Category: R

The Luminance Illusion With gganimate

Published 2018-08-23 by Kevin Feasel

David Smith highlights an example of the luminance illusion:

Colin created this animation in R using the gganimate package (available on GitHub from author Thomas Lin Pederson), and the process is delightfully simple. It begins with a chart of 10 “points”, each being the same grey square equally spaced across the shaded background. Then, a simple command animates the transitions from one point to the next, and interpolates between them smoothly:
library(gganimate)
gg_animated <- gg + transition_time(t) + ease_aes('linear')

Check it out, both as a parlor trick and a way of getting a grip on the gganimate package.

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Styling In ggplot2

Published 2018-08-23 by Kevin Feasel

The folks at Jumping Rivers show an example of creating a nice-looking plot with ggplot2:

The changes we’ve made so far would impossible for any package to do for us – how would the package know the plot title? We can now improve the look and feel of the plot. There are two ways of complementary ways of doing this: scales and themes. The ggplot scales control things like colours and point size. In the latest version of ggplot2, version 3.0.0, the Viridis colour palette was introduced. This palette is particularly useful for creating colour-blind friendly palettes
g + scale_colour_viridis_d() # d for discrete

With a few lines of code, those default graphs can look a lot nicer.

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Matrix Math In R

Published 2018-08-22 by Kevin Feasel

Dave Mason continues his series on matrices in R:

Math operations between matrices is possible too. Here, the same matrix is added to itself. Since it’s the same matrix, they obviously have the same number of elements. The first element is added to the first element, the second element is added to the second element, etc.
> #Add two matrices.
> some_numbers + some_numbers [,1] [,2] [,3] [,4] [,5] [,6]
[1,] 2 4 6 8 10 12
[2,] 14 16 18 20 22 24
[3,] 26 28 30 32 34 36
[4,] 38 40 42 44 46 48

This follows from Dave’s prior posts, but you can see some of the pieces start to fit together.

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Dealing With Multicollinearity With R

Published 2018-08-21 by Kevin Feasel

Chaitanya Sagar explains the concept of multicollinearity in linear regressions and how we can mitigate this issue in R:

Perfect multicollinearity occurs when one independent variable is an exact linear combination of other variables. For example, you already have X and Y as independent variables and you add another variable, Z = a*X + b*Y, to the set of independent variables. Now, this new variable, Z, does not add any significant or different value than provided by X or Y. The model can adjust itself to set the parameters that this combination is taken care of while determining the coefficients.
Multicollinearity may arise from several factors. Inclusion or incorrect use of dummy variables in the system may lead to multicollinearity. The other reason could be the usage of derived variables, i.e., one variable is computed from other variables in the system. This is similar to the example we took at the beginning of the article. The other reason could be taking variables which are similar in nature or which provide similar information or the variables which have very high correlation among each other.

Multicollinearity can make regression analysis trickier, and it’s worth knowing about. H/T R-bloggers.

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Including R Visuals In Power BI Dashboards

Published 2018-08-21 by Kevin Feasel

Parker Stevens shows how to include R visuals in a Power BI dashboard:

Let’s finish up this post with a quick example of how to code the elusive line chart with two y-axes. This always seems to be asked in the forums and it’s pretty easy to implement.
Follow the same steps as shown above to bring in a new R visual. Since we need a column to pass into the visual and open up the editor, let’s just throw in the Angle field that we made previously. With the code editor available we can start writing the R script. In this example, we are going to need some data that is available in a specific R package, called “ggplot2.” Go ahead and install the package by typing the following code the same way we installed scatterplot3d:
install.packages(“ggplot2”)

There are two interesting examples here, including one which accepts an external parameter.

