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R Consortium
Registrace 24. 03. 2017
The R Consortium, Inc. is a group organized under an open source governance and foundation model to support the worldwide community of users, maintainers and developers of R software. Its members include leading institutions and companies dedicated to the use, development and growth of R.
The R language is an open source environment for statistical computing and graphics. The R community has enjoyed significant growth, with more than 2 million users worldwide. A broad range of organizations have adopted the R language as a data science platform, including biotech, finance, research and high technology industries. The R language is often integrated into third-party analysis, visualization and reporting applications, and runs on a wide variety of computing platforms.
The central mission of the R Consortium is to work with and provide support to the R Foundation and key organizations and groups developing, maintaining, distributing and using R software.
The R language is an open source environment for statistical computing and graphics. The R community has enjoyed significant growth, with more than 2 million users worldwide. A broad range of organizations have adopted the R language as a data science platform, including biotech, finance, research and high technology industries. The R language is often integrated into third-party analysis, visualization and reporting applications, and runs on a wide variety of computing platforms.
The central mission of the R Consortium is to work with and provide support to the R Foundation and key organizations and groups developing, maintaining, distributing and using R software.
R-based Test Submission Package for FDA Evaluation: A Milestone in R-based Regulatory Submissions
This demo highlights the efforts led by Joel Laxamana, a statistical programmer at Genentech, to develop an R-based approach for submitting clinical trial packages to the FDA. Traditionally, sponsors have used proprietary tools like SAS, but there is growing interest in open source software like R. The R Consortium R submission Working Group is creating R-based submission packages to improve transparency and reproducibility in the approval process. Their initiatives include pilot projects using R scripts and a Shiny app for submissions.
Main Sections
00:00 Introduction
04:11 The R Consortium R submission Working Group
04:57 Overview of Pilots
15:05 Open source language-based submissions to FDA & challenges
16:25 Pilot 3 Demonstration
56:08 Q&A
More resources
R Validation Hub Site: www.pharmar.org/
Main Site: www.r-consortium.org/
News: www.r-consortium.org/news
Blog: www.r-consortium.org/news/blog
Join: www.r-consortium.org/about/join
Twitter: rconsortium?lang=en
LinkedIn: www.linkedin.com/company/r-consortium
Mastodon: fosstodon.org/@RConsortium
Main Sections
00:00 Introduction
04:11 The R Consortium R submission Working Group
04:57 Overview of Pilots
15:05 Open source language-based submissions to FDA & challenges
16:25 Pilot 3 Demonstration
56:08 Q&A
More resources
R Validation Hub Site: www.pharmar.org/
Main Site: www.r-consortium.org/
News: www.r-consortium.org/news
Blog: www.r-consortium.org/news/blog
Join: www.r-consortium.org/about/join
Twitter: rconsortium?lang=en
LinkedIn: www.linkedin.com/company/r-consortium
Mastodon: fosstodon.org/@RConsortium
zhlédnutí: 514
Video
R/Medicine: Quarto for Reproducible Medical Manuscripts
zhlédnutí 2,9KPřed 5 měsíci
In this webinar, Mine Cetinkaya-Rundel, Professor of the Practice of Statistical Science at Duke University, presents a new capability in Quarto that provides a straightforward and user-friendly approach to creating reproducible manuscripts that are publication-ready for submission to science journals. This new feature, Quarto manuscripts, includes the ability to produce a bundled output contai...
Tidy Finance and Accessing Financial Data
zhlédnutí 921Před 5 měsíci
This webinar focused on Tidy Finance and accessing financial data. Christoph Scheuch, Head of Artificial Intelligence, wikifolio Financial Technologies AG, and co-author and maintainer of the Tidy Finance Project, introduced Tidy Finance and illustrated the underlying principles. Tidy Finance was an opinionated approach to empirical research in financial economics. It provided a fully transpare...
Escape the Data Dungeon: Unlock Scalable R Analytics and ML
zhlédnutí 377Před 5 měsíci
Tired of sluggish R data processing and limited Machine Learning (ML) options with large databases? Imagine swiftly predicting customer churn and deploying solutions with ease. Watch our in-depth webinar to see Oracle Machine Learning for R (OML4R) in action! Key topics include: - Seamless In-Database Access: Jump straight into your data without the drag of extractions. - Scalable High-Performa...
