Posted on Categories Opinion, StatisticsTags ,

Some Notes on GNU Licenses in R Packages

I was recently asked if Win-Vector LLC would move the R wrapr package from a GPL-3 license to an LGPL license. In the end I decided to move wrapr distribution to a “GPL-2 | GPL-3” license. This means the package is now available under both GPL-2 and GPL-3 licensing, allowing the user to pick which of these two licenses they wish to accept the software under. I decided to stick to “GPL-*” style licensing as I endorse the values underlying these licenses, and my (not-legal advice, I am not a lawyer!) opinion this is the licensing pattern closest to the license R itself is distributed under (and hence the closest to the values of the core R community).

Please read on for some background issues I found (not-legal advice, I am not a lawyer!)

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Posted on Categories OpinionTags , , 4 Comments on A Comment on Data Science Integrated Development Environments

A Comment on Data Science Integrated Development Environments

A point that differs from our experience struck us in the recent note regarding doing data science in Python:

A development environment [for Python] specifically tailored to the data science sector on the level of RStudio, for example, does not (yet) exist.

“What’s the Best Statistical Software? A Comparison of R, Python, SAS, SPSS and STATA” Amit Ghosh

Actually, Python has a large number of very capable integrated development environments, some of which are specifically tailored for data science. Please read on for a small list of tools, and my recommendations for a specific data science in Python toolchain.

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Posted on Categories Opinion, Practical Data Science, Pragmatic Data Science, Pragmatic Machine LearningTags , ,

A Kind Note That We Really Appreciate

The following really made my day.

I tell every data scientist I know about vtreat and urge them to read the paper.
Jason Wolosonovich

Jason, thanks for your support and thank you so much for taking the time to say this (and for your permission to quote you on this).

For those interested the R version of vtreat can be found here, the paper can be found here, and the in-development Python/Pandas version of vtreat can be found (with examples) here.

Chapter of 8 Zumel, Mount, Practical Data Science with R, 2nd Edition, Manning 2019 has a more operational discussion of vtreat (which itself uses concepts developed in chapter 4).

Posted on Categories Administrativia, Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, ProgrammingTags , , ,

Big News: Porting vtreat to Python

We at Win-Vector LLC have some big news.

We are finally porting a streamlined version of our R vtreat variable preparation package to Python.

vtreat is a great system for preparing messy data for supervised machine learning.

The new implementation is based on Pandas, and we are experimenting with pushing the sklearn.pipeline.Pipeline APIs to their limit. In particular we have found the .fit_transform() pattern is a great way to express building up a cross-frame to avoid nested model bias (in this case .fit_transform() != .fit().transform()). There is a bit of difference in how object oriented APIs compose versus how functional APIs compose. We are making an effort to research how to make this an advantage, and not a liability.

The new repository is here. And we have a non-trivial worked classification example. Next up is multinomial classification. After that a few validation suites to prove the two vtreat systems work similarly. And then we have some exciting new capabilities.

The first application is going to be a shortening and streamlining of our current 4 day data science in Python course (while allowing more concrete examples!).

This also means data scientists who use both R and Python will have a few more tools that present similarly in each language.

Posted on Categories data science, Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, Statistics, TutorialsTags , , ,

An Ad-hoc Method for Calibrating Uncalibrated Models

In the previous article in this series, we showed that common ensemble models like random forest and gradient boosting are uncalibrated: they are not guaranteed to estimate aggregates or rollups of the data in an unbiased way. However, they can be preferable to calibrated models such as linear or generalized linear regression, when they make more accurate predictions on individuals. In this article, we’ll demonstrate one ad-hoc method for calibrating an uncalibrated model with respect to specific grouping variables. This "polishing step" potentially returns a model that estimates certain rollups in an unbiased way, while retaining good performance on individual predictions.

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Posted on Categories data science, Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, Statistics, TutorialsTags , , , , 1 Comment on Some Details on Running xgboost

Some Details on Running xgboost

While reading Dr. Nina Zumel’s excellent note on bias in common ensemble methods, I ran the examples to see the effects she described (and I think it is very important that she is establishing the issue, prior to discussing mitigation).

In doing that I ran into one more avoidable but strange issue in using xgboost: when run for a small number of rounds it at first appears that xgboost doesn’t get the unconditional average or grand average right (let alone the conditional averages Nina was working with)!

Let’s take a look at that by running a trivial example in R.

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Posted on Categories Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, Statistics, TutorialsTags , , , , , 2 Comments on Common Ensemble Models can be Biased

Common Ensemble Models can be Biased

In our previous article , we showed that generalized linear models are unbiased, or calibrated: they preserve the conditional expectations and rollups of the training data. A calibrated model is important in many applications, particularly when financial data is involved.

However, when making predictions on individuals, a biased model may be preferable; biased models may be more accurate, or make predictions with lower relative error than an unbiased model. For example, tree-based ensemble models tend to be highly accurate, and are often the modeling approach of choice for many machine learning applications. In this note, we will show that tree-based models are biased, or uncalibrated. This means they may not always represent the best bias/variance trade-off.

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Posted on Categories Expository Writing, Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, Statistics, TutorialsTags , , , ,

Link Functions versus Data Transforms

In the linear regression section of our book Practical Data Science in R, we use the example of predicting income from a number of demographic variables (age, sex, education and employment type). In the text, we choose to regress against log10(income) rather than directly against income.

One obvious reason for not regressing directly against income is that (in our example) income is restricted to be non-negative, a restraint that linear regression can’t enforce. Other reasons include the wide distribution of values and the relative or multiplicative structure of errors on outcomes. A common practice in this situation is to use Poisson regression, or generalized linear regression with a log-link function. Like all generalized linear regressions, Poisson regression is unbiased and calibrated: it preserves the conditional expectations and rollups of the training data. A calibrated model is important in many applications, particularly when financial data is involved.

Regressing against the log of the outcome will not be calibrated; however it has the advantage that the resulting model will have lower relative error than a Poisson regression against income. Minimizing relative error is appropriate in situations when differences are naturally expressed in percentages rather than in absolute amounts. Again, this is common when financial data is involved: raises in salary tend to be in terms of percentage of income, not in absolute dollar increments.

Unfortunately, a full discussion of the differences between Poisson regression and regressing against log amounts was outside of the scope of our book, so we will discuss it in this note.

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Posted on Categories Opinion, Programming, TutorialsTags , 11 Comments on Programming Over lm() in R

Programming Over lm() in R

Here is simple modeling problem in R.

We want to fit a linear model where the names of the data columns carrying the outcome to predict (y), the explanatory variables (x1, x2), and per-example row weights (wt) are given to us as string values in variables.

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