One of the most common tasks performed by data scientists and data analysts are prediction and machine learning. This course will cover the basic components of building and applying prediction functions with an emphasis on practical applications. The course will provide basic grounding in concepts such as training and tests sets, overfitting, and error rates. The course will also introduce a range of model based and algorithmic machine learning methods including regression, classification trees, Naive Bayes, and random forests. The course will cover the complete process of building prediction functions including data collection, feature creation, algorithms, and evaluation.
Predicting with Regression Multiple Covariates
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Del curso dictado por Johns Hopkins University
Practical Machine Learning
1976 calificaciones
De la lección
Week 2: The Caret Package
This week will introduce the caret package, tools for creating features and preprocessing.
Conoce a los instructores
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's about two things.
First it's about predicting with regression and using
multiple covariates, but more importantly it's about exploring a
data set and trying to identify which predictors are
the most important to include in our prediction model.
So we're again going to be using the wages data to try to
predict the wages of a group of men that come from the mid Atlantic.
This data set is available at the ISLR package which you can find here.
And it comes from the book Introduction to statistical learning.
So the first thing that we do is that we load
the data set in, and so here is the ISLR data set.
We're also loading the ggplot2 package for some
exploratory analysis, and we're loading the caret package.
We're doing prediction, and we're going to
subset the data set for exploration purposes to
just the part of the data set that isn't the variable we're trying to predict.
So we select out the log wage variable, which is
the variable that we're going to be predicting in this analysis.
Then we can look at a summary of the data set and
so we can already see some features, for example, we saw before,
that this data set has only males included in the data set
and that for example the region is entirely peopled from the mid Atlantic.
So to do a little bit more exploration, we first
need to train subset things into the training and test sets.
So we use that with the Create Data Partition function.
And we subset into a training and test set.
And so we're going to do all of our exploration again on the training set.
Because when we're building models, we're not going to use any of the test set.
We're only going to apply it once.
So the first thing that you can do is a feature plot.
So this feature plot says, shows a little bit
about how the variables are related to each other.
Sometimes this plot is useful and sometimes it isn't.
In this particular plot it's a little bit hard
to see because everything is so squished together but if
you make it on your own, by using this function
you'll see that it's a little bit easier to see.
So, for example, you can see that there appears
for the job class there appears to be this group,
appears to be a little bit higher than that
group for the job class in terms of the outcome.
And you can see that there is, at least
for this age variable the relationship to the outcome.
Again there seems to be some outlier group, two separate groups here that gives
us some indication that we might be able to use that variable to predict.
So the first thing that we can do is plot the variables versus weight age.
So this is plotting the wage variable versus the age
variable and you can see that there appears to be
some kind of trend which we saw in the previous
lectures, but there also is this set of points that's
outlined up here, and so the idea is that that
set of points that's outlined up there might be, something
that we can predict, but we would have to figure
out what variable it is that, is representing that chunk.
So, one way that you can do that is, you
plot one variable, one predictor, age versus the outcome, wage.
And then you color the points by another variable, in this case job class.
And you can see for example that it appears that most of these points up
here are blue instead of pink and so
that means they come from the information group.
So, this gives us some indication that the
information variable might be able to predict at least
some fraction of the variability that's in that top class up at the top of the plot.
You can also color it by education.
So, here I'm just doing a q plot again.
So I'm plotting age versus wage.
And I'm telling it to color the plot by education.
And, again, I'm only using the training set because we're trying
to, only look at training set for our development of our model.
And you can see that the advance degree, also explains,
a lot of the variation up here in the top group.
And so, some combination of, degree, and,
class of job, could explain why, the relationship
between age and wage isn't just a perfect relationship down here, in one big cloud.
So the next thing that we can do is fit a linear model with multiple variables in it
and so the idea here is, again, we're just
fitting lines, but now we're fitting more than one line.
And so the idea is, we have some intercept terms, so that's
just the baseline level of, wage that we might have, and then
we might have a, a relationship with the age of the person,
and then we might have relationship with what job class you're in.
So one way that we typically do that is, by fitting an indicator variable.
So an indicator variable is a variable
that's denoted like this in mathematical notation.
It just says, if the job class for the ith
person is equal to information, this variable's equal to one.
If the job class for the ith person is not equal to information, then
this information is equal to zero, and so this represents the difference in the
wages between the people with job class
equal to information versus job class equal
to not information, when you, fix all the other variables in the regression model.
You can also do this for education it's a little
bit more complicated road because there are multiple education levels.
