Before you can work with data you have to get some. This course will cover the basic ways that data can be obtained. The course will cover obtaining data from the web, from APIs, from databases and from colleagues in various formats. It will also cover the basics of data cleaning and how to make data “tidy”. Tidy data dramatically speed downstream data analysis tasks. The course will also cover the components of a complete data set including raw data, processing instructions, codebooks, and processed data. The course will cover the basics needed for collecting, cleaning, and sharing data.
The data.table Package
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Из курса от партнера Johns Hopkins University
Getting and Cleaning Data
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Week 1
In this first week of the course, we look at finding data and reading different file types.
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Jeff Leek, PhDAssociate Professor, Biostatistics
Bloomberg School of Public Health
Roger D. Peng, PhDAssociate Professor, Biostatistics
Bloomberg School of Public Health
Brian Caffo, PhDProfessor, Biostatistics
Bloomberg School of Public Health
This lecture is about the data.table package which is a often faster more
memory efficient version of the data frames that you're commonly using when
your analyzing data NR.
So the data.table inherits from a data frame so
all functions that accept that data.frame should work on data.table.
And there's a pretty steady set of updates to data that table in case it
doesn't work.
It's written in C so
it can be much, much faster than some of the functions that are done in data.frame.
It's much, much faster at subsetting, grouping variables, and
updating variables than data frames are but it requires you
to learn a little bit of a new syntax so there's a little bit of a learning curve.
So if we load the data.table package we can create a data frame like this.
This is the usual way that we create a data frame.
And if we look at that we see it has, you know, three variables, x, y,
and z stored in each of the columns.
And we can also create a data table, and we create it in exactly the same way.
And so we just pass it the arguments for the variables that we want to create.
And if you look at the top of that data frame you see it looks
very similar to what you would expect if you had created a data frame.
So one thing that you can do is see all of that data that tables in memory, so
you do that with the tables command.
It has an s at the end, it's different than the table command.
And so what it'll tell you is the name of the data table, how many rows,
how many megabytes how many columns and if there's a key.
And so I'll talk a little bit more about what I mean by a key in a minute.
So the first thing that you might want to be able to do is subset rows and
so just like with.
Subsetting the rows in the data frame.
You can subset with the first spot in the square brackets, before the comma.
You can also subset just like you did rows, like you did with the data frame,
in a similar way, by accessing a particular element, y, and
looking at only the values where y is equal to a.
One thing that is a little bit different is when you subset with only one index,
it subsets based on the rows.
So if I do this data table, I take the second or third element,
that's going to take the second and third rows that come out of that data table.
What happens when you try to subset columns,
if you just try to subset columns the way you're used to in data frames,
this is where they really diverge data table and data frame.
It's not actually trying to subset the columns using the same subsetting
function that happens with data frame, it does something a little bit different.
And so what it's using is expressions to be able to summarize the data in various,
different ways.
So, any expression is
some set of statements that are between curly brackets, like this.
So here's an example of an statement that says print ten and
then five, and so this actually prints out ten.
But when you tell k to print, it just prints out the variable five at the end.
So, this will come into a play in a minute when we try to use expressions to
summarize data sets.
So for example, you can, instead of putting an index here in the second
part of the brackets, you can actually pass a list of functions that you want
to perform where the functions are applied to variables named by columns.
So here x is one of the variables in the data table and
z is one of the variables in the data table.
And note we don't have to use parentheses, or sorry, quotation marks.
It will just recognize what the variables.
That you're trying to use R.
And so, this will report the mean of the x values and the sum of the z values.
You can also do that to perform pretty much any function.
You can say, for example, get a table of the y values.
And so, anytime you pass a list into this second argument,
it'll perform those functions and return the values.
That's good for summarizing data.
Another thing that it does very fast and
very memory efficiently is to add a new column.
So suppose you wanted to add a new column to your data table where a new column was
equal to this z variable squared you can use this command where it's
colon equals to add that variable w to the data table.
And the nice thing is is usually when you're adding a new variable to a data
frame, R will copy over the entire data frame and add a new variable to it,
so you get two copies of the the data frame and memory.
So when dealing with big data sets,
this is obviously going to cause lots of memory problems,
which you don't have with data table because a new copy isn't being created.
You have to be a little bit careful with that though, so
suppose we set a second data table to be assigned to the first data table.
And then we make a change to the first data table.
