This November 2nd-7th, 2020, the 5th edition of the Brazilian Conference on Data Journalism and Digital Methods (Coda.Br) will be taking place with 50 national and international guest speakers and 16 workshops. Coda.Br is the largest data journalism conference in Latin America and this year will be completely online.
Organized by Open Knowledge Brasil and Escola de Dados (School of Data Brazil), Coda.Br boasts the support of multiple large scale associations including the Brazilian Association of Investigative Journalism (Abraji), R Consortium, Hivos Institute, Embassy of the Netherlands and the United States Consulate.
For 2020, the conference will be offering main panels, keynote presentations, lightning talks, and a ceremony to announce the winners of Cláudio Weber Abramo Data Journalism Award. Coda.Br and its partners will also be offering 150 free yearly subscriptions to the School of Data Brazil membership program, granting free access to all event activities.
Tickets will be available for R$180 (1 year subscription to Escola de Dados membership, which allows access to workshops and the event chat, among other benefits) and R$40 (workshops only). This translates approximately to USD$32 and $7, respectively.
The R/Pharma virtual conference this year was held October 13-15th, 2020. R/Pharma focuses on the use of R in the development of pharmaceuticals, covering topics from reproducible research to drug discovery to genomics and beyond.
Over 1,000 people signed up for the 3 day, free event this year!
Designed to be a smaller conference with maximum interaction opportunities, R/Pharma was a free event that allowed keynote speakers in the R world to present their research and findings in ways that allowed for maximum viewer participation.
All presentations are given in ways that showcase using R as a primary tool within the development process for pharmaceuticals.
The deadline for submitting proposals is midnight, October 1st, 2020.
The September 2020 ISC Call for Proposals is now open. The R Consortium’s Infrastructure Steering Committee (ISC) solicits progressive, pioneering projects that will benefit and serve the R community and ecosystem at large. The ISC’s goal is to foster innovation and help bring your ideas into tangible realities.
Although there is no set theme for this round of proposals, grant proposals should be focused in scope. If you are currently working on a larger project, consider breaking it into smaller, more manageable subprojects for a given proposal. The ISC encourages you to “Think Big” but create reasonable milestones. The ISC favors grant proposals with meaningful detailed milestones and justifiable grant requests, so please include measurable objectives attached to project milestones, a team roster, and a detailed projection of how grant money would be allocated. Teams with detailed plans and that can point to previous successful projects are most likely to be selected.
To submit a proposal for ISC funding, read the Call for Proposals page and submit a self-contained pdf using the online form.
In HTML vignettes, you can also use web dependencies. On a pkgdown website, you might encounter some incompatibilities between your, say, HTML widgets, and Boostrap (that powers pkgdown).
Web dependency management
Here’s an example from the applause package. This package wraps applause-button, a zero-configuration button for adding applause/claps/kudos to web pages and blog posts. It was also created to demonstrate how to package a web component in an R package using htmltools. For a full walk through of the package development process, see the dev log in the package README.
The HTML dependency for applause-button is provided in the html_dependency_applause() function. htmltools tracks all of the web dependencies being loaded into a document, and conflicts are determined by the name of the dependency where the highest version of a dependency will be loaded. For this reason, it’s important for package authors to use the package name as known on npm or GitHub and to ensure that the version is up to date.
The package, src, and script or stylesheet arguments work together to locate the dependency’s resources: htmlDependency() finds the package‘s installation directory (i.e. inst/), then finds the directory specified by src, where the script (.js) and/or stylesheet (.css) files are located. The src argument can be a named vector or a single character of the directory in your package’s inst folder. If src is named, the file element indicates the directory in the inst folder, and the href element indicates the URL to the containing folder on a remote server, like a CDN.
To ship dependencies in your package, copy the dependencies into a sub-directory of inst in your package (but not inst/src or inst/lib, these are reserved directory names1). As long as the dependencies are a reasonable size2, it’s best to include the dependencies in your R package so that an internet connection isn’t strictly required. Users who want to explicitly use the version hosted at a CDN can use shiny::createWebDependency().
Finally, it’s important that the HTML dependency be provided by a function and not stored as a variable in your package namespace. This allows htmltools to correctly locate the dependency’s files once the package is installed on a user’s computer. By convention, the function providing the dependency object is typically prefixed with html_dependency_.
