Merge pull request #462 from hdolinh/2023-10-delta

2023 10 delta

materials/DESCRIPTION

@@ -11,12 +11,18 @@ Imports:
     curl,
     dataone,
     datapack,
+    doParallel,
     dplyr,
     DT,
     EML,
     filelock,
     forcats,
+    foreach,
+    furrr,
+    future,
+    ggiraph,
     ggplot2,
+    ggExtra,
     ggforce,
     ggmap,
     ggpmisc,
@@ -30,10 +36,13 @@ Imports:
     knitr,
     knitcitations,
     leaflet,
+    mapview,
+    palmerpenguins,
+    parallel,
     parsedate,
     pdftools,
     pins,
-    plyt,
+    plyr,
     qualtRics,
     readr,
     reshape2,
@@ -44,13 +53,14 @@ Imports:
     solrium,
     stringi,
     stringr,
+    tidycensus,
     tidyr,
     tidytext,
+    tigris,
     textdata,
     wordcloud,
     viridis,
-    xml
-
+    XML
 Remotes: 
     rstudio/bookdown
 License: Apache License (>= 2)

materials/_quarto.yml

@@ -23,27 +23,24 @@ 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/2023-10-delta
 
   chapters:
     - index.qmd # preface
-    - session_01.qmd # collaborating using git & github and merge conflicts
-    - session_02.qmd # social aspects of collaboration
-    - session_03.qmd # thinking preferences
-    - session_04.qmd # synthesis
-    - session_05.qmd # publishing to web
-    - session_06.qmd # data vis
-    - session_07.qmd # systematic reviews
-    - session_08.qmd # synthesis
-    - session_09.qmd # spatial data
-    - session_10.qmd # intro to meta-analysis
-    - session_11.qmd # text data
-    - session_12.qmd # census data
-    - session_13.qmd # reproducible surveys
-    - session_14.qmd # spatial demographis specialist
-    - session_15.qmd # synthesis
-    - session_16.qmd # shiny
-    - session_17.qmd # 2FA setup
+    - session_01.qmd # census maps
+    - session_02.qmd # message box
+    - session_03.qmd # synthesis
+    - session_04.qmd # flexdashboard
+    - session_05.qmd # shiny
+    - session_06.qmd # practice: shiny + flexdashboard using design thinking
+    - session_07.qmd # synthesis
+    - session_08.qmd # reproducible workflows using targets
+    - session_09.qmd # parallel processing
+    - session_10.qmd # synthesis
+    - session_11.qmd # publishing data
+    - session_12.qmd # git workflows
+    - session_13.qmd # synthesis
+    - session_14.qmd # presentations and wrap-up
 
 
 bibliography: book.bib

materials/book.bib

@@ -273,3 +273,35 @@ @article{michener2015
     number = {10},
 
 }
+
+@article{borowiec2023,
+    doi = {10.1371/journal.pcbi.1011251},
+    author = {Borowiec, Brittney G.},
+    journal = {PLOS Computational Biology},
+    publisher = {Public Library of Science},
+    title = {Ten simple rules for scientists engaging in science communication},
+    year = {2023},
+    month = {07},
+    volume = {19},
+    url = {https://doi.org/10.1371/journal.pcbi.1011251},
+    pages = {1-8},
+    abstract = {null},
+    number = {7},
+
+}
+
+@article{brousil2023,
+	title = {Improving ecological data science with workflow management software},
+	author = {Brousil, Matthew R. and Filazzola, Alessandro and Meyer, Michael F. and Sharma, Sapna and Hampton, Stephanie E.},
+	year = {2023},
+	month = {04},
+	date = {2023-04-23},
+	journal = {Methods in Ecology and Evolution},
+	pages = {1381--1388},
+	volume = {14},
+	number = {6},
+	doi = {10.1111/2041-210x.14113},
+	url = {http://dx.doi.org/10.1111/2041-210X.14113},
+	langid = {en}
+}
+

materials/index.qmd

@@ -19,38 +19,27 @@ The [National Center for Ecological Analysis and Synthesis (NCEAS)](https://www.
 
 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 3: Scaling up and presenting synthesis
 
-### Week 2: Open Tools for Analysis and Visualization
-
-*Aug 28 - Sep 1, 2023*
-
-- Strengthen core knowledge of version control and workflow
-- Introduce metaanalysis concepts and tools
-- Approaches for geospatial visualization
-- Data tools for qualitative data
-
+*October 23 – 27, 2023*
 
-## Schedule
 
-UPDATE IMAGE WITH WEEK 2 SCHEDULE
+- Big data workflows and parallel computing
+- Presenting results using Shiny or flexdashboards
+- Revisit reproducible and git workflows
+- Synthesis presentations and next steps
 
-:::{.column-page}
-<!--![](images/schedule.png)-->
-:::
 
 
+## Schedule
 
-## Next training
 
 
-### Week 3: Scaling up and presenting synthesis
+:::{.column-page}
+![](images/schedule.png)
+:::
 
-*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
 
 
 ## Code of Conduct
@@ -66,7 +55,7 @@ These written materials are the result of a continuous and collaborative effort
 This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
 
 
-**Citation:** Halina Do-Linh, Carmen Galaz García, Matthew B. Jones, Camila Vargas Poulsen. 2023. Open Science Synthesis training Week 2. NCEAS Learning Hub & Delta Stewardship Council.
+**Citation:** Halina Do-Linh, Matthew B. Jones, Camila Vargas Poulsen. 2023. Open Science Synthesis training Week 3. 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.
 

materials/sections/closing-materials-openS.qmd

@@ -0,0 +1,35 @@
+## Material to include:
+
+- Project Messaging
+- Methods / Analytical Process
+- Next Steps
+
+### Project Messaging
+
+Present your message box. High Level. You can structure it within the envelope style visual format or as a section based document. 
+
+Make sure to include:
+
+- Audience
+- Issue
+- Problem
+- So What?
+- Solution
+- Benefits
+
+![](images/messagebox.png)
+
+### Methods / Analytical Process
+
+Provide an update on your approaches to solving your 'Problem'. How are you tackling this? If multiple elements, describe each. Present the workflow for your synthesis.
+
+![](images/workflows.png)
+
+### Next Steps
+
+Articulate your plan for the next steps of the project. Some things to consider as you plan:
+
+<!-- - The one-day workshop is January 24th
+- January deliverables include analyses and results
+    - What needs do you anticipate for data / code support
+- Project funding ends May 2022 -->