From Vision to Action: The R Pfizer R Center of Excellence-led Journey to R Adoption
zhlédnutí 727Před 6 měsíci
The upcoming webinar by the R consortium titled “From Vision to Action: The R Pfizer R Center of Excellence-led Journey to R Adoption” is not just a case study of Pfizer’s journey. It’s a platform for sharing valuable insights and strategies applicable across industries and experience levels. Participants will understand the importance of an engaged R community and learn practical approaches to...
High performance programming in R
zhlédnutí 838Před 6 měsíci
In this webinar, Benedikt discussed how comma-separated values (CSV) files were commonly used when working with data files, as they were easy to read for humans and supported by tools like Excel or R. However, these files had a downside in terms of performance and file size. To address this, the industry developed binary formats that were more efficient. Benedikt focused on the Arrow R package ...
Visualizing Survival Data with the {ggsurvfit} R Package
zhlédnutí 2KPřed 6 měsíci
This webinar focused on the {ggsurvfit} R package, a tool designed to simplify the creation of time-to-event or survival analysis summary figures using {ggplot2}. It emphasized the package’s capability to produce high-quality, publication-ready Kaplan-Meier plots and other survival analysis figures with ease and efficiency. Overall, the webinar promised to be an informative session for statisti...
R/Insurance Series: R Performance culture
zhlédnutí 430Před 6 měsíci
In this webinar, Benedikt covered how performance fitted into R’s design, what tools were available to tune it, and examples of what other aspects should have been considered beyond pure runtime. Main Sections 00:00 Introduction 01:12 Background to Swiss Re's R Community 06:08 R is designed for flexibility, but can have high performance 09:06 The R ecosystem provides guidance and tools 11:48 Tr...
R/Insurance Series: From programming in R to putting R into production
zhlédnutí 668Před 7 měsíci
In this webinar, Georgios illustrated ways to document and test the solution and made it available to others using R’s frameworks for packaging, Web API creation, and graphical user interface generation (Shiny). Main Sections 00:00 Introduction 02:19 Background 02:45 Running examples for webinars 1 & 2 04:26 where we ended in webinar 1 05:15 Today: Putting R into production 08:33 Iteration with...
R/Insurance Series: From Excel to Programming in R
zhlédnutí 1,2KPřed 7 měsíci
This webinar demonstrated the instances where employing the R programming language was advantageous and a feasible method for integrating Excel and R approaches. Agenda: Welcome Webinar presentation Q&A Main Sections 00:00 Introduction 02:17 Background 03:17 Running example for webinars 1 & 2 07:00 Calculating EMI in Excel and R is similar 09: 35 Vectorization in R 17:27 Putting all together in...
The Adoption of R in Japan's Pharma Industry Confirmation
zhlédnutí 365Před 7 měsíci
The Adoption of R in Japan’s Pharma Industry talk and panel discussion was led by key industry experts from the JPMA R Task Force Team. The webinar explored the usage and adoption of R in the pharmaceutical industry, specifically focusing on the findings of the JPMA Drug Evaluation Committee, R Task Force Team, and the JPMA Report. The report referenced various open source works and publication...
Cleaning Medical Data with R
zhlédnutí 4KPřed 8 měsíci
In this workshop you will learn how to import messy data from an Excel spreadsheet, and develop the R skills to turn this mess into tidy data ready for analysis. If your answer to any of the following questions is “yes”, then this is the right workshop for you. (1) Do you frequently receive untidy data for analysis in Excel spreadsheets? (2) Does this drive you slightly batty?(3) Do you want to...
Automated Reporting with Quarto
zhlédnutí 947Před 8 měsíci
Quarto is a recently released open source publishing system that allows you to dynamically create static or interactive documents and automatically update reports when data changes. Quarto supports dozens of static and dynamic output formats including HTML, PDF, MS Word, slides, dashboards, scientific articles and more. The aim of the workshop is to provide a basic introduction to Quarto and to...