Using an HTML dependency
Functions that provide HTML dependencies like html_dependency_applause() aren’t typically called by package users. Instead, package authors provide UI functions that construct the HTML tags required for the component, and the HTML dependency is attached to this, generally by including the UI and the dependency together in an htmltools::tagList().
Note that package authors can and should attach HTML dependencies to any tags produced by package functions that require the web dependencies shipped by the package. This way, users don’t need to worry about having to manually attach dependencies and htmltools will ensure that the web dependency files are added only once to the output. This way, for instance, to include a button, using the applause package an user only needs to type in e.g. their Hugo blog post3 or Shiny app:
Some web dependencies only need to be included in the output document and don’t require any HTML tags. In these cases, the dependency can appear alone in the htmltools::tagList(), as in this example from xaringanExtra::use_webcam(). The names of these types of functions commonly include the use_ prefix.
How do you test JS code for your package, and how do you test your package that helps managing JS dependencies? We’ll simply offer some food for thought here. If you bundle or help bundling an existing JS library, be careful to choose dependencies as you would with R packages. Check the reputation and health of that library (is it tested?). If you are packaging your own JS code, also make sure you use best practice for JS development. 😉 Lastly, if you want to check how using your package works in a Shiny app, e.g. how does that applause button turn out, you might find interesting ideas in the book “Engineering Production-Grade Shiny Apps” by Colin Fay, Sébastien Rochette, Vincent Guyader and Cervan Girard, in particular the quote “instead of deliberately clicking on the application interface, you let a program do it for you”.
The resources for learning we found are mostly related to Shiny, but might be relevant anyway.
Different problem, using JS libraries in Rmd documents
More as a side-note let us mention the htmlwidgets package for adding elements such as leaflet maps to your HTML documents and Shiny apps.
When learning a new language, using a playground is great. Did you know that the js4shiny package provides a JS playground you can use from RStudio? Less new things at once if you already use RStudio, so more confidence for learning!
The second COVID-19 Data Forum, co-sponsored by the Stanford Data Science Institute and the R Consortium, was held August 13, 2020. This series of forums brings together experts working to collect and curate data needed to drive scientific research and formulate effective public health responses to the pandemic.
The forum utilized Zoom as the video platform and allowed keynote speakers to present, as well as interact during a Q&A session.
The moderator was Sherri Rose, an associate professor at Stanford University in the Center for Health Policy and Center for Primary Care and Outcomes Research and Co-Director of the Health Policy Data Science Lab.
Speakers covered topics such as current issues facing researchers during the COVID-19 pandemic such as data sharing or research duplication, how phenotype impacts severity of cases, and data inequality for under-serviced communities. Speakers also answered questions from the moderator and the chat about their work and ways individuals can get involved at all R literacy levels.
This fall, the R Consortium’s support for advancing data science in medicine continues with the third of three exceptional events, pulling together experts in their fields, including the Covid-19 Data Forum, R/Medicine, and R/Pharma.
What is R/Pharma?
R/Pharma is an ISC working group under the R Consortium. The entire event is a community-lead effort and 100% volunteer run. R/Pharma is vendor neutral and very much an academic conference. Harvard has been very helpful in hosting the event.
August 27-29, 5:30am PDT / 8:30am EDT / 2:30pm CEST – Register now!
Brought to you by the Children’s Hospital of Philadelphia, Yale School of Public Health, and the R Consortium, the R/Medicine conference encourages the adoption of statistical modeling and reproducible data processing in clinical practice.
R is the gold standard in reproducible research in academia and industry and has powerful capabilities to create highly-customizable interactive analytic dashboards, as well as predictive models that employ machine learning, deep learning, and artificial intelligence.
Presentations will showcase how the R ecosystem is currently leveraged in medical applications including clinical trial design and analysis, personalized medicine, the development of machine learning models using laboratory and patient record data, and reproducible research.
