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From the course by Johns Hopkins University

Reproducible Research

2592 оценки

Johns Hopkins University

Reproducible Research

2592 оценки

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 2: Markdown & knitr

This week we cover some of the core tools for developing reproducible documents. We cover the literate programming tool knitr and show how to integrate it with Markdown to publish reproducible web documents. We also introduce the first peer assessment which will require you to write up a reproducible data analysis using knitr.

Coding Standards in R8:58

R Markdown Demonstration7:23

knitr (part 1)7:04

knitr (part 2) 4:10

knitr (part 3) 4:46

knitr (part 4) 9:29

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

[BLANK_AUDIO]

Markdown is a really useful language for

creating documents without having to deal with

a lot of the overhead and kind

of complications of using standard markup languages.

The idea behind Markdown is that it's

a, you know, it's a simplified markup language.

And it really, the, the goal is to, to allow you to focus on just writing

your content and not have to worry about

things like tags or other things like that.

And so Markdown, you'll notice, is very simple.

And we use it a lot here.

All of the slides for the course are written in Markdown And a nice thing

about Markdown is that it's very easy to

integrate it with Rcode, and other programming languages.

So, in this lecture I'm just going to talk about the very basics of Markdown.

But of course it, beyond the basics actually there's not a whole lot.

So that's what makes Markdown so, so nice.

And then once I'll just talk a little bit about kind of the basic aspects and give,

give you a few pointers on kind of where you can go to learn about more.

So,

so just to start off with, Markdown is

a text to HTML conversion tool for web writers.

Markdown allows you to write easy, using an easy to use, read,

easy to write, plain text format and then convert to structurally valid XHTML.

So the idea is that, so the, John Gruber, the creator of Markdown, wanted people

to be able to focus on writing their content, and not other kind of aspects.

And so, the basic syntax for Markdown is fairly simple.

For, so,

you can you can format text, for example with italics

using the asterisks here and then the text will be italicized.

You can do things like create bold face with the,

with the double asterisk and the text will appear bold.

You can create headings.

There are different sizes, so if you're familiar with

HTML you can think of this as H1, H2, H3.

So the two hashes, this is a secondary heading.

The three hashes is a tertiary heading.

And then a single hash, which I didn't put here

is a, is like a main heading, a primary heading.

And so you can see that there are different sizes here.

You can create very simple unordered lists by putting

a little indicator there, like a hyphen or an asterisk.

It doesn't really matter what the the character is that you

use there as long as it's kind of consistent across the list.

So you can create an unordered list like this by

just just starting it right away, there's no other formatting element.

You can create an ordered list here by just doing one, two, and three.

And the, and, and the truth is actually,

although it's a little, it's not immediately clear here

the numbering doesn't have to actually be in order.

As long as you use a number as the kind of character that, kind

of, that indents the line it will cr-, the Markdown will create an ordered list.

And so, if you decide that oh, you know, you want to stick something in

between one and two, you don't have to renumber every element on the list.

You can just stick another item there under the first item.

And it could be another one, or it could be four, it could be

any number, the numbers don't have to be in order, but when you process

the document Markdown will automatically order the list in the right way.

You can of course put links into a document,

this is very important if you're creating web documents.

And there are two ways to create links.

The first way I've got here puts the text in square

brackets, and then immediately following that puts the URL in parenthesis.

So, here I can see Johns Hopkins Bloomberg School of Public Health.

And and the URL is right next to it, and

then Download R with the R website right next to that.

And so and then it'll be formatted in an HTML

document in the usual way.

The text will be highlighted, and underlined.

The other way to to create links in a Markdown

document is to put the, again, the text in square brackets.

And then, and right next to it in square brackets put

a number which is going to be like an identifier for that link.

And then later on, perhaps at the bottom of the document you

can put the actual URL for for the length that you meant.

So, number one here is for R

bloggers and at the bottom of the document I might

put a number one and then the R bloggers URL.

And then the second link here is for Simply Statistics,

so for number two I put the Simply Statistics URL.

The basic idea with this type of linking is that it makes

the text in your document a little bit cleaner and easier to read.

Especially if you have very long URL's.

And you, and you don't necessarily want to put all these really

long URL's in the document so it makes it hard to read.

This makes it a little bit easier to read, while your

editing the document and puts all the links down at the bottom.

Lastly new lines can be created in the text document by

just putting a double space at the end of a line.

So I just do first line, second line like

this with just, with no space after the first line.

All the lines will run together like that.

But if I put two spaces after the first line then

you'll get a kind of a new line put in between.

So just the, that's going to be just an easy gotcha, that

can be the people who newly come into Markdown will often discover.

So that's just a really,

really quick overview of Markdown.

Here's some basic resources of the

official Markdown documentation on, on Jon-,

John Grubers website, is very easy to read, it's very, it's relatively short.

You'll be able to learn it within minutes.

You already know most of it just by readin-, by looking at this lecture.

And then, Github has its own kind of

Markdown flavor, with a few kind of enhancements.

So if you're going to be using Github and documenting things in

Github it might be useful to check out their Markdown guide.

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