclusions of the paper was that conservatives seemed to be more prone to this effect than liberals, it’s an important point.
  3. A new paper with a broader sample suggest the “backfire effect” is actually fairly rare. Last year, two researchers (Porter and Wood) polled 8,100 people from all walks of life on 36 political topics and found…..WMDs in Iraq were actually the only issue that provoked a backfire effect. A great Q&A with them can be found here. This is fascinating if it holds up because it means the original research was mostly confirmed, but any attempt at generalization was pretty wrong.
  4. When correcting facts, phrasing mattered One of the more interesting parts of the Porter/Wood study was when the researchers described how they approached their corrections. In their own words “Accordingly, we do not ask respondents to change their policy preferences in response to facts–they are instead asked to adopt an authoritative source’s description of the facts, in the face of contradictory political rhetoric“. They reject heartily “corrections” that are aimed at making people change their mind on a moral stance (like say abortion) and focus only on facts. Even with the WMD question they found that the more straightforward and simple the correction statement, the more people of all political persuasions accepted it.
  5. The 4 study authors are now working together In an exceptionally cool twist, the authors who came to slightly different conclusions are now working together. The Science of Us gives the whole story here, but essentially Nyhan and Reifler praised Porter and Wood’s work, then said they should all work together to figure out what’s going on. They apparently gathered a lot of data during the height of election season and hopefully we will see those results in the near future.

I think this is an important set of points, both because it’s heartwarming (and intellectually awesome!) to see senior researchers accepting that some of their conclusion may be wrong and actually working with others to improve their own work. Next, I think it’s important because I’ve heard a lot of people in my personal life commenting that “facts don’t work” so they basically avoid arguing with those who don’t agree with them. If it’s true that facts DO work as long as you’re not focused on getting someone to change their mind on the root issue, then it’s REALLY important that we know that. It’s purely anecdotal, but I can note that this has been my experience with political debates. Even the most hardcore conservatives and liberals I know will make concessions if you clarify you know they won’t change their mind on their moral stance.

Calling BS Read-Along Week 7: Big Data

Welcome to the Calling Bullshit Read-Along based on the course of the same name from Carl Bergstorm and Jevin West  at the University of Washington. Each week we’ll be talking about the readings and topics they laid out in their syllabus. If you missed my intro and want the full series index, click here or if you want to go back to Week 6 click here.

Well hello week 7! This week we’re taking a look at big data, and I have to say this is the week I’ve been waiting for. Back when I first took a look at the syllabus, this was the topic I realized I knew the least about, despite the fact that it is rapidly becoming one of the biggest issues in bullshit today. I was pretty excited to get in to this weeks readings, and I was not disappointed. I ended up walking away with a lot to think about, another book to read, and a decent amount to keep me up at night.

Ready? Let’s jump right in to it!

First, I suppose I should start with at least an attempt at defining “big data”. I like the phrase from the Wiki page here “Big data usually includes data sets with sizes beyond the ability of commonly used software tools to capture, curate, manage, and process data within a tolerable elapsed time.” Forbes goes further and compiles 12 definitions here. If you come back from that rabbit hole, we can move in to the readings.

The first reading for the week is “Six Provocations for Big Data” by danah boyd and Kate Crawford. The paper starts off with a couple of good quotes (my favorite: ” Raw data is both an oxymoron and a bad idea; to the contrary, data should be cooked with care”) and a good vocab word/warning for the whole topic: apophenia, the tendency to see patterns where none exist. There’s a lot in this paper (including a discussion about what Big Data actually is), but the six provocations the title talks about are:

  1. Automating Research Changes the Definition of Knowledge Starting with the example of Henry Ford using the assembly line, boyd and Crawford question how radically Big Data’s availability will change what we consider knowledge. If you can track everyone’s actual behavior moment by moment, will we end up de-emphasizing the why of what we do or broader theories of development and behavior? If all we have is a (big data) hammer, will all human experience end up looking like a (big data) nail?
  2. Claims to Objectivity and Accuracy are Misleading I feel like this one barely needs to be elaborated on (and is true of most fields), but it also can’t be said often enough. Big Data can give the impression of accuracy due to sheer volume, but every researcher will have to make decisions about data sets that can introduce bias. Data cleaning, decisions to rely on certain sources, and decisions to generalize are all prone to bias and can skew results. An interesting example given was the original Friendster (Facebook before there was Facebook for the kids, the Betamax to Facebook’s VHS for the non-kids). The developers had read the research that people in real life have trouble maintaining social networks of over 150 people, so they capped the friend list at 150. Unfortunately for them, they didn’t realize that people wouldn’t use online networks the same way they used networks in real life. Perhaps unfortunately for the rest of us, Facebook did figure this out, and the rest is (short term) history.
  3. Bigger Data are Not Always Better Data Guys, there’s more to life than having a large data set. Using Twitter data as an example, they point out that large quantities of data can be just as biased (one person having multiple accounts, non-representative user groups) as small data sets, while giving some people false confidence in their results.
  4. Not all Data are Equivalent With echos of the Friendster example from the second point, this point flips the script and points out that research done using online data doesn’t necessarily tell us how people interact in real life. Removing data from it’s context loses much of it’s meaning.
  5. Just Because it’s Accessible Doesn’t Make it Ethical The ethics of how we use social media isn’t limited to big data, but it definitely has raised a plethora of questions about consent and what it means for something to be “public”. Many people who would gladly post on Twitter might resent having those same Tweets used in research, and many have never considered the implications of their Tweets being used in this context. Sarcasm, drunk tweets, and tweets from minors could all be used to draw conclusions in a way that wouldn’t be okay otherwise.
  6. Limited Access to Big Data Creates New Digital Divides In addition to all the other potential problems with big data, the other issue is who owns and controls it. Data is only as good as your access to it, and of course nothing obligates companies who own it to share it, or share it fairly, or share it with people who might use it to question their practices. In assessing conclusions drawn from big data, it’s important to keep all of those issues in mind.

The general principles laid out here are a good framing for the next reading the Parable of the Google Flu, an examination of why Google’s Flu Trends algorithm consistently overestimated influenza rates in comparison to CDC reporting. This algorithm was set up to predict influenza rates based on the frequency of various search terms in different regions, but over 108 weeks examined it overestimated rates 100 times, sometimes by quite a bit. The paper contains a lot of interesting discussion about why this sort of analysis can err, but one of the most interesting factors was Google’s failure to account for Google itself. The algorithm was created/announced in 2009, and some updates were announced in 2013. Lazer et al point out that over that time period Google was constantly refining its search algorithm, yet the model appears to assume that all Google searches are done only in response to external events like getting the flu. Basically Google was attempting to change the way you search, while assuming that no one could ever change the way you search. They call this internal software tinkering “blue team” dynamics, and point out that it’s going to be hell on replication attempts. How do you study behavior across a system that is constantly trying to change behavior? Also considered are “red team” dynamics, where external parties try to “hack” the algorithm to produce results they want.

Finally we have an opinion piece from a name that seems oddly familiar, Jevin West, called “How to improve the use of metrics: learn from game theory“. It’s short, but got a literal LOL from me with the line “When scientists order elements by molecular weight, the elements do not respond by trying to sneak higher up the order. But when administrators order scientists by prestige, the scientists tend to be less passive.” West points out that when attempting to assess a system that can respond immediately to your assessment, you have to think carefully about what behavior your chosen metrics reward. For example, currently researchers are rewarded for publishing a large volume of papers. As a result, there is concern over the low quality of many papers, since researchers will split their findings in to the “least publishable unit” to maximize their output. If the incentives were changed to instead have researchers judged based on only their 5 best papers, one might expect the behavior to change as well. By starting with the behaviors you want to motivate in mind, you can (hopefully) create a system that encourages those behaviors.

