diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..db75bfb Binary files /dev/null and b/.DS_Store differ diff --git a/404.qmd b/404.qmd new file mode 100644 index 0000000..08fe1c4 --- /dev/null +++ b/404.qmd @@ -0,0 +1,10 @@ +--- +title: "404 - Page Not Found" +format: html +--- + +Sorry, but the page you are looking for does not exist. + +R you sure that's the correct address? + +Please double-check the URL or go back to our [homepage](/). diff --git a/RConsortium_Horizontal_Pantone.png b/RConsortium_Horizontal_Pantone.png new file mode 100644 index 0000000..3a28eb0 Binary files /dev/null and b/RConsortium_Horizontal_Pantone.png differ diff --git a/RConsortium_Horizontal_Pantone.webp b/RConsortium_Horizontal_Pantone.webp new file mode 100644 index 0000000..2ab1bd7 Binary files /dev/null and b/RConsortium_Horizontal_Pantone.webp differ diff --git a/README.md b/README.md new file mode 100644 index 0000000..f57ebd8 --- /dev/null +++ b/README.md @@ -0,0 +1,121 @@ +# Development Server for R Consortium Website + +This is a new Quarto-based website which updates and supersedes the original website [here:](https://www.r-consortium.org/) + +R Consortium Blog - [How to upload your blog post to a quarto-based website](https://oppkeyquarto.netlify.app/blog/how_to_post.html) + +## Contributing to this website + +This website is being built members of the R Consortium, R-Ladies Gaborone and other volunteer contributors. Thank you! If you want to help contribute to the site, please use the following workflow. + +### Workflow for making contributions + +#### 1\. Clone this website + +#### 2\. Make a branch + +Make a branch and edit your branch locally. + +To preview the website locally you can execute this quarto command in your terminal: + +#### 3\. Commit your changes + +Make your changes locally save them and commit them. Be sure to make your commit message descriptive of the work you did. + +#### 4\. Do a Pull Request + +Do a pull request from your local copy to make sure branch is in sync with the website branch. We will review your Pull Request! + +## What is the R Consortium? + +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](https://oppkeyquarto.netlify.app/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 R Consortium’s mission is to promote the R language and to develop the technical and social infrastructure required to support the R ecosystem and the R Community. Its activities and programs include: + +Promoting the growth and development of R as a leading platform for data science and statistical computing. +[Members of the R Consortium](https://oppkeyquarto.netlify.app/members) are recognized as supporters of the R Project and the R community, and the R Consortium represents its members to the R community and to the media. +Supporting and collaborating with the [R Foundation](https://www.r-project.org/foundation/), the governing body of the R Project. + +The R Foundation maintains a permanent seat on the board of the R Consortium, as an open communication channel for R Consortium members. + +Funding projects to enhance R and support its users. + +Projects are proposed by the R community at large, and selected for funding by the Infrastructure Steering Committee. R Consortium members nominate the selection committee and provide funds for project grants with their membership dues. (Here is a list of [projects funded by the R Consortium](https://oppkeyquarto.netlify.app/all-projects/funded-projects) to date.) + +Fostering the continued growth of R community and the data science ecosystem. + +The R Consortium sponsors R-related conferences (including useR!), meetings (including SatRDays and RLadies), and local user groups worldwide. + +Enabling the use of R in commercial environments, and fostering collaboration between companies investing in R. +R Consortium committees are developing programs for R language certification and training, consulting, and employment. + +The mission of the R Consortium is formally defined in the [R Consortium bylaws](rc-docs/Bylaws-GU-Draft-7-9-2024.docx.pdf) (PDF) and the [Infrastructure Steering Committee charter](rc-docs/ISC-Charter-08-11-23.pdf) (PDF). + +## Main Links + +Main Site: [https://www.r-consortium.org/](https://www.r-consortium.org/) +News: [https://www.r-consortium.org/news](https://www.r-consortium.org/news) +Blog: [https://www.r-consortium.org/news/blog](https://www.r-consortium.org/news/blog) +Join: [https://www.r-consortium.org/about/join](https://www.r-consortium.org/about/join) +Twitter: [https://twitter.com/rconsortium?lang=en](https://twitter.com/rconsortium?lang=en) +LinkedIn: [https://www.linkedin.com/company/r-consortium/](https://www.linkedin.com/company/r-consortium/) +Mastodon: [https://fosstodon.org/@RConsortium](https://fosstodon.org/@RConsortium) + +--- + +## Development Section + +## Quarto Project hosted with Netlify + +## Live site here: [https://oppkeyquarto.netlify.app/](https://oppkeyquarto.netlify.app/) + +## Running locally + +Clone repo + +Use `quarto preview` to run locally. Ensure you are in the root directory of the Quarto project where the _quarto.yml file is located. + +If you use `quarto serve` you may get the error: + +ERROR: No input passed to serve. +If you are attempting to preview a website or book use the quarto preview command instead. + +## Setup for Contributors + +Install R using sudo apt-get install r-base and sudo apt-get install r-base-dev + +Install R packages on Linux; type R in console and then install.packages('rmarkdown') + +GGPLOT2 installation: install.packages("ggplot2") + +dygraphs installation : install.packages("dygraphs") + +## Project Setup + +The .gitignore of this project is setup to ignore `_site/` and `.quarto/` + +![gitignore](image.png) + +- `_site/` is also known as `docs/` in other quarto projects + +- `_site` was specified as netlify publish directory on the website + +## Notable findings + +- Only the freeze directory is needed when hosting on netlify using the [plugin](https://github.com/quarto-dev/netlify-plugin-quarto) + +- Can use the "local only" ignoring files strategy. Each person adds `_freeze/` to the exclude file and only have one person who is reponsible for rendering and uploading to netlify + +![exclude](image-1.png) + +- When adding a new post these are the files that are added and the ones that are modified, I *manually* modified README.md and _quarto.yml + +![modified](image-2.png) + +- Second time after initial setup these are the files that need to be added, my observation from this is that it's possible that only during initial setup merge conflicts are a problem due to `site_libs/` directory. I think `site_libs/` is modified only when someone sets up quarto. I can try git_ignoring that directory and see if it causes a build failure or not on netlify. Maybe when someone is setting up R and the libraries on their computer it downloads and modifies this directory. + +![sitelibs](image-3.png) + +![sitelib2](image-4.png) diff --git a/_freeze/posts/Slides-Post/index/execute-results/html.json b/_freeze/posts/Slides-Post/index/execute-results/html.json new file mode 100644 index 0000000..c88bd9a --- /dev/null +++ b/_freeze/posts/Slides-Post/index/execute-results/html.json @@ -0,0 +1,18 @@ +{ + "hash": "dc5c034a21ea83b8633e4ba12d88926c", + "result": { + "markdown": "---\ntitle: \"Regulatory Repositories\"\nauthor:\n - name: Coline Zeballos\n affiliations: \n - name: Roche\n - name: Yann Féat\n affiliations:\n - name: mainanalytics\nformat: revealjs\n---\n\n\n## Introduction\n\n- R has a meticulously maintained ecosystem, which is immensely valuable in a regulatory space\n- In a regulatory setting, the trust of any software needs to be thoroughly documented (NOTE: replace with more precise wording based on HA documents)\n\n::: {.notes}\nColine\n:::\n\n## Goals\n\n- Provide a community-maintained catalog of package quality indicators (\"risk metrics\")\n- Serve quality indicators in a standard format\n- Thoroughly document the system used to perform quality assessment\n- Demonstrate how regulatory-ready risk assessments can be provided using public quality indicators\n- Serve subsets of packages that conform to a specified risk tolerance\n- Improve transparency of industry R package adoption, endorsement and regulator interaction\n\n::: {.notes}\nColine\n:::\n\n## An evolving R ecosystem\n\n- (NOTE: show interaction between CRAN, RVH Reg R Repo (us), RC Submissions WG, RC Repositories WG, pharmaverse, other?)\n\n# Interacting with the repo\n\n## Packages risk filters\n\n::: columns\n::: {.column width=\"50%\"}\n- Helper package for system administrators\n- Restricts packages available for installation to those fitting in a policy\n- Uses packages metadata in the repo\n- May be use together with manual checks (e.g. read a statistical review)\n:::\n::: {.column width=\"50%\"}\n- Example of automated filter for safety-critical activities:\n - Acceptance Criteria 1: “Code Coverage > 95% ”\n - Acceptance Criteria 2: “Package documentation available”\n:::\n:::\n\n::: {.notes}\nYann\n:::\n\n## Usage\n\n\n::: {.cell}\n\n:::\n\n\n::: columns\n::: {.column width=\"40%\"}\n### Unfiltered\n\n::: {.cell}\n\n```{.r .cell-code}\navailable.packages()\n```\n:::\n\n:::\n\n::: {.column