Tag Archives: R software

Recommended: Textbook Examples Applied Survival Analysis

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I’m teaching an online workshop for The Analysis Factor on survival analysis. It’s not announced yet, and I have a LOT of work to do before it is ready. One thing that will save me time is that I am taking many of my examples from the excellent textbook, Applied Survival Analysis Second Edition. One nice perk of this book is that the helpful folks at UCLA have taken every textbook example, and written up code (with comments!) to reproduce the book’s results. With the exception of a few advanced methods in later chapters, where only one or two software packages have the right capability, the code is written in parallel in R, SAS, SPSS, and Stata. They also have links to the raw data at the publishers website, and datasets stored in SAS format and SPSS format. How nice! Browse around and you’ll find software code for all the examples in other popular statistics textbooks as well.

Warning! The R examples look like they are from the first edition, not the second edition. A small nitpick for an otherwise very nice resource. Continue reading →

PMean: Peer grading in Introduction to R, SPSS, SAS

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I’ve gotten some helpful feedback that I need to encourage more interactions among students in the on-line classes, Introduction to R, Introduction to SPSS, and Introduction to SAS. No just interactions of the students with the teacher, but interactions between the students.

In many online classes this is done by encouraging online discussion of the material in the class. This is not so easy, however, for these three classes. I can just imagine myself posting the following on Blackboard. “Tell me what you think about the read.csv function in R.”

There are a couple of ways, however, that make sense for technical classes like these. Continue reading →

PMean: Changes to the Introduction to R, SAS, and SPSS classes

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I have helped develop and have taught (along with other faculty in our department) three one credit hour pass/fail classes: Introduction to R, Introduction to SPSS, and Introduction to SAS. These classes were developed back in 2014-2015 and they are in need of some serious updates. I will try to outline some of the updates that I think these classes need in this blog post. Continue reading →

Recommended: Cleaning Words with R: Stemming, Lemmatization & Replacing with More Common Synonym

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In many text mining or natural language processing applications, you will have problems with words that are very similar, but which are counted separately. An example might be the words win, winner, and winning. You can combine these words into a single category using stemming. This blog post gives a nice overview of stemming. Continue reading →

PMean: Do you need to name your function arguments in R?

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If you program anything in R, you’ll end up calling a lot of functions. You pass your data or your constants to these functions, and you can do it in one of two ways. You can either pass the data/constants in the order in which the function expects the arguments or you can match each data/constant value with a particular argument name. This came up in the context of a question: do I need to save everything using

save.image(file=”foo.RData”)

or can I save it with

save.image(“foo.RData”)? Continue reading →

PMean: My work on a CTSA grant

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I’m on a Clincal and Translational Science Award (CTSA) research grant (5UL1TR000001-05, formerly 1U54RR031295-01A1), which is pretty cool. My name is even mentioned a few times in the grant. I thought that as I plan what I would do for this grant, I would see what the grant promised and write down what, exactly, that those promises mean. As I talk with various people (especially Russ Waitman, who is supervising my work on this grant), I will revise and update my plans. Still, I thought it would be valuable to put some thoughts down now, both to help me focus on what I should be doing and to offer an early draft of those ideas to the various people that I will end up interacting with. Continue reading →

PMean: Losing track of your transformed variables in R

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I got an interesting question from one of my students, and it illustrates a subtle issue that may confuse beginning R programmers. The student was trying to compute a ratio of brain weight to body weight in a small data set, but then was unable to calculate any summary statistics on that ratio. Here’s what caused the problem. Continue reading →