In addition to those readings, there are two recommend readings that are worth noting. The first is Cathy O’Neil’s Weapons of Math Destruction (a book I’ve started but not finished), which goes in to quite a few examples of problematic algorithms and how they effect our lives. Many of O’Neil’s examples get back to point #6 from the first paper in ways most of don’t consider. Companies maintaining control over their intellectual property seems reasonable, but what if you lose your job because your school system bought a teacher ranking algorithm that said you were bad? What’s your recourse? You may not even know why you got fired or what you can do to improve. What if the algorithm is using a characteristic that it’s illegal or unethical to consider? Here O’Neil points to sentencing algorithms that give harsher jail sentences to those with family members who have also committed a crime. Because the algorithm is supposedly “objective”, it gets away with introducing facts (your family members involvement in crimes you didn’t take part in) that a prosecutor would have trouble getting by a judge under ordinary circumstances. In addition, some algorithms can help shape the very future they say they are trying to predict. Why are Harvard/Yale/Stanford the best colleges in the US News rankings? Because everyone thinks they’re the best. Why do they think that? Look at the rankings!

Finally, the last paper is from Peter Lawrence with “The Mismeasurement of Science“. In it Lawrence lays out an impassioned case that the current structure around publishing causes scientists to spend too much time on the politics of publication and not enough on actual science. He also questions heavily who is rewarded by such a system, and if those are the right people. It reminded me of another book I’ve started but not finished yet “Originals: How Non-Conformists Move the World”. In that book Adam Grant argues that if we use success metrics based on past successes, we will inherently miss those who might have a chance at succeeding in new ways. Nicholas Nassim Taleb makes a similar case in Antifragile, where he argues that some small percentage of scientific funding should go to “Black Swan” projects….the novel, crazy, controversial destined-to-fail type research that occasionally produces something world-changing.

Whew! A lot to think about this week and these readings did NOT disappoint. So what am I taking away from this week? A few things:

  1. Big data is here to stay, and with it come ethical and research questions that may require new ways of thinking about things.
  2. Even with brand new ways of thinking about things, it’s important to remember the old rules and that many of them still apply
  3. A million plus data points does not  =/= scientific validity
  4. Measuring systems that can respond to being measured should be approached with some idea of what you’d like that response to be, along with some plans for change if you have unintended consequences
  5. It is increasingly important to scrutinize sources of data, and to remember what might be hiding in “black box” algorithms
  6. Relying too heavily on the past to measure the present can increase the chances you’ll miss the future.

That’s all for this week, see you next week for some publication bias!


I Got a Problem, Don’t Know What to do About It

Help and feedback request! This past weekend I encountered an interesting situation where I discovered that a study I had used to help make a point in several posts over the years has come under some scrutiny (full story at the bottom of the post). I have often blogged about meta-science, but this whole incident got me thinking about meta-blogging, and what the responsibility of someone like me is when you find out a study you’ve leaned on may not be as good as you thought it was. I’ve been poking around the internet for a few days, and I really can’t find much guidance on this.

I decided to put together a couple quick poll questions to gauge people’s feelings on this. Given that I tend to have some incredibly savvy readers, I would also love to hear more lengthy opinions either in the comments or sent to me directly.  The polls will stay open for a month, and I plan on doing a write up of the results. The goal of these poll questions is to assess a starting point for error correction, as I completely acknowledge the specifics of a situation may change people’s views. If you have strong feelings about what would make you take error correction more or less seriously, please leave it in the comments!

Why I’m asking (aka the full story)

This past weekend I encountered a rather interesting situation that I’m looking for some feedback on. I was writing my post for week 6 of the Calling BS read-along, and remembered an interesting study that found that  people were more likely to find stories with “science pictures” or graphs credible than those that were just text. It’s a study I had talked about in one of my Intro to Internet Science posts  and I have used it in presentations to back up my point that graphs are something you should watch closely. Since the topic of the post was data visualization and the study seemed relevant, I included it in the intro to my write up.

The post had only been up for a few hours when I got a message from someone tipping me off that the lab the study was from was under some scrutiny for some questionable data/research practices. They thought I might want to review the evidence and consider removing the reference to the study from my post. While the study I used doesn’t appear to be one of the ones being reviewed at the moment, I did find the allegations against the lab concerning. Since the post didn’t really change without the citation, I edited the post to remove the citation and replaced it with a note alerting people the paragraph had been modified. I put a full explanation at the bottom of the post that included the links to a summary of the issue and the research lab’s response.

