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Posts by Matt Parkes

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Two main frameworks that shape research assessment in the NLs are moving to open research information in line with the #BarcelonaDeclaration: the new SEP protocol and NWO's evidence based CV.

A blog (w/ @ludowaltman.bsky.social) about context and importance:

upstream.force11.org/research-eva...

3 hours ago 1 2 0 0
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Sage Journals: Discover world-class research Subscription and open access journals from Sage, the world's leading independent academic publisher.

🆕 New publication!

Our researchers explored how #Bayesian methods are used in confirmatory #ClinicalTrials.
The most common reasons for choosing Bayesian methods were making probability statements about the interventions or the flexibility to adapt the trial design.

🔗 Read more: buff.ly/wHnFcuC

1 day ago 2 1 0 0
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Branded Figures and Tables in R and Python with Quarto – Mickaël CANOUIL Style ggplot2, plotnine, gt, and great_tables outputs using Quarto’s brand feature by reading brand configuration from the QUARTO_EXECUTE_INFO environment variable at render time.

New blog post: Branded Figures and Tables in R and Python with Quarto.

Style your figures and tables to match your brand automatically at render time, with light/dark mode support.

mickael.canouil.fr/posts/2026-0...

#Quarto #Python #RStats #Brand

6 days ago 36 13 2 2

Many folk are surprised to discover thay Risk of Bias assessment tools tend not to interrogate the question “Did this study actually happen? And are its results trustworthy enough to believe?”

Jack’s Cochrane endorsed INSPECT-SR checks have done a lot to mainstream such Trustworthiness Assessment.

1 week ago 30 10 3 0
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A passenger flight from Costa Rica to Atlanta got the chance to witness Artemis launch.

I imagine how painful it was to be sitting on the wrong side of that plane!

2 weeks ago 638 141 14 8
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*Sharing code for research publications*
Here's the process that I've ended up with, through various collaborators like Robert Forkel, @simongreenhill.bsky.social , Stephen Francis Mann and others.
Not perfect perhaps, but works pretty ok.
A student asked, so I made this illustration.

3 weeks ago 48 12 0 0
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EMA consults on virtual control groups to help reduce animal use in medicines development | European Medicines Agency (EMA) A draft qualification opinion for the new testing method is open for consultation

We have just launched an open consultation on virtual animal control groups to help reduce animal use in medicines development.

Check it out now! 👇
❗Consultation open until 12 May 2026.

3 weeks ago 19 9 0 0
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Wealth, shown to scale Wealth inequality in the United States is out of control. Here we visualize the issue in a unique way.

Wealth, shown to scale eattherichtextformat.github.io/1-pixel-weal...

3 weeks ago 1 1 0 0
CERN to host Europe’s flagship open access publishing platform In an important step for open science, CERN has been selected to host a new phase of Open Research Europe (ORE), an initiative supported by the European Commission and a new funding consortium of Euro...

Open Research Europe is re-launching with a new platform, and broader set of supporters, this fall. It uses the publish-review-curate model. "Publishing will remain completely free for both European Commission-funded researchers and authors from participating countries." home.cern/news/news/ce...

3 weeks ago 7 11 1 1
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From Protocol to Analysis Plan: Development and Validation of a Large Language Model Pipeline for Statistical Analysis Plan Generation using Artificial Intelligence (SAPAI) | Petrina C. Are you a trial statistician who’s tired of manually transferring details from a protocol to a blank analysis plan template? Have you ever wished AI could draft that first version for you?   Introdu...

We’ve just released a pre-print reporting the development and validation of an AI tool to write statistical analysis plans from protocols.

www.linkedin.com/feed/update/...

Thread 👇

1 month ago 0 2 1 0

The #NIHR are currently advertising several funding committee vacancies including a number to serve on the #BMBR (Better Methods Better Research) funding Committee. If you are interested in supporting the funding of methods research in the UK, please consider applying.
www.nihr.ac.uk/get-involved...

1 month ago 0 3 0 0
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What Makes an Estimand Useful? Guidance on the Choice of Intercurrent Event Strategies While the use of estimands in randomized trials is increasing, there is little guidance on which intercurrent event strategies should be used. The article by Fleming et al. seeks to address this gap....

COMMENTARY: What Makes an Estimand Useful? Guidance on the Choice of Intercurrent Event Strategies @brennankahan.bsky.social @suziecro.bsky.social

onlinelibrary.wiley.com/doi/full/10....

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Data Organization in Spreadsheets
Karl W. Broman
& Kara H. Woo
Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018

    1. Introduction
    2. Be Consistent
    3. Choose Good Names for Things
    4. Write Dates as YYYY-MM-DD
    5. No Empty Cells
    6. Put Just One Thing in a Cell
    7. Make it a Rectangle
    8. Create a Data Dictionary
    9. No Calculations in the Raw Data Files
    10. Do Not Use Font Color or Highlighting as Data
    11. Make Backups
    12. Use Data Validation to Avoid Errors
    13. Save the Data in Plain Text Files

ABSTRACT

Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.

