Posted on Categories Programming, Statistics, Tutorials, UncategorizedTags , 4 Comments on What does it mean to write “vectorized” code in R?

What does it mean to write “vectorized” code in R?

One often hears that R can not be fast (false), or more correctly that for fast code in R you may have to consider “vectorizing.”

A lot of knowledgable R users are not comfortable with the term “vectorize”, and not really familiar with the method.

“Vectorize” is just a slightly high-handed way of saying:

R naturally stores data in columns (or in column major order), so if you are not coding to that pattern you are fighting the language.

In this article we will make the above clear by working through a non-trivial example of writing vectorized code.

Continue reading What does it mean to write “vectorized” code in R?

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We try to keep this blog mostly technical and business (as we assume that is what our readers are here for).

However, this post is going to be an exception.

I’ve just got back from photographing the Rotary Club of San Francisco‘s 2018 Holiday Party. We had a special guest SF Mayor London Breed (shown here with Rotary Club of San Francisco President Rhonda Poppen).

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I am proud to say I have been a member of this organization for over 10 years. It is where I do my volunteer work both in San Francisco and internationally.

In particular I am thrilled to be supporting the efforts of a number of Rotarians and Roots of Peace in their latest effort to remediate farmland in Vietnam (with the help and permission of the Vietnamese government). These people are working hard to undo some of the pain and misery of unexploded ordinance (UXO). I’ll be helping with some administrative tasks and these people will be training hundreds of farmers to move into profitable world market crops.

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Pictured above Heidi Kuhn and Christian Kuhn of Roots of Peace.

Posted on Categories Statistics, Tutorials, UncategorizedTags , , ,

R tip: Make Your Results Clear with sigr

R is designed to make working with statistical models fast, succinct, and reliable.

For instance building a model is a one-liner:

model <- lm(Petal.Length ~ Sepal.Length, data = iris)

And producing a detailed diagnostic summary of the model is also a one-liner:


# Call:
# lm(formula = Petal.Length ~ Sepal.Length, data = iris)
# Residuals:
#      Min       1Q   Median       3Q      Max 
# -2.47747 -0.59072 -0.00668  0.60484  2.49512 
# Coefficients:
#              Estimate Std. Error t value Pr(>|t|)    
# (Intercept)  -7.10144    0.50666  -14.02   <2e-16 ***
# Sepal.Length  1.85843    0.08586   21.65   <2e-16 ***
# ---
# Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# Residual standard error: 0.8678 on 148 degrees of freedom
# Multiple R-squared:   0.76,   Adjusted R-squared:  0.7583 
# F-statistic: 468.6 on 1 and 148 DF,  p-value: < 2.2e-16

However, useful as the above is: it isn’t exactly presentation ready. To formally report the R-squared of our model we would have to cut and paste this information from the summary. That is a needlessly laborious and possibly error-prone step.

With the sigr package this can be made much easier:

Rsquared <- wrapFTest(model)

# [1] "F Test summary: (R2=0.76, F(1,148)=468.6, p<1e-05)."

And this formal summary can be directly rendered into many formats (Latex, html, markdown, and ascii).

render(Rsquared, format="html")

F Test summary: (R2=0.76, F(1,148)=468.6, p<1e-05).

sigr can help make your publication workflow much easier and more repeatable/reliable.

Posted on Categories UncategorizedTags , , 9 Comments on For loops in R can lose class information

For loops in R can lose class information

Did you know R‘s for() loop control structure drops class annotations from vectors? Continue reading For loops in R can lose class information

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Our Differential Privacy Mini-series

We’ve just finished off a series of articles on some recent research results applying differential privacy to improve machine learning. Some of these results are pretty technical, so we thought it was worth working through concrete examples. And some of the original results are locked behind academic journal paywalls, so we’ve tried to touch on the highlights of the papers, and to play around with variations of our own.

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  • A Simpler Explanation of Differential Privacy: Quick explanation of epsilon-differential privacy, and an introduction to an algorithm for safely reusing holdout data, recently published in Science (Cynthia Dwork, Vitaly Feldman, Moritz Hardt, Toniann Pitassi, Omer Reingold, Aaron Roth, “The reusable holdout: Preserving validity in adaptive data analysis”, Science, vol 349, no. 6248, pp. 636-638, August 2015).

    Note that Cynthia Dwork is one of the inventors of differential privacy, originally used in the analysis of sensitive information.

  • Using differential privacy to reuse training data: Specifically, how differential privacy helps you build efficient encodings of categorical variables with many levels from your training data without introducing undue bias into downstream modeling.
  • A simple differentially private-ish procedure: The bootstrap as an alternative to Laplace noise to introduce privacy.

Our R code and experiments are available on Github here, so you can try some experiments and variations yourself.

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