I didn’t stop thinking about it though. There’s not much I could have done about using the study originally….I started citing it almost a full year before concerns were raised, and the “visuals influence perception” point seemed reasonable. I’ll admit I missed the story about the concerns with the research group, but even if I’d seen it I don’t know if I would have remembered that they were the ones who had done that study. Now that I know though, I’ve been mulling over what the best course of action is in situations like this. As someone who at least aspires to blog about truth and accuracy, I’ve always felt that I should watch my own blogging habits pretty carefully. I didn’t really question removing the reference, as I’ve always tried to update/modify things when people raise concerns. I also don’t modify posts after they’ve been published without noting that I’ve done so, other than fixing small typos. I feel good about what I did with that part.

What troubled me more was the question of “how far back to I go?” As I mentioned, I know I’ve cited that study previously. I know of at least one post where I used it, and there may be more. Given that my Intro to Internet Science series is occasionally assigned by high school teachers, I feel I have some obligation to go a little retro on this.


Current hypothesis (aka my gut reaction)

My gut reaction here is that I should probably start keeping an updates/corrections/times I was wrong page just to discuss these issues. While I think notations should be made in the posts themselves, some of them warrant their own discussion. If I’m going to blog about where others go wrong, having a dedicated place to discuss where I go wrong seems pretty fair.  I also would likely put some links to my “from the archives” columns to have a repository for posts that have more updates versions. Not only would this give people somewhere easy to look for updates, give some transparency to my own process and weaknesses, but it would also probably give me a better overview of where I tend to get tripped up and help me improve. If I get really crazy I might even start doing root cause analysis investigations in to my own missteps. Thoughts on this or examples of others doing this would be appreciated.


Calling BS Read-Along Week 6: Data Visualization

Welcome to the Calling Bullshit Read-Along based on the course of the same name from Carl Bergstorm and Jevin West  at the University of Washington. Each week we’ll be talking about the readings and topics they laid out in their syllabus. If you missed my intro and want the full series index, click here or if you want to go back to Week 5 click here.

Oh man oh man, we’re at the half way point of the class! Can you believe it? Yup, it’s Week 6, and this week we’re going to talk about data visualization. Data visualization is an interesting topic because good data with no visualization can be pretty inaccessible, but a misleading visualization can render good data totally irrelevant. Quite the conundrum. [Update: a sentence that was originally here has been removed. See bottom of the post for the original sentence and the explanation] It’s easy to think of graphics as “decorations” for the main story, but as we saw last week with the “age at death graph”, sometimes those decorations get far more views than the story itself.

Much like last week, there’s a lot of ground to cover here, so I’ve put together a few highlights:

Edward Tufte The first reading is the (unfortunately not publicly available) Visual Display of Quantitative Information by the godfather of all data viz Edward Tufte.  Since I actually own this book I went and took a look at the chapter, and was struck by how much of his criticism was really a complaint about the same sort of “unclarifiable unclarity” we discussed in Week 1 and 2. Bad charts can arise because of ignorance of course, but frequently they exist for the same reason verbal or written bullshit does. Sometimes people don’t care how they’re presenting data as long as it makes their point, and sometimes they don’t care how confusing it is as long as they look impressive. Visual bullshit, if you will. Anything from Tufte is always worth a read, and this book is no exception.

Next up are the “Tools and Tricks” readings which are (thankfully) quite publicly available. These cover a lot of good ground themselves, so I suggest you read them.

Misleading axes The first reading goes through the infamous but still-surprisingly-commonly-used case of the chopped y-axis. Bergstrom and West put forth a very straightforward rule that I’d encourage the FCC to make standard in broadcasting: bar charts should have a y-axis that starts at zero, line charts don’t have to. Their reasoning is simple: bar charts are designed to show magnitude, line charts are designed to show variation, therefore they should have different requirements. A chart designed to show magnitude needs to show the whole picture, whereas one designed to show variation can just show variation. There’s probably a bit of room to quibble about this in certain circumstances, but most of the time I’d let this bar chart be your guide:

They give several examples of charts, sometimes published or endorsed by fairly official sources screwing this up, just to show us that no one’s immune. While the y-axis gets most of the attention, it’s worth noting the x-axis should be double check too. After all, even the CDC has been known to screw that up. Also covered are the problems with multiple y-axes, which can give impressions about correlations that aren’t there or have been scaled-for-drama. Finally, they cover what happens when people invert axes and just confuse everybody.

