Articles by Radford Neal

Critique of “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period” — Part 3: Estimating reproduction numbers

June 24, 2020 | 0 Comments

This is the third in a series of posts (previous posts: Part 1, Part 2) in which I look at the following paper: Kissler, Tedijanto, Goldstein, Grad, and Lipsitch, Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period, Science, vol. 368, pp. 860-868, 22 May 2020 (released online 14 April 2020).  The paper is also available […]
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Critique of “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period” — Part 2: Proxies for incidence of coronaviruses

June 17, 2020 | 0 Comments

This is the second in a series of posts (previous post: Part 1) in which I look at the following paper: Kissler, Tedijanto, Goldstein, Grad, and Lipsitch, Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period, Science, vol. 368, pp. 860-868, 22 May 2020 (released online 14 April 2020).  The paper is also available here, ...
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Critique of “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period” — Part 1: Reproducing the results

May 27, 2020 | 0 Comments

I’ve been looking at the following paper, by researchers at Harvard’s school of public health, which was recently published in Science: Kissler, Tedijanto, Goldstein, Grad, and Lipsitch (2020) Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period (also available here, with supplemental materials here). This is one of ...
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Automatic differentiation in pqR

July 6, 2019 | 0 Comments

I’ve released a version of my pqR implementation of R that has extensions for automatic differentiation. This is not a stable release, but it can be downloaded from pqR-project.org — look for the test version at the bottom — and installed the same as other pqR versions (from source, so ...
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Faster garbage collection in pqR

November 29, 2018 | 0 Comments

The latest version of pqR and the version before as well use a new garbage collector, and new memory layouts for R objects, which both reduce memory usage and considerably speed up garbage collection. Here, I’ll give an overview of how the new scheme works, and present some performance ...
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The new pqR parser, and R’s “else” problem

November 27, 2018 | 0 Comments

The latest version of pqR (mostly) solves R’s “else” problem, by modifying the new parser previously introduced in pqR.  I’ll explain the “else” problem and solution here, and also present other advantages of pqR’s parser over the R Core parser, including a big speed advantage in one ...
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New version of pqR, with major speed improvements

November 25, 2018 | 0 Comments

I’ve released pqR-2018-11-18, a new version of my variant implementation of R.  You can install it on Linux, Windows, or Mac as described at pqR-project.org. Installation must currently be from source, similarly to source installs of R Core versions of R. This version has some major ...
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New release of pqR — faster, and now compatible with R-2.15.1

October 8, 2016 | 0 Comments

I have released a new version of my “pretty quick” R interpreter, pqR-2016-10-05. One major change with this version is that pqR, which was based on R-2.15.0, is now compatible with R-2.15.1.  This allows for an increased number of packages in the pqR repository. This release also has ...
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Fixing R’s design flaws in a new version of pqR

June 25, 2016 | 0 Comments

I’ve released a new version of my pqR implementation of R. This version introduces extensions to the R language that fix some long-standing design flaws that were inherited from S. These language extensions make it easier to write reliable programs, that work even in edge cases, such as data ...
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Has there been a ‘pause’ in global warming?

December 19, 2015 | 0 Comments

As I discussed in my previous post, records of global temperatures over the last few decades figure prominently in the debate over the climate effects of CO2 emitted by burning fossil fuels. I am interested in what this data says about which of the reasonable positions in this debate is ...
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What can global temperature data tell us?

December 3, 2015 | 0 Comments

Debates about anthropogenic climate change often centre around data on changes in global temperatures over the last few decades. There are good scientific reasons to look at this data, but it also plays a prominent role in political advocacy, sometimes fairly, sometimes not so fairly. This is the first in ...
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Exact computation of sums and means

May 21, 2015 | 0 Comments

A while ago, I came across a mention of the Python math.fsum function, which sums a set of floating-point values exactly, then rounds to the closest floating point value. This seemed useful. In particular, I thought that if it’s fast enough it could be used instead of R’...
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How large vectors in R might be stored compactly

April 30, 2015 | 0 Comments

Vectors in R can currently have elements of two sizes — 8-byte double-precision floating-point elements for `numeric’ vectors, or 4-byte elements for `integer’ or `logical’ vectors.  You can also have vectors whose elements are 1-byte `raw’ values, but these raw vectors don’t support negative numbers, or NA values, so they ...
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New release of pqR, with a curated repository

June 21, 2014 | 0 Comments

I have released a new version, pqR-2014-06-19, of my speedier, “pretty quick”, implementation of R.  This and the previous release (pqR-2014-02-23) are maintenance releases, with bug fixes, improved documentation, and better test procedures. The result is that pqR now works with a large collection of 3438 packages. ... [Read more...]

Inaccurate results from microbenchmark

February 2, 2014 | 0 Comments

The microbenchmark package is a popular way of comparing the time it takes to evaluate different R expressions — perhaps more popular than the alternative of just using system.time to see how long it takes to execute a loop that evaluates an expression many times. Unfortunately, when used in the ... [Read more...]

New version of pqR, now with task merging

January 1, 2014 | 0 Comments

 I’ve now released pqR-2013-12-29, a new version of my speedier implementation of R.  There’s a new website, pqR-project.org, as well, and a new logo, seen here. The big improvement in this version is that vector operations are sped up using task merging. With task merging, ... [Read more...]

Deferred evaluation in Renjin, Riposte, and pqR

July 24, 2013 | 0 Comments

The previously sleepy world of R implementation is waking up.  Shortly after I announced pqR, my “pretty quick” implementation of R, the Renjin implementation was announced at UserR! 2013.  Work also proceeds on Riposte, with release planned for a year from now. These three implementations differ greatly in some respects, but ... [Read more...]
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