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Faster User-Defined Functions In SparkR

Published 2018-08-20 by Kevin Feasel

Liang Zhang and Hossein Falaki note a major performance improvement for functions in SparkR using the latest version of the Databricks Runtime:

SparkR offers four APIs that run a user-defined function in R to a SparkDataFrame
dapply()
dapplyCollect()
gapply()
gapplyCollect()
dapply() allows you to run an R function on each partition of the SparkDataFrame and returns the result as a new SparkDataFrame, on which you may apply other transformations or actions. gapply() allows you to apply a function to each grouped partition consisting of a key and the corresponding rows in a SparkDataFrame. dapplyCollect() and gapplyCollect()are shortcuts if you want to call collect() on the result.
The following diagram illustrates the serialization and deserialization performed during the execution of the UDF. The data gets serialized twice and deserialized twice in total, all of which are row-wise.
By vectorizing data serialization and deserialization in Databricks Runtime 4.3, we encode and decode all the values of a column at once. This eliminates the primary bottleneck which row-wise serialization, and significantly improves SparkR’s UDF performance. Also, the benefit from the vectorization is more drastic for larger datasets.

It looks like they get some pretty serious gains from this change.

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Subsetting Matrices In R

Published 2018-08-20 by Kevin Feasel

Dave Mason continues his look at matrices in R:

We can extract an entire row from a matrix. To do this, specify the desired row only within the square brackets [ ]. The placeholder where you would otherwise specify the column is left empty.
> #Points scored by Kendrick Perkins.
> points_scored_by_quarter[1,]
1st 2nd 3rd 4th 2 2 6 0
> points_scored_by_quarter["Perkins",]
1st 2nd 3rd 4th 2 2 6 0 
Conversely, we can extract a column from a matrix. Specify the column within the square brackets [ ]and omit the row. The result is a vector, thus the pivot effect–the row names are displayed in the output (not the column name).

Dave points out that working with matrices is basically an extension of working with vectors.

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Microsoft R Open 3.5.1

Published 2018-08-16 by Kevin Feasel

David Smith announces Microsoft R Open 3.5.1:

Microsoft R Open 3.5.1 has been released, combining the latest R language engine with multi-processor performance and tools for managing R packages reproducibly. You can download Microsoft R Open 3.5.1 for Windows, Mac and Linux from MRAN now. Microsoft R Open is 100% compatible with all R scripts and packages, and works with all your favorite R interfaces and development environments.
This update brings a number of minor fixes to the R language engine from the R core team. It also makes available a host of new R packages contributed by the community, including packages for downloading financial data, connecting with analytics systems, applying machine learning algorithms and statistical models, and many more. New R packages are released every day, and you can access packages released after the 1 August 2018 CRAN snapshot used by MRO 3.5.1 using the checkpoint package.

Read on for more and check out the updates.

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Performing Linear Regression With Power BI

Published 2018-08-16 by Kevin Feasel

Jason Cantrell shows how to create a simple linear regression in Power BI:

Linear Regression is a very useful statistical tool that helps us understand the relationship between variables and the effects they have on each other. It can be used across many industries in a variety of ways – from spurring value to gaining customer insight – to benefit business.
The Simple Linear Regression model allows us to summarize and examine relationships between two variables. It uses a single independent variable and a single dependent variable and finds a linear function that predicts the dependent variable values as a function of the independent variables.

If you want real linear regression, drop in an R or Python script.

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Principal Component Analysis With Faces

Published 2018-08-14 by Kevin Feasel

Mic at The Beginner Programmer shows us how to creepy PCA diagrams with human faces:

PCA looks for a new the reference system to describe your data. This new reference system is designed in such a way to maximize the variance of the data across the new axis. The first principal component accounts for as much variance as possible, as does the second and so on. PCA transforms a set of (tipically) correlated variables into a set of uncorrelated variables called principal components. By design, each principal component will account for as much variance as possible. The hope is that a fewer number of PCs can be used to summarise the whole dataset. Note that PCs are a linear combination of the original data.
The procedure simply boils down to the following steps

Scale (normalize) the data (not necessary but suggested especially when variables are not homogeneous).
Calculate the covariance matrix of the data.
Calculate eigenvectors (also, perhaps confusingly, called “loadings”) and eigenvalues of the covariance matrix.
Choose only the first N biggest eigenvalues according to one of the many criteria available in the literature.
Project your data in the new frame of reference by multipliying your data matrix by a matrix whose columns are the N eigenvectors associated with the N biggest eigenvalues.
Use the projected data (very confusingly called “scores”) as your new variables for further analysis.

I like the explanations provided, and the data set is definitely something I’m not used to seeing with PCA. H/T R-bloggers

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