create 2023-08-usgs event (#323)

* add usgs logo to index page * update index text to reflect openS USGS CAP program * title change for data management session * setup chapters; update titles; add css styling sheet * include combined dmp lesson in session 2 * specify width and height styling for slide deck * remove references.bib and use book.bib instead * create test slide deck to embed in synthesis lesson * embed slide deck in session 1 * text changes
NCEAS · Jul 31, 2023 · 6b5f351 · 6b5f351
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diff --git a/materials/_quarto.yml b/materials/_quarto.yml
@@ -3,7 +3,7 @@ project:
   output-dir: _book
 
 book: 
-  title: "NCEAS Open Science Synthesis for the Delta Science Program"
+  title: "NCEAS openS for the Climate Adaptation Postdoctoral (CAP) Fellows: Future of Aquatic Flows Cohort"
   # date: "April 3, 2023"
   reader-mode: false
 
@@ -14,7 +14,7 @@ book:
   favicon: cover.png # learning hub logo
 
   sidebar:
-    title: "Course Materials"
+    title: "Session Materials"
     style: "floating"
     search: true
     tools:
@@ -23,35 +23,20 @@ book:
       - icon: twitter
         href: https://twitter.com/ucsb_nceas
       - icon: github
-        href: https://github.com/NCEAS/nceas-training/tree/2023-06-delta
+        href: https://github.com/NCEAS/nceas-training/tree/2023-08-usgs
 
   chapters:
     - index.qmd # preface
-    - session_01.qmd # rstudio server setup + mini intro to R programming
-    - session_02.qmd # git setup
-    - session_03.qmd # r intro to quarto
-    - session_04.qmd # LEGO® reproducibility activity
-    - session_05.qmd # Accesing and publishing data
-    - session_06.qmd # logic modeling
-    - session_10.qmd # synthesis
-    - session_09.qmd # data modeling essentials
-    - session_16.qmd # FAIR and CARE
-    - session_07.qmd # git and github intro
-    - session_08.qmd # programmatic data access
-    - session_13.qmd # synthesis
-    - session_11.qmd # clean and wrangle data
-    - session_12.qmd # r practice: clean and wrangling
-    - session_14.qmd # r functions
-    - session_15.qmd # r packages
-    - session_13.qmd # synthesis
-    - session_19.qmd # reproducible papers
+    - session_01.qmd # successful synthesis science
+    - session_02.qmd # data management essentials
 
 
 bibliography: book.bib
 
 format:
   html:
     theme: cosmo
+    css: style.css
     # Note HD: latex rendering issues, maybe with column-margin
   # pdf:
   #   documentclass: scrreprt

diff --git a/materials/images/usgs-logo.png b/materials/images/usgs-logo.png
diff --git a/materials/index.qmd b/materials/index.qmd
@@ -3,83 +3,63 @@
 ::: column-margin
 ![](cover.png){width="80%" fig-align="center"}
 
-![](images/delta/delta-logo.png){width="80%" fig-align="center"}
-
+![](images/usgs-logo.png){width="80%" fig-align="center"}
 :::
 
 ## About this training
 
-NCEAS Open Science Synthesis training consists of three 1-week long workshops, geared towards early career researchers. Participants engage in a mix of lectures, exercises, and synthesis research groups to undertake synthesis while learning and implementing best practices for open data science.
-
+The **NCEAS openS Program** consists of three 1-week long workshops, geared towards early career researchers. Participants engage in a mix of lectures, exercises, and synthesis research activities to conduct synthesis science and implement best practices in open data science.
 
-<!-- CoreR A five-day immersion in R programming for environmental data science. Researchers will gain experience with essential data science tools and best practices to increase their capacity as collaborators, reproducible coders, and open scientists.-->
+openS has been adapted to coincide with each USGS CAP training, for a total of four training sessions across 2 years.
 
 ## Why NCEAS
-The [National Center for Ecological Analysis and Synthesis (NCEAS)](https://www.nceas.ucsb.edu/), a research affiliate of UCSB, is a leading expert on interdisciplinary data science and works collaboratively to answer the world's largest and most complex questions. The NCEAS approach leverages existing data and employs a team science philosophy to squeeze out all potential insights and solutions efficiently - this is called [synthesis science](https://www.nceas.ucsb.edu/our-approach).
-
-NCEAS has over 25 years of success with this model among working groups and environmental professionals. Together with the Delta Science Program and the Delta Stewardship Council we are excited to pass along skills, workflows, mindsets learn throughout the years.
-
-
-## Week 1: Open Data and Synthesis
-
-*June 26-30, 2023*
-
-Learning Objectives:
-
- - Implement reproducible scientific workflows throughout all aspects of a project
- - Increase your familiarity and confidence with data science tools
- - Effectively manage and wrangle data using `tidy` data practices
- - Accessing, interpreting and developing metadata for synthesis research
- - Organize and initiate synthesis projects
-
-
-## Schedule
 
-<!--- UPDATE IMAGE WITH CLASSROOM and KEY COLORS -->
+The [National Center for Ecological Analysis and Synthesis (NCEAS)](https://www.nceas.ucsb.edu/), a research affiliate of the University of California, Santa Barbara, is a leading expert on interdisciplinary data science and works collaboratively to answer the world's largest and most complex questions. The NCEAS approach leverages existing data and employs a team science philosophy to squeeze out all potential insights and solutions efficiently - this is called [synthesis science](https://www.nceas.ucsb.edu/our-approach).
 
