Category: R

Sahir Bhatnagar uses heatmaply to generate heatmaps:

In every statistical analysis, the first thing one should do is try and visualise the data before any modeling. In microarray studies, a common visualisation is a heatmap of gene expression data.

In this post I simulate some gene expression data and visualise it using theheatmaply package in R by Tal Galili. This package extends the plotly engine to heatmaps, allowing you to inspect certain values of the data matrix by hovering the mouse over a cell. You can also zoom into a region of the heatmap by drawing a rectangle over an area of your choice

This went way past my rudimentary heatmap skills, so it’s nice to see what an advanced user can do.

Saravanan Subramanian has an introduction to data frames in R:

The R data frame is a high level data structure which is equivalent to a table in database systems.  It is highly useful to work with machine learning algorithms, and it’s very flexible and easy to use.

The standard definition of data frames are a “tightly coupled collections of variables which share many of the properties of matrices and of lists, used as the fundamental data structure by most of R‘s modeling software.”

Data frames are a powerful abstraction and make R a lot easier for database professionals than application developers who are used to thinking iteratively and with one object at a time.

Julie Koesmarno shows how to install an R package on a SQL Server 2016 instance which has SQL Server R Services installed:

When you start playing with R in SQL Server, sooner or later you would need to install some packages, for example ggplot2. You may run into a problem that sounds like this “Error in library(“ggplot2”) : there is no package called ‘ggplot2’“.

The following script is used in the iris_demo.sql (SQLServer2016CTP3Samples\Advanced Analytics\iris_demo.sql), and would cause a missing library error if you don’t have the packages installed on SQL Server R Services yet.

Julie shows two methods, one a Good Idea and the other a Bad(?) Idea.

Achim Rumberger shows how to map German postal codes using R:

Just at this time Ari published his webinar about getting shape files into R. Which also includes a introduction to shape files to get you going, if you are new to it, as I am. I remembered Ari from his mail course introducing his great R-package (choroplethr). By the way this is a terrible name, being a biologist by heart, I always type “chloroplethr”, as in “chlorophyll”, and this is not found by the R package manager. [Editor’s note: I agree!]

Next question, where do I get the shapefiles, describing Germany? A major search engine was of great help here. http://www.suche-postleitzahl.org/downloads?download=zuordnung_plz_ort.csv . Germany has some 8700 zip code areas, so expect some time for rendering the file, if you do on your computer. Right on this side one can also find a dataset which might act as a useful warm up practice to display statistical data in a geographical context. Other sources are https://datahub.io/de/dataset/postal-codes-de

This is really cool.

Nina Zumel delves into principal component regression using R (via R Bloggers):

Data tends to come from databases that must support many different tasks, so it is exactly the case that there may be columns or variables that are correlated to unknown and unwanted additional processes. The reason PCA can’t filter out these noise variables is that without use of y, standard PCA has no way of knowing what portion of the variation in each variable is important to the problem at hand and should be preserved. This can be fixed through domain knowledge (knowing which variables to use), variable pruning and y-aware scaling. Our next article will discuss these procedures; in this article we will orient ourselves with a demonstration of both what a good analysis and what a bad analysis looks like.

All the variables are also deliberately mis-scaled to model some of the difficulties of working with under-curated real world data.

This does read like an academic paper, so it’s pretty heavy reading.  It’s also very good reading from a great writer, so take some time and give it a read if you do data analysis.

The Revolution Analytics blog has a Microsoft-driven article on estimating bike rental demand with Microsoft R Server:

In addition to the original features in the raw data, we add number of bikes rented in each of the previous 12 hours as features to provide better predictive power. We create acomputeLagFeatures() helper function to compute the 12 lag features and use it as the transformation function in rxDataStep().

Note that rxDataStep() processes data chunk by chunk and lag feature computation requires data from previous rows. In computLagFeatures(), we use the internal function .rxSet() to save the last n rows of a chunk to a variable lagData. When processing the next chunk, we use another internal function .rxGet() to retrieve the values stored in lagData and compute the lag features.

This is a great article for anybody wanting to dig into analytics, because they show their work.

R 3.3.0 is now available:

As this is a major release, you’ll need to re-install any packages you were using (and perhaps wait a little while until package authors make any compatibility fixes needed for version 3.3.0). If you’re on the Windows platform, Tal Galili’s installr package automates the process for you. If you are using the checkpoint package (on any platform) you can simply increment the checkpoint date to anytime after May 2, 2016.

(For Microsoft R Open users, the next version to be released will be MRO 3.2.5, and MRO 3.3.0 will follow soon thereafter.)

For more information about R 3.3.0, including the detailed list of changes and bug fixes, follow the link to the announcement from the R Core Group below.

David Smith also notes that R Tools for Visual Studio 0.3 has been released:

R Tools for Visual Studio, the open-source extenstion to Visual Studio that provides an IDE for the R language, has been upgraded to include several new features.

The latest update, RTVS 0.3, now includes:

• An R package manager, allowing you to review, install, and uninstall packages using a convenient user interface.

• The Variable Explorer now allows you to open data-frames for viewing in an Excel workbook.

• New toolbar buttons to run selected code, source the current script, import data from a URL or file, and start/stop a Shiny app.

This is a great time to get interested in R.  If you’re familiar with Visual Studio, Microsoft is making great strides toward integrating things nicely.