Publications by Radford Neal
New version of pqR, with major speed improvements
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 speed improvements, as well as some new features. I’ll de...
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The new pqR parser, and R’s “else” problem
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 context. The “else” problem in R Probably m...
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Faster garbage collection in pqR
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 comparisons with R-3.5.1. Some more details are presen...
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Automatic differentiation in pqR
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 you’ll need C and Fortran compilers). Note that thi...
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Critique of “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period” — Part 1: Reproducing the results
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...
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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
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 ...
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Critique of “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period” — Part 3: Estimating reproduction numbers
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 av...
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Critique of “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period” — Part 4: Modelling R, seasonality, immunity
In this post, fourth in a series (previous posts: Part 1, Part 2, Part 3), I’ll finally talk about some substantive conclusions of 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 onli...
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New version of pqR, with automatic differentiation and arithmetic on lists
I’ve released pqR-2020-07-23, 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 preliminary implementations of automatic differentiation and of arithme...
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