-:::{.column-page}
-![](images/schedule.png)
-:::
-
-
-
-## Next trainings
-
-### Week 2: Open Tools for Analysis and Visualization
+NCEAS has over 25 years of success with this model among working groups and environmental professionals, and we are excited to pass on this cumulative expertise to you.
 
-*Aug 28 - Sep 1, 2023*
+## Week One: Successful Synthesis and Data Management Best Practices
 
-- Strengthen core knowledge of version control and workflow
-- Introduce metaanalysis concepts and tools
-- Approaches for geospatial visualization
-- Data tools for qualitative data
+### Learning Objectives:
 
+-   Implement reproducible scientific workflows throughout all aspects of a project
+-   Increase your familiarity and confidence with data science tools
+-   Effectively manage and wrangle data using `tidy` data practices
+-   Accessing, interpreting and developing metadata for synthesis research
+-   Organize and initiate synthesis projects
 
-### Week 3: Scaling up and presenting synthesis
+### Schedule
 
-*October 23 – 27, 2023*
-
-- Handling missing data
-- Big data workflows and parallel computing
-- Building scientific websites with R and Shiny
-- Synthesis presentations and next steps
++-----------------+-----------------+-----------------------------------------------------------+--------------------------------------------------+
+| Date            | Time            | Session Title                                             | Lead Facilitator                                 |
++=================+=================+===========================================================+==================================================+
+| Monday 08/21    | Block 3         | Successful Synthesis Science                              | Halina Do-Linh, Data Training Program Manager    |
+|                 |                 |                                                           |                                                  |
+|                 | 1:45PM-3:15PM   |                                                           |                                                  |
++-----------------+-----------------+-----------------------------------------------------------+--------------------------------------------------+
+| Tuesday 08/22   | Block 2         | Panel for PIs: Successful Mentorship in Synthesis Science | Halina Do-Linh, Data Training Program Manager    |
+|                 |                 |                                                           |                                                  |
+|                 | 10:45AM-12:15PM |                                                           |                                                  |
++-----------------+-----------------+-----------------------------------------------------------+--------------------------------------------------+
+| Wednesday 08/23 | Block 1         | Data Management Essentials                                | Camila Vargas Poulsen, Data Training Coordinator |
+|                 |                 |                                                           |                                                  |
+|                 | 9AM-10:30AM     |                                                           |                                                  |
++-----------------+-----------------+-----------------------------------------------------------+--------------------------------------------------+
 
+: {tbl-colwidths="\[15, 25, 30, 30\]"}
 
 ## Code of Conduct
 
 By participating in this activity you agree to abide by the [NCEAS Code of Conduct](https://www.nceas.ucsb.edu/sites/default/files/2021-11/NCEAS_Code-of-Conduct_Nov2021_0.pdf).
 
-
-
 ## About this book
 
 These written materials are the result of a continuous and collaborative effort at NCEAS with the support of DataONE, to help researchers make their work more transparent and reproducible. This work began in the early 2000's, and reflects the expertise and diligence of many, many individuals. The primary authors for this version are listed in the citation below, with additional contributors recognized for their role in developing previous iterations of these or similar materials.
 
 This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
 
+**Citation:** Halina Do-Linh, Camila Vargas Poulsen. 2023. openS for USGS Climate Adaptation Postdoctoral (CAP) Fellows Program. Week One. NCEAS Learning Hub & USGS Climate Adaptation Science Centers (CASCs).
 
-**Citation:** Halina Do-Linh, Carmen Galaz García, Matthew B. Jones, Camila Vargas Poulsen. 2023. Open Science Synthesis training Week 1. NCEAS Learning Hub & Delta Stewardship Council.
-
-**Additional contributors:** Ben Bolker, Julien Brun, Amber E. Budden,  Jeanette Clark, Samantha Csik, Stephanie Hampton, Natasha Haycock-Chavez, Samanta Katz, Julie Lowndes, Erin McLean, Bryce Mecum, Deanna Pennington, Karthik Ram, Jim Regetz, Tracy Teal, Daphne Virlar-Knight, Leah Wasser.
+**Additional contributors:** Ben Bolker, Julien Brun, Amber E. Budden, Jeanette Clark, Samantha Csik, Carmen Galaz García, Stephanie Hampton, Natasha Haycock-Chavez, Matthew B. Jones, Samanta Katz, Julie Lowndes, Erin McLean, Bryce Mecum, Deanna Pennington, Karthik Ram, Jim Regetz, Tracy Teal, Daphne Virlar-Knight, Leah Wasser.
 