Because a copy hasn't been made, if we go back and
look at the first data table, obviously we've made a change to that,
we've changed the Y variable to be all equal to's.
But the second data table was assigned to be the first data table and
since a copy wasn't made, we've actually changed data table two as well.
So you have to be able to, if you're trying to create a copy you have to
explicitly do that with the copy function.
So if you use the function copy you'd be able to copy the data table over.
So the next thing that you can do is you can actually perform multiple step
functions to create new variables.
So for example here I have an expression.
See it starts with the curly bracket and it ends with a curly bracket.
And each statement is followed by a semi-colon.
So the first statement is I'm going to assign to the temporary variable,
the values of X plus Z, and
then I'm going to take the log base two of that temporary variable plus five.
And so as you remember, the last thing that gets returned from this
expression in the evaluation of this last statement.
And so what ends up happening is
this variable m will be assigned to be log base two of x plus z plus five.
So those sorts of multi step
operations can be handled very easily with data table.
You can also do plyr like operations.
So for example we can add to this data table a variable like A which is
created in zero,
equal to true when X is greater than zero and false when X is less than zero.
So now we have a binary value A that we can work with.
So suppose we want to summarize another variable by the cases where
when X is greater than 0 versus the cases where X is less than 0.
So for example we can take the mean of X + W and
we can do it grouped by a variable A.
And so what that's gonna do is it's gonna take the mean of X plus W when A is equal
to true, and it's gonna place that mean in all the rows where A is equal to true.
Then it's gonna take the mean of X plus W where A is equal to false.
And place that mean in all the rows where A is equal to false.
So it creates a new variable that's equal to the aggregated mean,
aggregated over the variable that you used by 4.
There's some special variables and
data table that allow you to do something's really fast.
So one is a .N is an integer linked one and
it's a containment number of times that a particular group appears and so for
example if I created data table that has a large
number of As, Bs, and Cs in it, so about 100,000 A B and Cs.
Then what I can do is, if I want to count the number
of times each of those letters appear I can use data table,
dot N, and then grouped by the X variable.
And then what that will do is it will count,
dot N is just count the number of times grouped by the X variable.
It does that very fast as opposed to the equivalent operation,
which is just doing that table of DT dollar sign X.
A unique aspect of data tables is that they have keys,
so if you set the key, it's possible to subset and
sort a data table much more rapidly than you would be able to do with a data frame.
Here, I'm going to create a data table, and it's going to have a variable X.
And it's gonna have a variable Y and I'm gonna set the key for
the data table to be the variable X.
Then if I want a subset on the basis of x or if I put in
quoted a here, it knows to go and look in the key, and the key is x, and
it very quickly subsets the data to only the values of x that are equal to a.
You can also use keys to facilitate joints between data tables so for
example here I've created two data tables where they have a variable X and
a variable Y and in this case the second data table has a variable Z.
And so I can set the key in both cases to be equal to x, so
the same key for both data tables.
And then I can merge them together.
This is actually quite a bit faster than merging with the data frame
as long as you have the same key for both data tables.
It can be very fast.
It can also be advantageous to use data tables if you want to be able to read
things fast from the disk.
So here I've created a big data frames.
So it's a data frame with two very large variables in it.
And then I set up a temporary file with this command right here.
And I write our big data frame apps that file.
Then I'm going to time how long it takes to read it in using the fread command.
The fread command could be applied to reading data tables,
just like basically a drop-in substitute for read.table tab separated files.
And so you can see it takes about .32 seconds.
If I tried to do that same operation, if I just tried to read that table that file,
it would come in quite a bit slower,
well a little more than ten times slower to be able to read that file in.
So it's actually much faster to read files with data, data.table as well.
To summarize data table can be both faster and
more memory efficient than data frames.
Although it requires you to learn a little bit of use syntax, and
sometimes to be a little bit careful in terms of copying over data tables.
The latest developments can be found on the development version of the package.
Which can be found at this website right here.
They've already started to develop a melt like operations and
decast like operations for data tables and they're gonna continually
update that packages it's a very rapidly developing package.
And then this website here is very nice cause it gives you comprehensive-ish
list of all the differences between data.table and data frames.
And so, that would be very useful if you're transitioning from
using data frames to using data table.
The notes that I've used today are very largely based on the notes that
Raphael Gottardo has put up here on GitHub, and they were originally from
Kevin Ushey, and I think that both of them deserve credit for
the excellent notes that I've largely copied here for this lecture.
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