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How To Set Up Continuous Integration to Make Your Code More Robust, More Maintainable, and Easier to Publish

Series
Department of Statistics
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Dr Fergus Cooper, Research Software Engineer, Oxford RSE Group, gives a talk for the department of Statistics on 5th June 2020.
Following on from Graham Lee's talk on automated testing, we will use GitHub actions to automate the testing of a small Python project. We will: recap why this might be a good idea; walk through setting up a workflow on GitHub; test our code against multiple Python versions on multiple operating systems; and integrate other services such as code coverage and automated documentation generation.

Dr Fergus Cooper is a member of the Oxford Research Software Engineering group, which he co-founded in 2018 after finishing a DPhil in the Mathematical Institute. His research background is computational biology where he developed agent-based models of the developing tooth placode. He is now a passionate advocate for software best practices in academia, and will talk to anyone about modern C++."

Episode Information

Series
Department of Statistics
People
Fergus Cooper
Keywords
statistics
coding
continuous integration
GitHub
Python
Department: Department of Statistics
Date Added: 10/06/2020
Duration: 00:44:46

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Developing better code with automated testing

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Department of Statistics
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Graham Lee, Research Software Engineer, Oxford RSE Group, gives talk for the department of Statistics on 22nd May 2020.
Abstract: If we want reliable, reproducible simulations and data analysis software, we need to know that we have implemented our code correctly. Further, we need to be confident that changes we make to the code do not introduce unintended flaws. Automated testing is a technique widely used in industry to capture information about the expected behaviour of software and ensure that the system retains that behaviour through its evolution. In this talk, Graham explores the application of the technique to scientific software.

Episode Information

Series
Department of Statistics
People
Graham Lee
Keywords
statistics
software engineering
coding
Department: Department of Statistics
Date Added: 10/06/2020
Duration: 00:45:23

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Cluster-Randomised Test Negative Designs: Inference and Application to Vector Trials to Eliminate Dengue

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Department of Statistics
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Nick Jewell, University of California, Berkeley School of Public Health, gives a talk for the departmental of Statistics on 28th May 2020.
Abstract: The successful introduction of the intracellular bacterium Wolbachia into Aedes aegypti mosquitoes enables a practical approach for dengue prevention through release of Wolbachia-infected mosquitoes. Wolbachia reduces dengue virus replication in the mosquito and, once established in the mosquito population, it is possible that this will provide a long-term and sustainable approach to reducing or eliminating dengue transmission. A critical next step is to assess the efficacy of Wolbachia deployments in reducing dengue virus transmission in the field. I will describe and discuss the statistical design of a large-scale cluster randomised test-negative parallel arm study to measure the efficacy of such interventions. Comparison of permutation inferential approaches to model based methods will be described. Extensions to allow for individual covariates, and alternate designs such as the stepped wedge approach, will also be briefly introduced. There are also interesting questions regarding interrupted time-series methods associated with analysing pilot site data.

Episode Information

Series
Department of Statistics
People
Nick Jewell
Keywords
statistics
dengue fever
Medicine
tropical diseases
mosquitoes
Department: Department of Statistics
Date Added: 10/06/2020
Duration: 01:02:53

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MCMC for Hierachical Bayesian Models Using Non-reversible Langevin Methods

Series
Department of Statistics
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Radford M. Neal (University of Toronto), gives a talk for the department of Statistics.
Hamiltonian Monte Carlo (HMC) is an attractive MCMC method for continuous distributions because it makes use of the gradient of the log probability density to propose points far from the current point, avoiding slow exploration by a random walk (RW). The Langevin method - equivalent to HMC with one leapfrog step - also uses gradient information, but is slow due to RW behaviour. In this talk, I discuss how the Langevin method can be made competitive with HMC using two modifications that suppress RW behaviour by making the Markov chain no longer be time-reversible. This modified Langevin method can be better than HMC when it is necessary to combine gradient-based updates with other updates. One use is when other updates are required for discrete variables. Another application is learning of hierarchical Bayesian neural networks models, for which hyperparameters controlling the properties of the function learned are difficult to update using HMC. If they are instead updated by, for example, Gibbs sampling, these updates can be done more often, improving sampling efficiency, when a non-reversible Langevin method is used rather than HMC with long trajectories.

Episode Information

Series
Department of Statistics
People
Radford M Neal
Keywords
statistics
Bayesian
MCMC
Langevin methods
hierarchical Bayesian
Department: Department of Statistics
Date Added: 10/06/2020
Duration: 01:04:36

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The role of the Today programme in a national crisis

Series
Reuters Institute for the Study of Journalism
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Sarah Sands, editor of the Today programme, on the role of the BBC flagship radio news show

Episode Information

Series
Reuters Institute for the Study of Journalism
People
Sarah Sands
Keywords
reuters institute
journalism
bbc
news
Department: Department of Politics and International Relations (DPIR)
Date Added: 09/06/2020
Duration: 00:57:08

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Fact checking a global story

Series
Reuters Institute for the Study of Journalism
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Clara Jiménez Cruz is co-founder and head of Maldita.es, a Spanish non-profit news organisation focused on stopping disinformation through fact-checking and data journalism

Episode Information

Series
Reuters Institute for the Study of Journalism
People
Clara Jiménez Cruz
Keywords
reuters institute
journalism
fact checking
Department: Department of Politics and International Relations (DPIR)
Date Added: 09/06/2020
Duration: 00:59:26

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What I learned by watching the American press try to cover Donald Trump

Series
Reuters Institute for the Study of Journalism
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Journalism lecturer and prominent media critic Jay Rosen outlines his thoughts on the US press's coverage of President Trump

Episode Information

Series
Reuters Institute for the Study of Journalism
People
Jay Rosen
Keywords
reuters institute
trump
journalism
Department: Department of Politics and International Relations (DPIR)
Date Added: 09/06/2020
Duration: 00:58:33

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Reporting pandemics: Measles and Coronavirus in the Pacific Islands

Series
Reuters Institute for the Study of Journalism
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Lagipoiva Cherelle Jackson, investigative reporter from Samoa speaks about reporting on the twin pandemics in the Pacific Islands

Episode Information

Series
Reuters Institute for the Study of Journalism
People
Lagipoiva Cherelle Jackson
Keywords
reuters institute
journalism
coronavirus
Department: Department of Politics and International Relations (DPIR)
Date Added: 09/06/2020
Duration: 00:55:32

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Buliding a global media brand

Series
Reuters Institute for the Study of Journalism
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Senior Editor at the Atlantic Prashant Rao discusses broadening the reach of the publication beyond the US

Episode Information

Series
Reuters Institute for the Study of Journalism
People
Prashant Rao
Keywords
reuters institute
journalism
Department: Department of Politics and International Relations (DPIR)
Date Added: 09/06/2020
Duration: 00:58:44

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Brexit in a time of crisis

Series
Reuters Institute for the Study of Journalism
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Anand Menon discusses whether the coronavirus pandemic has distracted attention from the Brexit negotiations

Episode Information

Series
Reuters Institute for the Study of Journalism
People
Anand Menon
Keywords
reuters institute
journalism
Brexit
Department: Department of Politics and International Relations (DPIR)
Date Added: 09/06/2020
Duration: 00:54:20

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