Merge pull request #473 from NCEAS/2023-08-delta

merging 2023 08 delta to have lessons developed for this training on main

.github/workflows/main.yml

@@ -7,11 +7,12 @@ on:
 jobs:
   dispatch:
     runs-on: ubuntu-latest
+
     steps:
     - name: Repository Dispatch
       uses: peter-evans/[email protected]
       with:
         token: ${{ secrets.RRCOURSE }}
         repository: nceas/repro-research-course
         event-type: quarto
-        client-payload: '{"branch": "${{ github.ref_name }}"}'
+        client-payload: '{"branch": "${{ github.ref_name }}"}'

materials/DESCRIPTION

@@ -42,6 +42,7 @@ Imports:
     parsedate,
     pdftools,
     pins,
+    quanteda,
     plyr,
     qualtRics,
     readr,

materials/_quarto.yml

@@ -3,7 +3,7 @@ project:
   output-dir: _book
 
 book: 
-  title: "NCEAS openS for the Climate Adaptation Postdoctoral (CAP) Fellows: Future of Aquatic Flows Cohort"
+  title: "NCEAS Open Science Synthesis for the Delta Science Program"
   # date: "April 3, 2023"
   reader-mode: false
 
@@ -14,7 +14,7 @@ book:
   favicon: cover.png # learning hub logo
 
   sidebar:
-    title: "Session Materials"
+    title: "Course Materials"
     style: "floating"
     search: true
     tools:
@@ -24,25 +24,28 @@ book:
         href: https://twitter.com/ucsb_nceas
       - icon: github
 
-        href: https://github.com/NCEAS/nceas-training/tree/2023-10-delta
+        href: https://github.com/NCEAS/nceas-training/tree/2023-08-delta
 
   chapters:
     - index.qmd # preface
-    - 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
-
+    - session_01.qmd # collaborating using git & github and merge conflicts
+    - session_02.qmd # publishing to web
+    - session_03.qmd # data viz
+    - session_04.qmd # Practice session
+    - session_05.qmd # synthesis: setting goals
+    - session_07.qmd # thinking preferences
+    - session_06.qmd # social aspects of collaboration
+    - session_08.qmd # synthesis: data policies
+    - session_09.qmd # synthesis
+    - session_10.qmd # spatial data
+    - session_11.qmd # census data
+    - session_12.qmd # text data
+    - session_13.qmd # reproducible surveys
+    - session_14.qmd # synthesis
+    # - session_15.qmd # synthesis
+    - session_16.qmd # shiny
+    - session_17.qmd # 2FA setup + reset token
+
 
