Merge pull request #53 from Openscapes/julie-epa-june

Julie updates June 2024 to prep EPA PDF

_quarto.yml

@@ -63,11 +63,11 @@ website:
         contents:
          - href: "additional-lessons/code-of-conduct.qmd"
            text: Code of Conduct
-         - href: "additional-lessons/r-for-scicomm.qmd"  
-           text: R for SciComm
+         - href: "additional-lessons/reporting-scicomm.qmd"  
+           text: Reporting and SciComm
          - href: "additional-lessons/documentation.qmd"  
            text: Documentation
-      - community-lessons/index.qmd
+      - forked-lessons/index.qmd
       - section: how-do-i/index.qmd
         contents:        
          - href: "how-do-i/setup-rstudio-github.qmd"   

additional-lessons/reporting-scicomm.qmd

@@ -0,0 +1,23 @@
+---
+title: Quarto/RMarkdown for reporting & science communication
+---
+
+We can use Quarto and RMarkdown as powerful tools for reporting and science communication. So much potential for public communication, lab protocols and documents, etc. with R and Python workflows.
+
+We've talked and taught about this in different places: 
+
+- [Documenting things: openly for future us](https://openscapes.github.io/documenting-things/#/title-slide) - September 19, 2023, at posit::conf(2023) shared practical tips and repeatable strategies (from impact of NASA Openscapes & beyond)
+- [Data science as an entryway to open publishing](https://docs.google.com/presentation/d/1Jv0akRHEnjG_4t_9P7t93682BCBJskYnRu_7EnaeDQI/edit?usp=sharing) - May 27, 2020: Fireside Chat co-presented with Dr. Nick Tierney at Open Publishing Fest.
+- These 2019 Champions [slides](https://docs.google.com/presentation/d/1efJj7Dxg_g4ZRZT2b1agDQrT3DN5lVcNvv25IWcyGlw/edit?usp=sharing) show some early descriptions for teaching  
+
+
+## Further resources
+
+Strategies with RMarkdown also apply to Quarto
+
+- [RMarkdown](https://rmarkdown.rstudio.com) - RStudio (2021)
+- [How I teach RMarkdown](https://www.apreshill.com/blog/2020-05-how-i-teach-r-markdown/) - Hill (2020)
+- [R Markdown for scientists](https://rmd4sci.njtierney.com) - Tierney (2020)
+- [R for Excel Users](https://rstudio-conf-2020.github.io/r-for-excel) - Lowndes & Horst (2020)
+- [RMarkdown website tutorial](http://jules32.github.io/rmarkdown-website-tutorial) - Lowndes (2016) 
+- [Academic Publications with R Markdown](https://danovando.github.io/publications-with-rmarkdown/presentations/pubs-with-rmarkdown#9)- Ovando 2020

core-lessons/better-science.qmd

@@ -5,7 +5,7 @@ aliases:
   - ../better-science.html    
 ---
 
-Better science is less time is science that is more efficient, reproducible, open, inclusive, and kind. There are growing examples of better science in less time in environmental and Earth science, and beyond, including [Our path to better science in less time using open data science tools](https://www.nature.com/articles/s41559-017-0160) (Lowndes et al. 2017).
+Better science is less time is science that is more efficient, reproducible, open, inclusive, and kind. There are growing examples of better science in less time in environmental and Earth science, and beyond, including from the Ocean Health Index team: [Our path to better science in less time using open data science tools](https://www.nature.com/articles/s41559-017-0160) (Lowndes et al. 2017).
 
 ::: {.callout-warning icon="false"}
 ## Slides
@@ -18,25 +18,26 @@ Better science is less time is science that is more efficient, reproducible, ope
 
 [Better science for future us](https://youtu.be/gIvvzp7d9CQ?feature=shared&t=1) (22 min). Julie Lowndes shares part of her path to open science with the Ocean Health Index and Openscapes Champions success stories from 3 NOAA Fisheries teams 1) at the end of their cohort; 2) 2 months after their cohort; 3) several years after their cohort.
 
