Reproducible Research: Concepts and Ideas (part 1)

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From the course by Johns Hopkins University

Reproducible Research

2953 ratings

Johns Hopkins University

Reproducible Research

2953 ratings

Course 5 of 10 in the Specialization Data Science

This course focuses on the concepts and tools behind reporting modern data analyses in a reproducible manner. Reproducible research is the idea that data analyses, and more generally, scientific claims, are published with their data and software code so that others may verify the findings and build upon them. The need for reproducibility is increasing dramatically as data analyses become more complex, involving larger datasets and more sophisticated computations. Reproducibility allows for people to focus on the actual content of a data analysis, rather than on superficial details reported in a written summary. In addition, reproducibility makes an analysis more useful to others because the data and code that actually conducted the analysis are available. This course will focus on literate statistical analysis tools which allow one to publish data analyses in a single document that allows others to easily execute the same analysis to obtain the same results.

From the lesson

Week 1: Concepts, Ideas, & Structure

This week will cover the basic ideas of reproducible research since they may be unfamiliar to some of you. We also cover structuring and organizing a data analysis to help make it more reproducible. I recommend that you watch the videos in the order that they are listed on the web page, but watching the videos out of order isn't going to ruin the story.

Introduction1:57

What is Reproducible Research About?8:19

Reproducible Research: Concepts and Ideas (part 1)7:11

Reproducible Research: Concepts and Ideas (part 2) 5:26

Reproducible Research: Concepts and Ideas (part 3) 3:26

Scripting Your Analysis 4:35

Structure of a Data Analysis (part 1)12:29

Structure of a Data Analysis (part 2)17:40

Organizing Your Analysis11:05

Meet the Instructors

Roger D. Peng, PhD
Associate Professor, Biostatistics
Bloomberg School of Public Health
Jeff Leek, PhD
Associate Professor, Biostatistics
Bloomberg School of Public Health
Brian Caffo, PhD
Professor, Biostatistics
Bloomberg School of Public Health

Hi, everyone.

This lecture will be about reproducible research, and I want to

just talk about some concepts and ideas that are, that

are related to reproducible research and in, just in case

you haven't heard about it or don't know what it is.

So the basic idea is that in science, replication is the most important element

of kind of verifying and validating findings that a scientist discover.

So if you claim that

x causes y, or that Vitamin C improves disease, or that this causes a problem.

What happens is that, you know, other

scientists that are independent of the original.

Will, will try to investigate that same question and

see if they come up with the same result.

And if lots of different people come up with the

same result and replicate the original finding, then we can

tend to think that, well, the original was probably true

and that this is a real relationship or real finding.

So the

ultimate standard in strengthening scientific evidence is replication.

And we, and the goal is to

have independent people to do independent things with

different data, different methods, and different laboratories

and see if you get the same result.

Because if a finding is robust to all these different things then it

is more likely to be true and the evidence is stronger in it's favor.

Replication is particularly important in studies that have, kind

of had big policy impacts or can influence regulatory types

of decisions. So, what's wrong with replication?

So there's really nothing wrong with it.

This is what science has been doing for a long time through hundreds of years.

And there's nothing wrong with it today.

But the problem is that it's very, it's becoming

more and more challenging to do replication or to

replicate other studies and because and part of the

reason is because studies are getting bigger and bigger.

In order to do big studies you need a lot of money and so there's a lot of money

involved and if you want to do ten versions of the same study, you need ten

times as much money and there's not as much money around as there used to be.

[COUGH] sometimes it's just, it's difficult to replicate

a study because you know, if the original

study took 20 years to do, it's difficult

to wait around another 20 years for replication.

So that can be a, a challenge.

Some studies are just plain unique.

So if you're looking at a unique situation in time or a unique population,

you can't readily replicate that situation.

So, there are a lot of good reasons why you can't replicate a study.

And so the idea said, well, if you can't replicate it is

the alternative just to do nothing, just let that study stand by itself?

And so the idea behind a reproducible research is to create a kind

of minimum standard or a middle ground where we won't be replicating the study,

but maybe we can do something in between.

So the basic problem is, you know, you have the gold standard, which is, which

is replication and then you have the, kind

of the, the worst standard which is nothing.

And so, what can we do that's in between the

gold standard and nothing, and that's where we're thinking is reproducibility.

So, that's how we can kind of bridge the gap between replication and nothing.

So, why do we need this kind of middle ground, which I haven't clearly

defined yet, but the basic idea is that, you know, you

make the data available for the original study, and you make the

computational methods available so that other people can can, can look at

your data and cam run the kind of analysis that you've run.

And to kind of come, come to the same findings that you found.

And so a lot of this, what reproducible research

is about is a validation of the data analysis.

Because you're not collecting independent data

using independent methods, you can, it's

a little bit more difficult to validate the, the question itself that

you're asking, but if you can take someone's data and repli, and

reproduce their findings, then you can in some sense validate the data analysis.

And so this involves having the data and

the code because, you know, most, more likely than

not, the analysis will have been done on the

computer using some sort of programming language like R.

And so you can take their code and their data and reproduce the findings that they

come up with, then you can at least

have confidence that the analysis was done appropriately.

And and that the correct methods were done, were used excuse me.

So what is driving this need for a middle

ground, this reproducibility middle ground between replication and doing nothing?

Well, there's a lot of new technologies on

the scene and in many different fields including, biology

and chemistry and environmental science, all kinds of areas.

These technology allow us to collect data at a much higher throughput.

And so we get these very complex and very high dimensional data sets.

Almost instantaneously compared to even just ten years ago.

And so, the technology has allowed us to create huge

data sets, at a, at essentially the touch of a button.

furthermore, we have computing power that allows us to take on

existing databases and merge them into, just, even bigger and bigger databases.

So we can take data that were previously, maybe,

inaccessible and create new data sets out of it.

So these new data sets are huge now.

and, in addition to allowing us to create new data sets

computing power allows us to, to to do more sophisticated analysis.

So the analysis themselves, the models that we fit and

the algorithms that we run, are much much more complicated than they use to be.

And so, having a basic understanding of these

algorithms is difficult, even for a sophisticated person.

So, understanding what someone did in an analysis of data will

require looking at code, looking at the computer programs that people used.

And so the, and so the bottom line with all these different

trends is that for every field x, there is now computational x.

There's computational biology, computational

astronomy, computational whatever is

you want, there is a computational version of it.

So one example from research that I've conducted

is in the area of air pollution and health.

Now air pollution and health is a, is a big field and it, and it involves

a kind of, is a confluence of features

that make reproducibility very important in this area.

The first that we're estimating very small,

but very important public health effects in the presence of a much stronger signal.

So you can think about air pollution as something that's,

you know, perhaps harmful but even if it were harmful

there are many other things that are going, that are

going to be more harmful that you have to worry about.

So pollution is going to be, not at the

very top of the list that's going to harm you.

The results of a lot of air

pollution research inform kind of substantial policy decisions.

Regulations will

be based on scientific research in this area.

And so these regulations can affect a lot of stakeholders

and, and furthermore, can cost billions of dollars to implement.

Finally, we use a lot of complex statistical methods to do a lot

of these stedies and so, and these

statistical methods are subjected to intense scrutiny.

So combinations of an, of an inherently

small signal large impacts, and complex statistical methods

almost require that the research that we do be reproducible.

And so one of the things that we've done and here at John's

Hopkins is to create what's called the

Internet-based Health and Air Pollution Surveillance System.

We make a lot of our data available, we make a

lot of our statistical methods in the form of R code

available so that they can be examined, and the data, and

many of the results that we produce can be reproduced by others.

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