Proportional Ink The next tool and trick reading comes with a focus on “proportional ink” and is similar to the “make sure your bar chart axis includes zero” rule the first reading covered. The proportional ink rule is taken from the Tufte book and it says: “The representation of numbers, as physically measured on the surface of the graphic itself, should be directly proportional to the numerical quantities represented”. 

[Added for clarity: While Tufte’s rule here can refer to all sorts of design choices, the proportional ink rule hones in on just one aspect: the shaded area of the graph.] This rule is pretty handy because it gives some credence to the assertion made in the misleading axes case study: bar charts need to start at zero, line charts don’t. The idea is that since bar charts are filled in, not starting them at zero violates the proportional ink rule and is misleading visually. To show they are fair about this, the case study also asserts that if you fill in the space under a line graph you should be starting at zero. It’s all about the ink.

Next, we dive in to the land of bubble charts, and then things get really murky. One interesting problem they highlight is that in this case following the proportional ink rule can actually lead to some visual confusion, as people are pretty terrible at comparing the sizes of circles. Additionally, there are two different ways to scale circles: area and radius. Area is probably the fairer one, but there’s no governing body enforcing one way or the other. Basically, if you see a graph using circles, make sure you read it carefully. This goes double for doughnut charts. New rule of thumb: if your average person can’t remember how to calculate the area of a shape, any graph made with said shape will probably be hard to interpret. Highly suspect shapes include:

  • Circles
  • Anything 3-D
  • Pie charts (yeah, circles with angles)
  • Anything that’s a little too clever

To that last point, they also cover some of the more dense infographics that have started popping up in recent years, and how carefully you must read what they are actually saying in order to judge them accurately. While I generally applaud designers who take on large data sets and try to make them accessible, sometimes the results are harder to wade through than a table might have been. My dislike for infographics is pretty well documented, so I feel compelled to remind everyone of this one from Think Brilliant:

Lots of good stuff here, and every high school math class would be better off if they taught a little bit more of this right from the start. Getting good numbers is one thing, but if they’re presented in a deceptive or difficult to interpret way, people can still be left with the wrong impression.

Three things I would add:

  1. Track down the source if possible One of the weird side effects of social media is that pictures are much easier to share now, and very easy to detach from their originators. As we saw last week with the “age at death” graph, sometimes graphs are created to accompany nuanced discussions and then the graph gets separated from the text and all context is lost. One of the first posts I ever had go somewhat viral had a graph in it, and man did that thing travel. At some point people stopped linking to my original article and started reporting that the graph was from published research. Argh! It was something I threw together in 20 minutes one morning! It even had axis/scale problems that I pointed out in the post and asked for more feedback! I gave people the links to the raw data! I’ve been kind of touchy about this ever since….and I DEFINITELY watermark all my graphs now. Anyway, my personal irritation aside, this happens to others as well. In my birthday post last year I linked to a post by Matt Stiles who had put together what he thought was a fun visual (now updated) of the most common birthdays. It went viral and  quite a few people misinterpreted it, so he had to put up multiple amendments.  The point is it’s a good idea find the original post for any graph you find, as frequently the authors do try to give context to their choices and may provide other helpful information.
  2. Beware misleading non-graph pictures too I talk about this more in this post, but it’s worth noting that pictures that are there just to “help the narrative” can skew perception as well. For example, one study showed that news stories that carry headlines like “MAN MURDERS NEIGHBOR” while showing a picture of the victim cause people to feel less sympathy for the victim than headlines that say “LOCAL MAN MURDERED”. It seems subconsciously people match the picture to the headline, even if the text is clear that the picture isn’t of the murderer. My favorite example (and the one that the high school students I talk to always love) is when the news broke that only .2% of Tennessee welfare applicants tested under a mandatory drug testing program tested positive for drug use. Quite a few news outlets published stories talking about how low the positive rate was, and most of them illustrated the story with a picture of a urine sample or blood vial. The problem? The .2% positive rate came from a written drug test. The courts in Tennessee had ruled that taking blood or urine would violate the civil rights of welfare applicants, and since lawmakers wouldn’t repeal the law, they had to test them somehow. More on that here. I will guarantee you NO ONE walked away from those articles realizing what kind of drug testing was actually being referenced.
  3. A daily dose of bad charts is good for you Okay, I have no evidence for that statement, I just like looking at bad charts. Junk Charts by Kaiser Fung and the WTF VIZ tumblr and Twitter feed are pretty great.