-[First Forays into the Cloud](https://youtu.be/2Yd0eR6M04Y) (19 min), by [Aronne Merrelli](https://clasp.engin.umich.edu/people/aronne-merrelli/) to the 2024 Cohort of NASA Openscapes Champions. Aronne is Assistant Research Scientist at the University of Michigan College of Engineering (Climate and Space Sciences and Engineering) and a 2023 NASA Openscapes Champion.
+[First Forays into the Cloud](https://youtu.be/2Yd0eR6M04Y) (19 min), by Aronne Merrelli to the 2024 Cohort of NASA Openscapes Champions. Aronne is Assistant Research Scientist at the University of Michigan College of Engineering (Climate and Space Sciences and Engineering) and a 2023 NASA Openscapes Champion.
 
 [My path to open science](https://youtu.be/AouW9A9QpVk) (7 min), by Stefanie Butland, Openscapes Team Member
 :::
 
 ::: {.callout-warning icon="false" collapse="true"}
 ## Additional slides
+
 These slides were contributed by guest instructors.
 
-[Empowering transformational science](https://docs.google.com/presentation/d/1SUMiQg0HhD19H-D6DDzTrFQVzub0kOINwJBG59uQCTw/edit#slide=id.p1) - [Dr. Chelle Gentemann](https://twitter.com/ChelleGentemann)
-::: 
+[Empowering transformational science](https://docs.google.com/presentation/d/1SUMiQg0HhD19H-D6DDzTrFQVzub0kOINwJBG59uQCTw/edit#slide=id.p1) - Dr. Chelle Gentemann
+:::
 
-Here we also introduce the [**Pathways concept**](/core-lessons/pathways.qmd) that teams will develop throughout the Champions program. The Pathway is based on Table 1 in Lowndes et al. 2017, and helps teams deliberately identify data workflow practices and next steps to facilitate efficiency and open culture in terms of reproduciblity, collaboration, communication, and culture.
+Here we also introduce the [**Pathways concept**](/core-lessons/pathways.qmd) that teams will develop throughout the Champions program. The Pathway is based on Table 1 in Lowndes et al. 2017, and helps teams deliberately identify data workflow practices and next steps to facilitate efficiency and open practices in terms of reproduciblity, collaboration, communication, and culture.
 
----
+------------------------------------------------------------------------
 
 ## Pathways to better science in less time {#pathways-better-science}
 
-[Figure 1](https://www.nature.com/articles/s41559-017-0160) of Lowndes et al. 2017 shows that open data science tools increased the ease of reproducibility and the ease of collaboration for the Ocean Health Index (OHI) team. But it was not the tools alone - it was the process the team co-created and prioritized.
+[Figure 1](https://www.nature.com/articles/s41559-017-0160/figures/1) of Lowndes et al. 2017 shows that open data science tools increased the ease of reproducibility and the ease of collaboration for the Ocean Health Index (OHI) team. But it was not the tools alone - it was the process the team co-created and prioritized.
 
 ### Create space
 
@@ -68,16 +69,16 @@ For the OHI team, we asked how to make sure everyone can participate as they nee
 
 Changing behavior/habits takes time, and is messy. Here is part of the story:
 
-![](images/ohi-transition-github.png){fig-align="center" width="376"}
+![Ocean Health Index (OHI) team's transition of code and shifting communication to GitHub](images/ohi-transition-github.png){fig-align="center" width="80%"}
 
 ## Ocean Health Index: behind the scenes
 
-Some key points to discuss from [Lowndes *et al. 2017, Nature Ecology & Evolution*: Our path to better science in less time using open data science tools](https://www.nature.com/articles/s41559-017-0160):
+Some key points to discuss from [Our path to better science in less time using open data science tools](https://www.nature.com/articles/s41559-017-0160) (Lowndes et al. 2017):
 
 -   Reproducibility & communication enabled by open tooling
 -   Shared practices are useful beyond shared projects
 
-If you're interested in more overview of the OHI setup, see this 2017 talk (25 mins): [OHI Better science in less time](https://www.youtube.com/watch?v=x4uzVAZvFCA)
+If you're interested in more overview of the OHI setup, see this 2017 talk (25 mins): [OHI Better science in less time](https://www.youtube.com/watch?v=x4uzVAZvFCA) or this 2021 Plenary at [Better Science for Future Us](https://docs.google.com/presentation/d/1HGw4P095-lblHiGQHXYidHiVysjrPxuojxTxKtE13vk/edit) at the inaugural Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology [SORTEE conference](https://www.sortee.org/events/) (30 minutes) ([video](https://osf.io/47req)).
 