So we create an indicator variable for, each of the different education
levels and so, here this is the sum of four indicator variables.
And so the, the variable's equal to one, if the education
for person I is equal to level K, that variables equal to one and zero otherwise.
So then we can fit the model just like we did before
so we have, we're using the train function in the caret package.
And we again use wage as the outcome and then tilde represents the formula
on the right, it's going to be used to predict the variable on the left.
So we use age, job class, and education.
So job class and education are both factor variables in r and so by
default it does, you know, it creates
these indicator variables like I've shown here.
So, that when it fits the model it takes that into account by automatically.
Again we're fitting the model on the training set
and we can look at the final model and
you can see now that the final model has
ten predictors even though we only put three variable
names into the formula and the reason is because
this, variable right here, got, actually received more than
one, predictor in the data set because of the
way that we had to create these indicator functions.
So then we can look at some diagnostic plots.
So this is very typical for when you're building these regression models.
The idea here is you can plot the fitted
values, so this is the predictions from our model on
the training set versus the residuals, that's the amount
of variation that's left over after you fit your model.
And so what you'd like to see is that.
This line would be centered at zero on this, axis because the residuals is the,
difference between our model prediction and our,
actual real values that we're trying to predict.
And here, you can see there's still a couple of outliers
up here that have been labeled for you in this plot.
And so, those variables might be variables that we
want to try to explore a little bit further and
see if we can identify any other predictors in
our data set that might be able to explain them.
The other thing that we can do is color by variables not just used in the model.
So for example here I'm plotting again the
fitted values from our model versus the residuals.
And so again, we like to see this laying on the zero
line because it's the difference between our fitted values and our real values.
And so, what we can do is plot on this plot, we can again plot
it by different variables, in this case, we can plot it by for example, race.
And so you can see that it seems like some of these
outliers up here may be explained by the race variable in the
data set and so these another exploratory technique plotting the fitted model
versus the residuals then coloring it
by different variables to identify potential trends.
Another thing that can be really useful
is plotting the fitted residuals versus the index.
And what do I mean by the index?
So the data set comes in a set of rows that you got in a particular order.
And so the index is just which row of the data set you're looking at.
And the y axis here is the residuals.
And so you can see that all the residuals seems to be happening, high residuals seem
to be happening down here at the right end of the high, the highest row numbers.
And you can also see a trend with respect to row numbers and so
whenever you can see a trend or a outlier like that with respect to the
row numbers, it suggests that there's a
variable missing from your model because you're
plotting the residuals here, so that's the
difference between the true values and the fitted.
And that shouldn't have any relationship to the order
in which the variables appear in your data set.
Unless, and this is what's typically you discover when you see
a trend like this, or outliers like this at one end of
this plot, that there's a relationship with respect to time, or
age, or some other continuous variable that the rows are ordered by.
So the other thing that you can do is plot the wage variable.
So this is the wage variable in the test
set versus the predicted values in the test set.
So ideally these two things would be very close to each other.
Ideally you'd have essentially a straight line on the 45
degree line where wage was exactly equal to our predictions.
Of course that isn't how it always works out.
And then in the test set, you can explore
and try to identify trends that you might have missed.
So, for example, here we're looking at the year
that the data was collected in the test set.
As a way of exploring how our model might have broken down.
Now something to keep in mind is that if you do
this sort of exploration in the test set, you can't then
go back and re-update your model in the training set because
that would be using the test set to rebuild your predictors.
This is more like a post-mortem on your analysis or a
way to try to determine whether your analysis worked or not.
If you want all of the covariants in your model building, one
thing that you can do is use this again in the training function.
You can pass it an outcome and then tilde and then if you put
a dot here instead of putting a set of variables separated by plus signs.
It says predict with all of the variables in the data set.
So, this is model fit with all of the variables and
so this is the wage variable and the predictions here and
so you can actually see that it does a little bit
better when you include all of the variables in the data set.
This is By default if you don't want to
try to do some sort of model selection in advance.
So linear regression is often useful in combination with other models.
It's a quite a simple model in the
sense that it always fits lines through the data.
And so it can be, capture a lot of variability
if the relationship between the predictors and the outcome is linear.
If it's not linear, then you can often miss
things, and it can be better blended with other models.
We'll talk about model blending later in the class.
Exploratory data analysis can be very useful with regression
models because, like, the plots we made with residuals
and so forth colored by different features, you can
try to identify the patterns in the data set.
There's more information in these three books, if you want to
go and find a lot more about regression modeling for prediction.
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