A Journey From Patchworks to Projects: A Ready-To-Use Project Template To Popularize Reproducible...
zhlédnutí 248Před 8 měsíci
This workshop introduces a minimal attrition approach to robust, reproducible research pipelines suitable for medical students and researchers with minimal coding experience. Participants will learn to create a package-driven R project integrated with GitHub, utilizing a variety of libraries for reproducibility. Key topics include {renv} for dependency management, {testthat} for automated testi...
Creating and Reasoning About Complex Clinical Trial Tables With rtables
zhlédnutí 234Před 8 měsíci
Gabe and Adrian will walk participants through the process of creating submission ready tables using the rtables framework. Specific topics will include both reasoning about and declaring table structure, and defining complex cell-value derivation instructions. Participants will get practice combining these topics to go from a LOPO style table and dataset specification to a publication ready ta...
Level Up Your Plots: Using Colour, Text Hierarchy and Annotations to Create Compelling and More
zhlédnutí 542Před 8 měsíci
Level Up Your Plots: Using Colour, Text Hierarchy and Annotations to Create Compelling and More
R/Adoption Series: R and Shiny in Regulatory Submissions
zhlédnutí 689Před 8 měsíci
R/Adoption Series: R and Shiny in Regulatory Submissions
Isoformic: Transcript Level RNA-seq Analysis for Human Data
zhlédnutí 337Před 8 měsíci
Isoformic: Transcript Level RNA-seq Analysis for Human Data
Tidy Transcriptomic Analysis of Single-cell and Bulk Data
zhlédnutí 152Před 8 měsíci
Tidy Transcriptomic Analysis of Single-cell and Bulk Data
High-Dimensional Propensity Score in Residual Confounding Control in Pharmacoepidemiologic Studies
zhlédnutí 331Před 8 měsíci
High-Dimensional Propensity Score in Residual Confounding Control in Pharmacoepidemiologic Studies
R validation Hub Community meeting wrapping up 2023 and welcoming 2024!
zhlédnutí 167Před 8 měsíci
R validation Hub Community meeting wrapping up 2023 and welcoming 2024!
GitHub Copilot in Rstudio, it's finally here!
zhlédnutí 13KPřed 10 měsíci
GitHub Copilot in Rstudio, it's finally here!
R Validation Hub Mini-Series Part II - Shiny for R Package Risk Assessment
zhlédnutí 483Před 11 měsíci
R Validation Hub Mini-Series Part II - Shiny for R Package Risk Assessment
R Validation Hub Mini-Series Part I - Risk Metrics and Risk Score Package
zhlédnutí 937Před 11 měsíci
R Validation Hub Mini-Series Part I - Risk Metrics and Risk Score Package
A Live Demonstration of the OHDSI PatientLevelPrediction R Package
zhlédnutí 605Před rokem
A Live Demonstration of the OHDSI PatientLevelPrediction R Package
Machine Learning for Risk Prediction using Oblique Random Survival Forests
zhlédnutí 1,8KPřed rokem
Machine Learning for Risk Prediction using Oblique Random Survival Forests
Analyzing Clinical and Genomic Oncological Data with {genieBPC} and {gnomeR}
zhlédnutí 200Před rokem
Analyzing Clinical and Genomic Oncological Data with {genieBPC} and {gnomeR}
Dengue Data Hub A Centralized Repository for Dengue related Data
zhlédnutí 231Před rokem
Dengue Data Hub A Centralized Repository for Dengue related Data
Starts 4:30
I watched this workshop. It is an excellent workshop. Thank you, speakers and R consortium sharing on youtube.
While I am a strong advocate of R, I wouldn't use R in this context. It's way too busy in its presentation. I think its value proposition is compromised by the obscurity of its presentation. In my opinion, I would use R for the generation of a data model, write a white paper on those findings, and for the data reporting, I would use a BI tool which I believe, if constructed correctly, would provide optimal insights and actionability.
This is really helpful! How does 0one justify the bullets to the left, as shown in 12:13. Most css formatting is being rejected: Caused by error: ! gridtext has encountered a tag that isn't supported yet: <ul> Only a very limited number of tags are currently supported.