Okay, that’s all for Week 6! We’re headed in to the home stretch now, hang in there kids.

Week 7 is up! Read it here.

Update from 4/10/17 3:30am ET (yeah, way too early): This post originally contained the following sentence in the first paragraph: “Anyway it’s an important issue to keep in mind since there’s evidence that suggests that merely seeing a graph next to text can make people perceive a story as more convincing and data as more definitive, so this is not a small problem.”  After I posted, it was pointed out to me that the study I linked to in that  sentence is from a lab whose research/data practices have recently come in for some serious questioning.  The study I mentioned doesn’t appear to be under fire at the moment, but the story is still developing and it seems like some extra skepticism for all of their results is warranted. I moved the explanation down here so as to not interrupt the flow of the post for those who just wanted a recap. The researcher under question (Brian Wansink) has issued a response here.

5 Things You Should Know About Statistical Process Control Charts

Once again I outdo myself with the clickbait-ish titles, huh? Sorry about that, I promise this is actually a REALLY interesting topic.

I was preparing a talk for a conference this week (today actually, provided I get this post up when I plan to), and I realized that statistical process control charts (or SPC charts for short) are one of the tools I use quite often at work but don’t really talk about here on the blog. Between those and my gif usage, I think you can safely guess why my reputation at work is a bit, uh, idiosyncratic. For those of you who have never heard of an SPC chart, here’s a quick orientation. First, they look like this:

(Image from, and excellent software for generating these)

The chart is used for plotting something over time….hours, days, weeks, quarters, years, or “order in line”…take your pick.  Then you map some ongoing process or variable you are interested in…..say employee sick calls. You measure employee sick calls in some way (# of calls or % of employees calling in) in each time period. This sets up a baseline average, along with “control limits”, which are basically 1, 2 and 3 standard deviation ranges. If at some point your rate/number/etc starts to go up or down, the SPC chart can tell you if the change is significant or not based on where it falls on the plot.  For example, if you have one point that falls outside the 3 standard deviation line, that’s significant. If two in a row fall outside the 2 standard deviation line, that’s significant as well. The rules for this vary by industry, and Wiki gives a pretty good overview here. At the end of this exercise you have a really nice graph of how you’re doing with a good visual of any unusual happenings, all with some statistical rigor behind it. What’s not to love?

Anyway, I think because they take a little bit of getting used to,  SPC charts do not always get the love they deserve. I would like to rectify this travesty, so here’s 5 things you should know about them to tempt you to go learn more about them:

  1. SPC charts are probably more useful for most business than hypothesis testing While most high school level statistics classes at least take a stab at explaining p-values and hypothesis testing to kids, almost none of them even show an example of a control chart. And why not? I think it’s a good case of academia favoring itself. If you want to test a new idea against an old idea or to compare two things at a fixed point in time p-values and hypothesis testing are pretty good. That’s why they’re used in most academic research. However, if you want see how things are going over time, you need statistical process control. Since this is more relevant for most businesses, people who are trying to keep track of any key metric should DEFINITELY know about these.   Six Sigma and many process improvement class teach statistical process control, but they still don’t seem widely used outside of those settings. Too bad. These graphs are  practical, they can be updated easily, and it gives you a way of monitoring what’s going on and lot of good information about how your process are going. Like what? Well, like #2 on this list:
  2. SPC charts track two types of variation Let’s get back to my sick call example. Let’s say that in any given month, 10% of your employees call in sick. Now most people realize that not every month will be exactly 10%. Some months it’s 8%, some months it’s 12%. What statistical process control charts help calculate is when those fluctuations are most likely just random (known as common cause variation) and the point at which they are probably not so random (special cause variation). It sets parameters that tell you when you should pay attention. They are better than p-values for this because you’re not really running an experiment every month….you just want to make sure everything’s progressing as it usually does. The other nice part is this translates easily in to a nice visual for people, so you can say with confidence “this is how it’s always been” or “something unusual is happening here” and have more than your gut to rely on.
  3. SPC charts help you test new things, or spot concerning trends quickly SPC charts were really invented for manufacturing plants, and were perfected and popularized in post-WWII Japan. One of the reasons for this is that they really loved having an early warning about when a machine might be breaking down or an employee might not be following the process. If the process goes above or below a certain red line (aka the “upper/lower control limit”) you have a lot of confidence something has gone wrong and can start investigating right away. In addition to this, you can see if a change you made helps anything. For example, if you do a handwashing education initiative, you can see what percentage of your employees call in sick the next month. If it’s below the lower control limit, you can say it was a success, just like with traditional p-values/hypothesis testing. HOWEVER, unlike p-values/hypothesis testing, SPC charts make allowances for time. Let’s say you drop the sick calls to 9% per month, but then they stay down for 7 months. Your SPC chart rules now tell you you’ve made a difference. SPC charts don’t just take in to account the magnitude of the change, but also the duration. Very useful for any metric you need to track on an ongoing basis.
  4. They encourage you not to fix what isn’t broken One of the interesting reasons SPC charts caught on so well in the manufacturing world is that the idea of “opportunity cost” was well established. If your assembly line puts out a faulty widget or two, it’s going to cost you a lot of money to shut the whole thing down. You don’t want to do that unless it’s REALLY broken. For our sick call example, it’s possible that what looks like an increase (say to 15% of your workforce) isn’t a big deal and that trying to interfere will cause more harm than good. Always good to remember that there are really two ways of being wrong: missing a problem that does exist, and trying to fix one that doesn’t.
  5. There are quite a few different types One of the extra nice things about SPC charts is that there are actually 6 types to chose from, depending on what kind of data you are working with. There’s a helpful flowchart to pick your type here, but a good computer program (I use QI macros) can actually pick for you. One of the best parts of this is that some of them can deal with small and varying sample sizes, so you can finally show that going from 20% to 25% isn’t really impressive if you just lowered your volume from 5 to 4.

So those are some of my reasons you should know about these magical little charts. I do wish they’d get used more often because they are a great way of visualizing how you’re doing on an ongoing basis.

If you want to know more about the math behind them and more uses (especially in healthcare), try this presentation. And wish me luck on my talk! Pitching this stuff right before lunch is going to be a challenge.

Calling BS Read-Along Week 5: Statistical Traps and Trickery

Welcome to the Calling Bullshit Read-Along based on the course of the same name from Carl Bergstorm and Jevin West  at the University of Washington. Each week we’ll be talking about the readings and topics they laid out in their syllabus. If you missed my intro and want the full series index, click here or if you want to go back to Week 4 click here.

Well hi there! Welcome to week 5 of the Calling Bullshit Read-Along. An interesting program note before we get started: there is now a “suitable for high school students” version of the Calling Bullshit website here. Same content, less profanity.

This week we dive in to a topic that could be its own semester long class “Statistical Traps and Trickery“. There are obviously a lot of ways of playing around with numbers to make them say what you want, so there’s not just one topic for the week. The syllabus gives a fairly long list of tricks, and the readings hit some highlights and link to some cool visualizations. One at a time these are:

Simpson’s Paradox This is a bit counterintuitive, so this visualization of the phenomena is one of the more helpful ones I’ve seen. Formally, Simpson’s paradox is when “the effect of the observed explanatory variable on the explained variable changes directions when you account for the lurking explanatory variable”. Put more simply, it is when the numbers look like there is bias in one direction, but when you control for another variable the bias goes in the other  direction. The most common real life example of this is when UC Berkeley got sued for discriminating against women in grad school admissions, only to have the numbers show they actually slightly favored women. While it was true they admitted more men than women, when you controlled for individual departments a higher proportion of women were getting in to those programs. Basically a few departments with lots of female applicants were doing most of the rejecting, and their numbers were overshadowing the other departments. If you’re still confused, check out the visual, it’s much better than words.