width=\"60%\"}\n### Filtered\n\n::: {.cell}\n\n```{.r .cell-code}\nfltr <- risk_filter(\n ReverseDependencies >= 0.99)\noptions(available_packages_filters = fltr)\navailable.packages()\n```\n:::\n\n:::\n:::\n\n::: {.notes}\nYann\n:::\n\n# Repository ‘back-end’\n\n## Repository forked from `r-hub/repos`\n\n![](resources/repos_pkgs.png)\n\n::: {.notes}\nYann\n:::\n\n## Packages cohort validation\n\n* Risk metrics calculated on packages with new versions and on their reverse dependencies\n* Uses the GitHub API to fetch new release assets\n\n\n::: {.notes}\nYann\n:::\n\n# Our roadmap\n\n## What's next\n\n* (NOTE: STAGE 1: Pipeline Integration)\n\n# Closing\n\n## Join us\n\n* (NOTE: link to GH join us issue, add R Consortium info)\n\n## Why Join the R Consortium\n* Community Leadership and Support\n* Funding Key Infrastructure and Projects\n* Influence Over Project Development\n![Elephant](elephant.png){width=300}\n\n## Thank you\n\n* (NOTE: List of Core team members)\n", + "supporting": [], + "filters": [ + "rmarkdown/pagebreak.lua" + ], + "includes": { + "include-after-body": [ + "\r\n\r\n\r\n" + ] + }, + "engineDependencies": {}, + "preserve": {}, + "postProcess": true + } +} \ No newline at end of file diff --git a/_freeze/posts/eriks-cool-post/index/execute-results/html.json b/_freeze/posts/eriks-cool-post/index/execute-results/html.json new file mode 100644 index 0000000..e54a028 --- /dev/null +++ b/_freeze/posts/eriks-cool-post/index/execute-results/html.json @@ -0,0 +1,20 @@ +{ + "hash": "b7a987f13e1e0b0853fadd7c96d0dad5", + "result": { + "markdown": "---\ntitle: \"My Cool Post\"\ndescription: \"R Code for Pharma\"\nauthor: \"Erik Rodriguez\"\ndate: \"10/03/2023\"\n---\n\n\n[Ivan Millanes](https://www.linkedin.com/in/ivan-millanes-a0b574155/?trk=pub-pbmap&originalSubdomain=ar) from the [R en Rosario](https://www.meetup.com/r-en-rosario/members/?op=leaders) recently talked to the R-Consortium. He shared the group’s vision to create an inclusive knowledge-sharing platform for a diverse R community in Rosario. In Argentina, the group welcomes participants and speakers at all experience levels. Ivan also uses R at work and builds Shiny applications for the pharmaceutical industry. \n\n![](https://www.r-consortium.org/wp-content/uploads/sites/13/2023/08/image.jpeg)\n\nIvan co-organizes R en Rosario and is one of the group’s founding members. He completed his Bachelor’s in Statistics at the National University of Rosario. Not to mention, Ivan has achieved multiple certifications in Machine Learning. Currently, he works as a R/Shiny developer at Appsilon. \n\n\n**_Please share your background and involvement with the RUGS group._**\n\n \nMy educational background is in Mathematics and Statistics. I first used R around six years ago during my studies and have since gained experience in R through different jobs. I have worked in various industries like marketing, healthcare, and insurance. I am currently working in the Pharmaceutical industry. \n\n![](https://www.r-consortium.org/wp-content/uploads/sites/13/2023/08/image-2.png)\n\n_R en Rosario Founding Members_\n\nWe started the R en Rosario User Group a couple of years ago, Argentina’s first R User Group. Later, other cities also started their R Users Groups, e.g., [Buenos Aires](https://www.r-consortium.org/blog/2022/12/15/r-en-buenos-aires-in-2023-compiling-a-list-of-latin-american-r-packages). We hosted a few virtual meetings during the pandemic but stopped after a few months. Now that everything is returning to normal, we plan to resume our meetings. We would like to host speakers from different industries who use R for their work. A networking session would follow these talks. \n\n\n**_What industry are you currently in? How do you use R in your work?_**\n\nI currently work in Pharma, where we develop [Shiny](https://shiny.posit.co/) applications using R.\n\nThe applications we develop have a similar workflow: we connect to SQL databases and produce some outputs the business needs in the form of PDFs or Word documents based on user choices for different parameters.\n\nWe use the [Rhino](https://cran.r-project.org/web/packages/rhino/index.html) package from [Appsilon](https://appsilon.com/) to develop the applications, as it provides a great framework for developing high-quality applications. We also use:\n\n- [R Markdown](https://rmarkdown.rstudio.com/) and [officer](https://cran.r-project.org/web/packages/officer/index.html) to generate PDF and Word reports from the app\n- [ggplot](https://ggplot2.tidyverse.org/) to create plots\n- [tidyverse](https://www.tidyverse.org/) packages (such as [dplyr](https://dplyr.tidyverse.org/)) to process data\n\nOne application we developed generates annual reports of different incidents in the laboratory. Before we developed the application, this process was manual and took time. With this app, they have a relatively simple interface where they can select the data they want to see in the report. They can download the reports and also get it sent to their system.