28:30 Quarto makes for great PDF output, as long as you keep and tweak the TeX file and correct the errors in there. 😅😂😢
How about just using duckdb and SQL?
The lecturer is awesome
Thank you for this thorough explanation. I sort of started using this workflow with a quarto website for consulting projects, which are less academic in nature, but many of these features work perfectly in that setting too. It's a great time to be alive.
Do you share the code for revealjs presentation?
multi-omics should be on the same sample using mixOmics?
Very good. Thanks for sharing this
Great. Thanks for sharing this
You are a genius! Fantastic video! Thanks!
I ran into a problem. When I render pdf files, the function tab_options(table.width = pct()" can only be used once. If more than once, I got the error as follow. No problem with HTML files. ERROR: compilation failed- error LaTeX Error: Command \holdLTleft already defined. Or name \end... illegal, see p.192 of the manual. See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.336 ewlength\holdLTleft ewlength\holdLTright\setlength\holdLTleft{\LTle... see table.log for more information.
Please share commands for forcasted value for every model
A neat question to answer. I'm using the duckplyr library and it's nice to not have to think about anything. It does make a strong argument for having a fast hard drive (an SSD is an order of magnitude faster than a traditional HDD, an M2 is an order of magnitude faster than that, and modern nvme drives are even faster).
Hello. I would like to ask a question, are there any test statistics to possibly use for underdispersed count data aside from generalized poisson model? Thanks!
Thanks
This is AWESOME! I have been using Quarto since it became available, but these new features are awesome! Thanks for providing outstanding explanation and examples.
can you share the code please, thank you for the nice presentation.
This talk blew my mind. Thank you very much!
Great webinar🎉❤
This is an amazing source and presentation. What I see dificult is to force fournals to work within this framework, when their business is upload plain PDFs to internet. I think reproducible manuscripts are a call for scientist to take the control again of scientific publishing basend on open and reproducible science. Thanks for sharing this amazing initiative.
Thanks. I got an error due to the embed part: ERROR: The cell fig-cars does not exist in notebook
I had trouble creating both html and pdf output. PDF was not rendering at all, and instead of html, I got an index.xml file. I found I could create either index.html or index.pdf by running the following code for each, respectively: quarto::quarto_render("index.qmd", output_format = "html") quarto::quarto_render("index.qmd", output_format = "pdf")
Thanks for the video. I missed the webinar. Just have to check it out ASAP
love it!
Thank you very much.
Is there a link to the scripts seen in this video?
Tidy Finance is great. But you took 17 Minutes to get to the actual features of your package. It would maybe be better to make several small videos on topics instead of a monolithic introduction of it.
great one, so it has access to my packages and their manuals? Or do i still have to post snipets of examples from those manuals for it to understand?
Amazing! Thanks. This is exactly my use case
You are very beautiful and very intelligent
Hello, is the repo still available? thanks :)
How to query multiple cancer studies or all the pan cancer studies and look for log2fold mRNA expression across all cancers? It takes only one study Id in cBioPortalData function
Thanks for the intro into it. chattr app wants to use the GPT-4 version in the chattr app. Do you know how to set it to use the free version? @ThomasMock
Can we change the legend labs as the argument legend.labs in ggsurvplot.
what is the 95 % confidence interval method used in survfit2 package ? is it based on greenwood formula?
Thanks
Thanks
Do you have spatial datasets on cancers, diabetes, heath indicators to predict output based on the data? Can you share datasets please i didn't find any spatial datasets on diseases..
Thanks for sharing? It is very nice to use ggplot2 gramar for modification of survival plot. However, is there any way for combing multiple survival objects with the ggsurvfit package? It could be done with survminer.
Thanks again for sharing!
Thank you for this!!
the Exercises/Data section has been updated with a link
Loved your presentation. Well done Sir!😊
This is a horrible video.
Hi, I am kindly asking for the link to the data
Hello, can anyone provide me the link to the data messy_uc.xlsx please?
Wonderful content and presentation. Thank you!!