Data Organization in Spreadsheets Karl W. Broman & Kara H. Woo Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018 1. Introduction 2. Be Consistent 3. Choose Good Names for Things 4. Write Dates as YYYY-MM-DD 5. No Empty Cells 6. Put Just One Thing in a Cell 7. Make it a Rectangle 8. Create a Data Dictionary 9. No Calculations in the Raw Data Files 10. Do Not Use Font Color or Highlighting as Data 11. Make Backups 12. Use Data Validation to Avoid Errors 13. Save the Data in Plain Text Files ABSTRACT Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.

Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice.

www.tandfonline.com/doi/full/10....

1 month ago 1050 402 31 47

We’re still going to be seeing p-values in table 1s when we’ve all turned to fossils and dust, aren’t we?

1 month ago 1 0 0 0
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Abstract submission – ICTMC 2026

⏰ Don't miss your chance to submit an abstract for the International Clinical Trials Methodology Conference 2026!

🗓️ The deadline is 22 April 2026

🔗 Find out more here: ictmc.org/abstract-sub...

#ICTMC2026 #TMRP #UKCTUNetwork

1 month ago 2 2 0 0
Box art for Quake 3 Arena

Box art for Quake 3 Arena

Box art for Donkey Kong Country 2

Box art for Donkey Kong Country 2

Box art for SimCity 3000

Box art for SimCity 3000

Box art for System Shock 2

Box art for System Shock 2

1 month ago 1 1 0 0

QTP with a game that has a 10/10 soundtrack

(too many to pick just one - love all these for different reasons)

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Do researchers share their code upon request? Does running their orginal code on the original data produce the original results? We provide evidence in a new Royal Society Open Science publication. Studying more than 1,000 articles which use data from the European Social Survey, we find that... 🧵

1 month ago 102 47 1 4

Sharing code is important for good science👇

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(Also, the SAP’s written in Quarto and rendered in HTML so it’s all purdy)

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C’mon folks, join in. It does feel scary, but it’s the right thing to do, and it feels good when you have.

Posted my first SAP online a couple of weeks ago, to go with the protocol (already online), code to follow in time when written. Do it!

1 month ago 1 0 1 0
Keep calm and be transparent: advice from scientists who retracted their papers Retractions correct the scientific record, but they have stigma attached to them. Some in the research community want that to change.

We're thrilled to announce the Ctrl-Z Award, a US$2,500 prize for researchers “who discover substantial errors in their published work and take meaningful steps to correct the scientific record."
Covered by @nature.com today; read more here: centerforscientificintegrity.org/2026/03/10/a...

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The image is an infographic titled "Open science creates economic value through reuse at scale," by PLOS. It highlights four benefits of reuse: prevents duplication of effort, accelerates research processes, compounds benefits through network effects, and enables reuse across sectors. The left side features a flowchart illustrating reuse from a single research output. On the right, a text box emphasizes that open science can enhance productivity and strengthen long-term performance when done correctly. A final note states, "Publishing is a vital part of the infrastructure that enables reuse at scale.

The image is an infographic titled "Open science creates economic value through reuse at scale," by PLOS. It highlights four benefits of reuse: prevents duplication of effort, accelerates research processes, compounds benefits through network effects, and enables reuse across sectors. The left side features a flowchart illustrating reuse from a single research output. On the right, a text box emphasizes that open science can enhance productivity and strengthen long-term performance when done correctly. A final note states, "Publishing is a vital part of the infrastructure that enables reuse at scale.

Open Science isn’t just a values choice. It’s an economic one.

We are sharing a new independent report by @technopolis-group.com on the economic benefits of #OpenScience and what drives value when research outputs are designed for reuse at scale: plos.io/4rdAxCY

1 month ago 12 14 1 0
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A few headline takeaways:

🔸 Biggest gains come from reuse beyond publications (data, code, software, workflows)
🔸Efficiency gains reduce duplication
🔸Open infrastructures enable innovation and spillovers
🔸Costs and benefits are unevenly distributed across the research ecosystem

1 month ago 1 1 1 0
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Scientific datasets are riddled with copy-paste errors Initial results from scanning through Excel files belonging to 600 published scientific papers.

If you want to take your mind off awful politics and look at awful science stuff instead, this is a good read: www.sciencedetective.org/scientific-d...

1 month ago 85 36 0 5
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PDF Accessibility and Standards – Quarto Quarto 1.9 brings PDF accessibility and standards support, building on new tagging features in LaTeX and Typst.

If you are interested in PDF accessibility, there has been some big progress in Quarto.

Take a look at the latest blog post: quarto.org/docs/blog/po...

#Quarto #Accessibility #LaTeX #Typst

1 month ago 19 6 0 1

Looking forward (!) to reading funding applications with AI-generated sample size calculations done at the 11th hour.

1 month ago 1 0 0 0

…and I’m not sure whether outsourcing that bit to an entropy engine is something I’m comfortable with, even though its’s appealing to think that something could make it faster and easier.

1 month ago 6 0 1 0

But I’m sure using this at scale is going to homogenise SAPs into long boring documents with lots of words but no meaning.

SAPs take ages to write, and it’s hard, and it’s a pain, but they force you to use your brain meat and work out all the thorny difficult stuff…

1 month ago 9 0 1 0

Rrrrrright. I mean, the words are all there. But they make no sense.

Primary analysis that doesn’t use MI but assumes MAR (so what are you doing with the missing values?!).

Like I said, complicated feelings. I’m sure someone’s going to have examples of where it works and where it doesn’t.

1 month ago 8 0 2 0