 This is a Quarto book. To learn more about Quarto books visit <https://quarto.org/docs/books>.
diff --git a/materials/sections/combined-dmp-metadata-publishing.qmd b/materials/sections/combined-dmp-metadata-publishing.qmd
@@ -1,7 +1,3 @@
----
-bibliography: references.bib
----
-
 ## Learning Objectives {.unnumbered}
 
 -   Understand the major components of the data life cycle and the data management plan

diff --git a/materials/sections/logic-modeling.qmd b/materials/sections/logic-modeling.qmd
@@ -1,8 +1,8 @@
 ## Learning Objectives {.unnumbered}
 
-- Provide an overview of Logic Models
-- Apply the principles of Logic Models to synthesis development
-- Refine synthesis group challenges
+-   Provide an overview of Logic Models
+-   Apply the principles of Logic Models to synthesis development
+-   Refine synthesis group challenges
 
 ## Logic Models
 
@@ -108,8 +108,8 @@ Often it is helpful to start with a brainstorming activity to list activities an
 
 Tools:
 
-- Powerpoint [logic model template](https://docs.google.com/presentation/d/1MBUy35QIAkA5FNCdRzWJM2aPaFXfUmGl/edit?usp=sharing&ouid=113328660159760492310&rtpof=true&sd=true)
-- [Mermaid flowcharts](https://mermaid.js.org/syntax/flowchart.html) embedded in [Quarto documents](https://quarto.org/docs/authoring/diagrams.html#mermaid)
+-   Powerpoint [logic model template](https://docs.google.com/presentation/d/1MBUy35QIAkA5FNCdRzWJM2aPaFXfUmGl/edit?usp=sharing&ouid=113328660159760492310&rtpof=true&sd=true)
+-   [Mermaid flowcharts](https://mermaid.js.org/syntax/flowchart.html) embedded in [Quarto documents](https://quarto.org/docs/authoring/diagrams.html#mermaid)
 
 ```{mermaid}
 flowchart LR

diff --git a/materials/session_01.qmd b/materials/session_01.qmd
@@ -1,8 +1,9 @@
 ---
-title: "RStudio Server Setup"
+title: "Successful Synthesis Science"
 title-block-banner: true
-
 ---
 
-{{< include /sections/rstudio-server-setup.qmd >}}
+<iframe class="slide-deck" src="slides/synthesis-science-slides.html"></iframe>
+
+{{< include /sections/logic-modeling.qmd >}}
 
diff --git a/materials/session_02.qmd b/materials/session_02.qmd
@@ -1,6 +1,6 @@
 ---
-title: "`Git` and GitHub Setup"
+title: "Data Management Essentials "
 title-block-banner: true
 ---
 
-{{< include /sections/git-setup.qmd >}}
+{{< include /sections/combined-dmp-metadata-publishing.qmd >}}
diff --git a/materials/slides/synthesis-science-slides.qmd b/materials/slides/synthesis-science-slides.qmd
@@ -0,0 +1,28 @@
+---
+title: "test presentation"
+author: "halina do-linh"
+format: 
+  revealjs:
+    embed-resources: true
+    controls: true
+editor: visual
+---
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into a finished presentation. To learn more about Quarto presentations see <https://quarto.org/docs/presentations/>.
+
+## Bullets
+
+When you click the **Render** button a document will be generated that includes:
+
+-   Content authored with markdown
+-   Output from executable code
+
+## Code
+
+When you click the **Render** button a presentation will be generated that includes both content and the output of embedded code. You can embed code like this:
+
+```{r}
+1 + 1
+```
diff --git a/materials/style.css b/materials/style.css
@@ -23,4 +23,27 @@ pre code {
 .aside {
   background-color: #bfbdbd;
   padding: 1em;
+}
+
+.slide-deck{
+  border: 3px solid #dee2e6;
+    border-top-color: rgb(222, 226, 230);
+    border-top-style: solid;
+    border-top-width: 3px;
+    border-right-color: rgb(222, 226, 230);
+    border-right-style: solid;
+    border-right-width: 3px;
+    border-bottom-color: rgb(222, 226, 230);
+    border-bottom-style: solid;
+    border-bottom-width: 3px;
+    border-left-color: rgb(222, 226, 230);
+    border-left-style: solid;
+    border-left-width: 3px;
+    border-image-source: initial;
+    border-image-slice: initial;
+    border-image-width: initial;
+    border-image-outset: initial;
+    border-image-repeat: initial;
+  width: 100%;
+  height: 475px;
 }