\n\n**_Why do industry professionals come to your user group? What is the benefit for attending?_**\n\nPeople from a diverse range of backgrounds attend our meetups. Some government officials use R to analyze traffic data for public services. Some people from the farming industry use R to interpret satellite images to understand crops. \n\nEven though statisticians founded this group, its purpose is to provide a platform for people from various backgrounds to learn R and use it for their work. We usually have around 20-30 people attending our meetups, and different companies provide space to host our meetups.\n\nNetworking is an important part of our meetups, allowing members to learn more about each other. \n\nWe also do not have any limit on the topics for these talks, and anyone who feels like sharing their work in R with the audience can give a talk. So everyone, at any experience level, is more than welcome to give a speech. We are not experts and are not looking for only experts to give talks. The idea is for people from different backgrounds to come together and learn from each other. \n\n![](https://www.r-consortium.org/wp-content/uploads/sites/13/2023/08/image-1.png)\n\n_R en Rosario Meeting Hosted by a Company_\n\n\n``` yaml\n---\ntitle: \"An Example Using the Tufte Style\"\nauthor: \"John Smith\"\nformat:\n html:\n grid:\n margin-width: 350px # <1>\n pdf: default\nreference-location: margin # <2>\ncitation-location: margin # <2>\n---\n```\n\nCool.\n\n\n# Figures\n\n## Margin Figures\n\nImages and graphics play an integral role in Tufte's work. To place figures in the margin you can use the **Quarto** chunk option `column: margin`. For example:\n\n\n::: {.cell .column-margin}\n\n```{.r .cell-code}\nlibrary(ggplot2)\nmtcars2 <- mtcars\nmtcars2$am <- factor(\n mtcars$am, labels = c('automatic', 'manual')\n)\nggplot(mtcars2, aes(hp, mpg, color = am)) +\n geom_point() + geom_smooth() +\n theme(legend.position = 'bottom')\n```\n\n::: {.cell-output-display}\n![MPG vs horsepower, colored by transmission.](index_files/figure-html/fig-margin-1.png){#fig-margin width=672}\n:::\n:::\n\n\nNote the use of the `fig-cap` chunk option to provide a figure caption. You can adjust the proportions of figures using the `fig-width` and `fig-height` chunk options. These are specified in inches, and will be automatically scaled down to fit within the handout margin.\n\n## Arbitrary Margin Content\n\nYou can include anything in the margin by places the class `.column-margin` on the element. See an example on the right about the first fundamental theorem of calculus.\n\n::: column-margin\nWe know from *the first fundamental theorem of calculus* that for $x$ in $[a, b]$:\n\n$$\\frac{d}{dx}\\left( \\int_{a}^{x} f(u)\\,du\\right)=f(x).$$\n:::\n\n\nYou can also add interactive plots. For example:\n\n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(dygraphs)\ndygraph(nhtemp) %>% \n dyRangeSelector(dateWindow = c(\"1920-01-01\", \"1960-01-01\"))\n```\n\n::: {#fig-temperatures-atTop .cell-output-display}\n```{=html}\n
\n\n```\n\n\nNew Haven Temperatures\n:::\n:::\n\n\n\n## Full Width Figures\n\nYou can arrange for figures to span across the entire page by using the chunk option `fig-column: page-right`.\n\n\n::: {.cell fig-column='page-right'}\n\n```{.r .cell-code}\nggplot(diamonds, aes(carat, price)) + geom_smooth() +\n facet_grid(~ cut)\n```\n\n::: {.cell-output-display}\n![A full width figure.](index_files/figure-html/fig-fullwidth-1.png){#fig-fullwidth width=1056}\n:::\n:::\n\n\nOther chunk options related to figures can still be used, such as `fig-width`, `fig-cap`, and so on. For full width figures, usually `fig-width` is large and `fig-height` is small. In the above example, the plot size is $11 \\times 3$.\n\n## Arbitrary Full Width Content\n\nAny content can span to the full width of the page, simply place the element in a `div` and add the class `column-page-right`. For example, the following code will display its contents as full width.\n\n``` md\n::: {.fullwidth}\nAny _full width_ content here.\n:::\n```\n\nBelow is an example:\n\n::: column-page-right\n*R is free software and comes with ABSOLUTELY NO WARRANTY.* You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see