The Will Rogers Phenomenon I love a good pop culture reference in my statistics (see here and here), and thus have a soft spot for the Will Rogers Phenomenon.  Based on the quote “When the Okies left Oklahoma and moved to California, they raised the average intelligence level in both states”, this classic paper points to an interesting issue raised by improvements in diagnostic technology. In trying to compare outcomes for cohorts of lung cancer patients from different decades, Feinstein realized that new imaging techniques were resulting in more patients being classified as having severe disease. While these patients were actually more severe than their initial classification, they were also less severe than their new classification. In other words, the worst grade 1 patients were now the best grade 3 patients , making it look like survival rates were improving for both the grade 1 group (who lost their highest risk patients) and group 3 (who gained less severe patients). Unfortunately for all of us, none of this represented a real change in treatment, it was just numerical reshuffling.

Lead time bias Also mentioned in the reading above, this is the phenomena of “improving” survival rates simply by catching diseases earlier. For example, let’s say you were unfortunate enough to get a disease that would absolutely kill you 10 years from the day you got it. If you get diagnosed 8 years in, it looks like you survived for 2 years. If everyone panics about it and starts testing everyone for this disease, they might start catching it earlier. If improved testing now means the disease is caught at the 4 year mark instead of the 8 year mark, it will appear survival has improved by 4 years. In some cases though, this doesn’t represent a real increase in the length of survival, just an increase in the length of time you knew about it.

Case Study: Musicians and mortality This case study combines a few interesting issues, and examines a graph of musician “average age at death” which went viral.

As the case study covers, there are a few issues with this graph, most notably that it right-censors the data. Basically, musicians in newer genres die young because they still are young. While you can find Blues artists in their 80s, there are no octogenarian rappers. Without context though, this graph is fairly hard to interpret correctly. Most notably quite a few people (including the Washington Post) confused “average age at death” with “life expectancy”, which both appear on the graph but are very different things when you’re discussing a cohort that is still mostly alive. While reviewing what went wrong in this graph is interesting, the best part of this case study comes at the end where the author of the original study steps in to defend herself. She points out that she herself is the victim of a bit of a bullshit two step. In her paper and the original article, she included all the proper caveats and documented all the shortcomings of her data analysis, only to have the image go viral without any of them. At that point people stopped looking at the source and misreported things, and she rightly objects to being blamed for that. This reminds me of something someone sent me a few years ago:

Case Study: On Track Stars Cohort Effects and Not Getting Cocky In this case study, Bergstrom quite politely takes aim at one of his own graphs, and points out a time he missed a caveat for some data. He had created a graph that showed how physical performance for world record holders declines with age:

He was aware of two possible issues in the data: 1) that it represents only the world records, not how individuals vary and 2) that it only showed elite athletes. What a student pointed out to him is that there was probably a lot of sample size variation in here too.  The cohort going for the record in the 95-100 year old age group is not the same size as the cohort going for the record in the 25-30 year old age group. It’s not an overly dramatic oversight, but it does show how data issues can slip in without you even realizing it.

Well those are all the readings for the week, but there were a few other things mentioned in the list of stats tricks that I figured I’d point to my own writings on:

Base Rate Fallacy: A small percentage of a large number is often larger than a large percentage of a small number. I wrote about this in “All About that Base Rate“.

Means vs Medians: It truly surprises me how often I have to point out to people how that average might be lying to you.

Of course the godfather of all of this is How to Lie With Statistics, which should be recommended reading for every high school student in the country.

While clearly I could go on and on about this, I will stop here. See you next week when we dive in to visualizations!

Week 6 is up, read it here!