Hosted by the COVID-19 Data Forum/Stanford Data Science Initiative/R Consortium
COVID-19 is the first pandemic to occur in the age of open data. Public health agencies around the world are releasing case counts to the public, and scientists are providing analyses and forecasts in real-time. However, the content of this data has so far been limited to simple metrics like cases, deaths, and hospitalizations at coarse geographic and demographic scales. To drive the next phase of COVID-19, scientists need access to higher-dimensional patient-level data, so we can understand how the virus causes disease, why are some more at risk than others, when and how is transmission occurring, what therapeutics are more likely to work, and what healthcare resources are being used. But sharing such data brings up tremendous challenges in terms of patient privacy and data standardization. The COVID-19 Data Forum, a collaboration between Stanford University and the R Consortium, is hosting the event “Beyond case counts: Making COVID-19 clinical data available and useful” to push the conversation forward on these issues. The event will include talks by representatives from international collaborative teams who are working to collect and share detailed clinical and biological data from individuals with COVID-19. The event will be open to the public, and is part of a continuing series focusing on data-related aspects of the scientific response to the pandemic.
Jenna Reps, Observational Health Data Sciences & Informatics (OHDSI) Consortium /Janssen R&D
Andrea Ganna, COVID-19 Host Genetics Initiative/Harvard Medical School/Finland Institute for Molecular Medicine
Ken Massey, EndPandemic National Data Consortium/Saama Technologies
Ryan Tibshirani, DELPHI epidemic forecasting group/Dept of Statistics, Carnegie Mellon University
On June 19th, 2020, we filmed a video for useR!2020 showcasing the communities and organizations we are involved in that are for Latin Americans or have Latin American participants. In this blog post, we wanted to highlight these initiatives and remind everyone that we are more than happy to help you launch similar initiatives in your local communities.
LatinR: LatinR is a trilingual international conference on the use of R in research and development across Latin America. Since launching in 2018, our annual meetings have been a starting point for new packages, local user groups, reading clubs, R-Ladies chapters, translations, and other initiatives in the region.
ConectaR: ConectaR 2019 took place during January 24-26, 2019 at the University of Costa Rica, in San José, Costa Rica. It was the first event in Central America endorsed by The R Foundation, and it was held completely in Spanish. You can find more information here.
satRday: SatRday is a conference about R and its applications, that happens all over the world, and it is organized by the local community. Two satRdays events happened in Latin America: in Santiago – Chile and São Paulo – Brazil. If you want to organize a satRday anywhere in Latin America, please get it touch so we can help each other!
R-Ladies: R-Ladies is a global organisation that promotes gender diversity in the R community. It has 123 active chapters in 51 countries around the world, of which 49 are found across 10 Latin American countries. Some Latin Americans are part of the R-Ladies Global Team, including its leadership. COVID-19 has not stopped us, instead, we have migrated online and fostered alliances among different chapters. All in an effort to give gender minorities in the R community the opportunity to learn R in a safe and supportive environment. Join us!
rOpenSci: R for open science, rOpenSci, provides free technical review of R packages to improve the quality of open source software in order to maximize readability, usability, usefulness, and minimize redundancy. Their peer-review process will soon be translated to Spanish and you can get involved!
RUGs: there are several R User Groups in Latin America, some of which are officially sponsored by the R Consortium. We believe that creating a welcoming space is crucial for keeping the ideas flowing, which allows for meaningful networking and, consequently, the development of new projects. We can help you start your own group!
R4DS in Spanish + datos package: the resources to learn R in English are many, awesome, online, and free. But in Latin America few people can afford to learn English, and the resources in Spanish are few. To help solve this problem, we community-translated to Spanish the “R for Data Science” book and developed a package with the translation of all the datasets used in it: datos. The workflow to contribute to the package was designed to engage first-time contributors, and is now guiding the development of a new version in Portuguese that will be released in the next few months.
#DatosDeMiércoles + #30díasdegráficos: The @R4DS_es Twitter account was created as a way to share projects like the R4DS translation and to developed initiatives to foster the Spanish-speaking R community, like #datosdemieRcoles, the Latin American cousin of #TidyTuesday. The idea is not only to use datasets that are in Spanish, but also datasets that are relevant for our Region. This initiative has been complemented with the 30 days plot challenge #30díasdegráficos. If you want to participate proposing a dataset for #datodemiéRcoles, please visit our github repo.