 bibliography: book.bib
 

materials/book.bib

@@ -274,6 +274,61 @@ @article{michener2015
 
 }
 
+
+@article{farrell2022,
+	title = {Past and future uses of text mining in ecology and evolution},
+	author = {Farrell, Maxwell J. and Brierley, Liam and Willoughby, Anna and Yates, Andrew and Mideo, Nicole},
+	year = {2022},
+	month = {05},
+	date = {2022-05-18},
+	journal = {Proceedings of the Royal Society B: Biological Sciences},
+	volume = {289},
+	number = {1975},
+	doi = {10.1098/rspb.2021.2721},
+	url = {http://dx.doi.org/10.1098/rspb.2021.2721},
+	langid = {en}
+}
+
+@article{froehlich2017,
+	title = {Public Perceptions of Aquaculture: Evaluating Spatiotemporal Patterns of Sentiment around the World},
+	author = {Froehlich, Halley E. and Gentry, Rebecca R. and Rust, Michael B. and Grimm, Dietmar and Halpern, Benjamin S.},
+	editor = {Somers, Christopher M.},
+	year = {2017},
+	month = {01},
+	date = {2017-01-03},
+	journal = {PLOS ONE},
+	pages = {e0169281},
+	volume = {12},
+	number = {1},
+	doi = {10.1371/journal.pone.0169281},
+	url = {http://dx.doi.org/10.1371/journal.pone.0169281},
+	langid = {en}
+}
+
+@article{vanhoutan2020,
+	title = {Sentiment Analysis of Conservation Studies Captures Successes of Species Reintroductions},
+	author = {Van Houtan, Kyle S. and Gagne, Tyler and Jenkins, Clinton N. and Joppa, Lucas},
+	year = {2020},
+	month = {04},
+	date = {2020-04},
+	journal = {Patterns},
+	pages = {100005},
+	volume = {1},
+	number = {1},
+	doi = {10.1016/j.patter.2020.100005},
+	url = {http://dx.doi.org/10.1016/j.patter.2020.100005},
+	langid = {en}
+}
+
+
+@misc{tidycensus2021,
+	title = {tidycensus: Load US Census Boundary and Attribute Data as ’Tidyverse’ and ’Sf’ -Ready Data Frames},
+	author = {Walker, Kyle, and Matt, Herman},
+	year = {2021},
+	howpublished = "\url{https://github.com/walkerke/tidycensus.}"
+}
+
+
 @article{halpern2023,
 	title = {Priorities for synthesis research in ecology and environmental science},
 	author = {Halpern, Benjamin S. and Boettiger, Carl and Dietze, Michael C. and Gephart, Jessica A. and Gonzalez, Patrick and Grimm, Nancy B. and Groffman, Peter M. and Gurevitch, Jessica and Hobbie, Sarah E. and Komatsu, Kimberly J. and Kroeker, Kristy J. and Lahr, Heather J. and Lodge, David M. and Lortie, Christopher J. and Lowndes, Julie S. S. and Micheli, Fiorenza and Possingham, Hugh P. and Ruckelshaus, Mary H. and Scarborough, Courtney and Wood, Chelsea L. and Wu, Grace C. and Aoyama, Lina and Arroyo, Eva E. and Bahlai, Christie A. and Beller, Erin E. and Blake, Rachael E. and Bork, Karrigan S. and Branch, Trevor A. and Brown, Norah E. M. and Brun, Julien and Bruna, Emilio M. and Buckley, Lauren B. and Burnett, Jessica L. and Castorani, Max C. N. and Cheng, Samantha H. and Cohen, Sarah C. and Couture, Jessica L. and Crowder, Larry B. and Dee, Laura E. and Dias, Arildo S. and {Diaz{-}Maroto}, Ignacio J. and Downs, Martha R. and Dudney, Joan C. and Ellis, Erle C. and Emery, Kyle A. and Eurich, Jacob G. and Ferriss, Bridget E. and Fredston, Alexa and Furukawa, Hikaru and {Gagné}, Sara A. and Garlick, Sarah R. and Garroway, Colin J. and Gaynor, Kaitlyn M. and {González}, {Angélica L.} and Grames, Eliza M. and {Guy{-}Haim}, Tamar and Hackett, Ed and Hallett, Lauren M. and Harms, Tamara K. and Haulsee, Danielle E. and Haynes, Kyle J. and Hazen, Elliott L. and Jarvis, Rebecca M. and Jones, Kristal and Kandlikar, Gaurav S. and Kincaid, Dustin W. and Knope, Matthew L. and Koirala, Anil and Kolasa, Jurek and Kominoski, John S. and Koricheva, Julia and Lancaster, Lesley T. and Lawlor, Jake A. and Lowman, Heili E. and {Muller{-}Karger}, Frank E. and Norman, Kari E. A. and Nourn, Nan and {O'Hara}, Casey C. and Ou, Suzanne X. and {Padilla{-}Gamino}, Jacqueline L. and Pappalardo, Paula and Peek, Ryan A. and Pelletier, Dominique and Plont, Stephen and Ponisio, Lauren C. and {Portales{-}Reyes}, Cristina and Provete, Diogo B. and Raes, Eric J. and {Ramirez{-}Reyes}, Carlos and Ramos, Irene and Record, Sydne and Richardson, Anthony J. and {Salguero{-}Gómez}, Roberto and Satterthwaite, Erin V. and Schmidt, {Chloé} and Schwartz, Aaron J. and See, Craig R. and Shea, Brendan D. and Smith, Rachel S. and Sokol, Eric R. and Solomon, Christopher T. and Spanbauer, Trisha and Stefanoudis, Paris V. and Sterner, Beckett W. and Sudbrack, Vitor and Tonkin, Jonathan D. and Townes, Ashley R. and Valle, Mireia and Walter, Jonathan A. and Wheeler, Kathryn I. and Wieder, William R. and Williams, David R. and Winter, Marten and Winterova, Barbora and Woodall, Lucy C. and Wymore, Adam S. and Youngflesh, Casey},

materials/index.qmd

@@ -3,36 +3,51 @@
 ::: column-margin
 ![](cover.png){width="80%" fig-align="center"}
 
-![](images/usgs-logo.png){width="80%" fig-align="center"}
+![](images/delta/delta-logo.png){width="80%" fig-align="center"}
 :::
 
 ## About this training
 
-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.
+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 activities to conduct synthesis science and implement best practices in open data science.
 
-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 2: Open Tools for Analysis and Visualization
+
+*Aug 28 - Sep 1, 2023*
+
+- Strengthen core knowledge of version control and workflow
+- Approaches for data visualization including geospatial data
+- Data tools for qualitative data
+- Building scientific websites with R and Shiny 
+
+## Schedule
+
+:::{.column-page}
+![](images/schedule.png)
+:::
+
+
+## Next training
+
 ### Week 3: Scaling up and presenting synthesis
 
 *October 23 – 27, 2023*
 
-
 - Big data workflows and parallel computing
+- GitHub Workflows
 - Presenting results using Shiny or flexdashboards
 - Revisit reproducible and git workflows
 - Synthesis presentations and next steps
 
 
-
-## Schedule
-
-
 ## 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).