 ### OHI pathway
 
@@ -89,12 +90,12 @@ If you're interested in more overview of the OHI setup, see this 2017 talk (25 m
 
 ### Reproducibility & communication enabled by open tooling
 
-RMarkdown to reimagine data analysis and communication. RMarkdown combines analyses & figures together, rendered to your reporting output of choice.
+RMarkdown/Quarto to reimagine data analysis and communication. RMarkdown/Quarto combines analyses & figures together, rendered to your reporting output of choice.
 
 An example: <http://ohi-science.org/betterscienceinlesstime/>
 
 -   Website built with R/RMarkdown & Github\
--   You can get started too: ([1-hour tutorial](https://jules32.github.io/rmarkdown-website-tutorial/))
+-   You can get started too: [1-hour RMarkdown tutorial](https://jules32.github.io/rmarkdown-website-tutorial/); [Quarto website tutorial](https://openscapes.github.io/quarto-website-tutorial/)
 
 ### Shared workflows not only useful for shared projects
 
@@ -117,26 +118,19 @@ And, critically:
 Here are a few examples to showcase what is possible and being done by the community.
 
 -   [Regime Shifts in R & Data Science within the BC Public Service Observations from the field](https://stephhazlitt.github.io/regime-shifts/slides#1) - Stephanie Hazlitt, Government of British Columbia, slides from CascadiaRconf keynote
--   [NMFSReports: Easily write NOAA reports and tech memos in R Markdown!](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/blob/main/presentations/2021-06-05%20NMFSReports%20-%20R%20Cascadia%20Conf.pdf) - Emily Markowitz, NOAA Alaska Fisheries Science Center, slides from CascadiaRconf talk
+-   [NMFSReports: Easily write NOAA reports and tech memos in R Markdown](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/blob/main/presentations/2021-06-05NMFSReports-RCascadiaConf.pdf)! - Emily Markowitz, NOAA Alaska Fisheries Science Center, slides from CascadiaRconf talk
 -   [Automated reporting in Tampa Bay with open science](https://www.openscapes.org/blog/2020/11/16/tampa-bay-reporting/) - Marcus Beck, Tampa Bay Estuary Program, Openscapes blog
     -   [TBEP's Data Management Workflow](https://tbep-tech.github.io/data-management-sop/workflow.html) and open science cake
--   [Regime Shifts in R & Data Science within the BC Public Service](https://stephhazlitt.github.io/regime-shifts/slides#1) - Steph Hazlitt CascadiaR keynote ([tweet](https://twitter.com/stephhazlitt/status/1401222464156299266))
 
 ## Further resources
 
 ### Not so standard deviation podcast
 
-Parker & Peng\
-<http://nssdeviations.com>\
-Great discussions about data concepts and "in the wild"\
-[Episode 9: Spreadsheet drama](http://nssdeviations.com/episode-9-spreadsheet-drama)
+Parker & Peng, <http://nssdeviations.com>. Great discussions about data concepts and "in the wild". Start with [Episode 9: Spreadsheet drama](http://nssdeviations.com/episode-9-spreadsheet-drama)
 
 ### Practical computing for biologists
 
-Haddock & Dunn\
-<http://practicalcomputing.org/>\
-Software & computing concepts already on your computer\
-Chapter 2: Regular expressions
+Haddock & Dunn, [http://practicalcomputing.org](http://practicalcomputing.org/){.uri}. Software & computing concepts already on your computer. Start with Chapter 2: Regular expressions
 
 ```{=html}
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