The Carpentries: The Carpentries builds global capacity in essential data and computational skills for conducting efficient, open, and reproducible research. Building a sustainable and active community in Latin America includes several initiatives: lesson translations, instructor training, workshop coordination, and fundraising. Get in touch with us through the mailing list and the carpentries-es channel at the Carpentries Slack workspace.
ReproHack: ReproHack is a growing community for researchers that are fighting the reproducibility crisis by sharing their experiences across disciplines. It is focused on organizing hackathons where participants attempt to reproduce published research from a list of proposed papers with public code and data. We are planning the first ReproHack in Spanish for October 2020 and you can get in touch with us through Twitter.
AI Inclusive: AI Inclusive is an organization that promotes diversity in the AI Community. We want to bring awareness around Artificial Intelligence issues and empower the community so they can enter in the AI field, a field that is not diverse at all. In December 2019, we had our launch events in Rio de Janeiro, Brazil and San Francisco, California. Follow us and join us!
Data Latam: in May 2016 we started with the first Data Latam podcast, aimed at offering an easy entry point, in Spanish, to those interested in data science. We always ask our interviewees: “How did you get where you are?”, and the diversity of stories has been enormous. Today Data Latam is a Latin American community of professionals and academics, who apply data science in their day to day work and we invite you to participate!
What happens in the R Community doesn’t stay in the R Community. All the good practices of inclusive and diverse communities learned in several of the initiatives presented before, generate strong work teams within and beyond the R community. There is still a lot to be done, but what we’ve already achieved is very encouraging and provides a solid foundation for the future.
These initiatives are sustained by many people making a great, mostly volunteer, effort behind the scenes. Some of the challenges that the communities face are translated into multiple positives, sustained, and a lot of invisible hard work. Some of them are: finding international funding due to limited local options, translating content, joining forces across organizations, organizing regional conferences, and becoming active developers of the technology.
The Latin American R community is growing fast and so does the responsibility to make this growth solid and safe. Some of the future work that we, as community builders, look forward to fulfilling are: consolidating regional conferences with support of international sponsors; acquiring funding to sustain translations; amplifying the voices of regional minorities; importing educational material and work opportunities; connecting expats with their local communities; helping other groups such as RUGs and RLadies; connecting with other initiatives such as R-Forwards, Africa-R, MiR, among others; Increase our and other minorities representation in the R Core Team, the R Foundation, and the R Consortium.
Thank you! Please watch our useR! 2020 video on YouTube.
We wanted to get a mid-year update and also more details on R communities in Southern Africa so we spoke with Dr. Heather Turner, chair of Forwards, a R Foundation taskforce for underrepresented groups. Dr. Turner is a Honorary Research Fellow of the Statistics Department at the University of Warwick, UK. She brings nearly 20 years of experience with R. Recently, Dr. Turner raised money to fund several workshops and talks in order to develop the R community in South Africa.
What were some of the interesting ways R is being used in Southern Africa?
R is being used in academia, government organisations, non-profits and businesses. It is perhaps not as common as SPSS or Python, but an enthusiastic community is growing. I was able to discover where R was being used through the people I met and the companies that hosted or supported some of the events. However, the Johannesburg satRday was my main opportunity to see how R was being used. Several of the talks had an African focus, such as Anelda van der Walt’s talk on the afrimapr project making it easier to map data by administrative regions:
Kirsty Lee Garcon’s talk on mapping African genomic data with the sf package:
And Astrid Radermacher’s talk on unravelling the mysteries of resurrection plants (specifically, a native African one) using various R packages:
Among the general R talks, I particularly enjoyed Diana Pholo’s talk “From Pythonista to Rtist”, which gave practical advice:
Drikus du Toit’s talk on SHAP: Interpreting ML Models with IML (), which looked at modelling whether a person would default on a loan.
And Roberto Bennetto’s talk on exploring the Corona outbreak with R, which, back in March 7, was one the first looks I’d had at data from the pandemic.
How has R literacy helped to empower women in areas like Johannesburg or Kampala where satRday events have been hosted?
Learning R is one way that women can unlock the power of data science. This can be directly applied to issues of gender equality as Caroline Akoth demonstrated through her talk on the work of Women in GIS, Kenya, at satRday Johannesburg.
Alternatively, it can give women the opportunity to lead the way to more open, reproducible practices, as satRday Kampala keynote Shelmith Kariuki recently demonstrated by extracting the Kenya Population and Housing Census results from PDF files and publishing them as tidy datasets in her rKenyaCensus package: https://github.com/Shelmith-Kariuki/rKenyaCensus
In general, expertise in R is a powerful skill that can help women to progress in their careers and make a difference in the world.
The satRday events play an important role in inspiring women to pursue data science and to take on responsibilities in the R community. After the satRday in Abidjan, three women joined the board of the Abidjan R Users group and they have already been active in planning and leading R training. The first satRdays in Africa were held in Cape Town and the organizing team made a concerted effort to have a strong representation of women in the program, inviting only women keynotes and proactively encouraging women to submit abstracts. This commitment to the inclusion of women has continued with the subsequent South African satRdays and has been very effective. It can be motivating for women in the audience to see women on stage; after the first Cape Town satRday, Theoni Photopoulou was inspired to start an R-Ladies group. She was joined by Megan Beckett and they co-founded R-Ladies Cape Town. Since then, there has been a symbiotic relationship between R-Ladies and satRdays in South Africa, where one helps to promote the other and both help to strengthen women’s R literacy and social networks.
The community and social network are just as important as R literacy. R-Ladies groups such as those in Cape Town and Johannesburg provide a particularly supportive space for women and gender minorities to learn R. But satRdays and regular R User Groups also help to connect women to R users outside their university or workplace. For some women, these connections have lead directly to new jobs requiring (more) R expertise. More generally, women can tap into their network to help them navigate interviews, negotiate competitive salaries and handle both technical and inter-personal issues that come up in their work.
As women learn more about R and are supported by the community, they become confident in themselves, impacting the wider community. For example, Astrid Radermacher, a co-organizer of R-Ladies Cape Town, has started to run free R classes at her institution and it is mostly women that attend. Shakirah Nakalungi, a co-organizer of the satRday in Kampala, is an ambassador for Zindi, a Kaggle-like platform focused on solving Africa’s most pressing problems. R-Ladies Johannesburg has partnered with ‘Women in Big Data’, ‘Coding Mamas’, ‘WiMLDS’ and other groups, widening their impact. In this way, women empowered by learning R pay it forward within the R community and beyond.
Your data (https://forwards.github.io/data/) shows that the average age for packet authors was approximately 39 years old. Has it been your experience that young adults find R to be daunting?
I don’t think that young adults find R to be daunting any more than older adults. The data you refer to is quite old now (from 2010); back then it was still unusual for R to be taught at undergraduate level. So most people would learn R during their postgraduate studies or later in life and it would take a few years to get to the stage where they might write a package, hence most package authors were over 25. I would expect the distribution to have shifted a little to younger ages these days, however the average age would still be relatively old, as thankfully writing an R package is not a fatal event and us older maintainers live on!
What has been the most gratifying part of putting on events like R-Ladies or satRday? The most frustrating?
The most gratifying part is people enjoying the event. It’s great when you get positive feedback or people post something online saying how they learnt something that they’re keen to try out or how they felt welcomed and supported by the folks at the event. The frustrating part is people wanting a lot more from you when you’ve volunteered to do a particular thing. On the one hand, it’s often something I would want to do and would be good at. On the other, the small asks add up and can become too much, so something has to give. This is challenging to me as a community organizer, it’s easiest to say “X is good at that, let’s ask them”, but we need to be respectful of people’s time and keep looking to bring new people in to share the work.
Do you see R being used more in Africa over the coming 3-5 years?
Yes I do. My impression is that R is not widely taught in universities across Africa, but initiatives like eR-Biostat are helping to change that. Often students will self-learn R, or learn through a one-off workshop perhaps by a visiting lecturer or run by the Carpentries. R users that are trying to encourage others to use or learn R can face a couple of frustrating attitudes. One is that R is only used in universities and is not useful in other sectors. Another is that R is something to be feared because increased automation may make people’s jobs redundant. Such attitudes are why I think it is critical to build the community around R, with R user groups, satRdays and online networks, so that people can see the variety of ways R is used and see that increasing data science literacy can lead to more interesting, skilled work. The R community is growing in Africa and I think this in turn will encourage wider adoption of R in the next few years.