fixing merge conflict, keeping ucsb-faculty branch version

NCEAS · Nov 13, 2023 · c7c8921 · c7c8921
2 parents 1e0c1e0 + cc5238b
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diff --git a/.github/workflows/main.yml b/.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 }}"}'
diff --git a/materials/DESCRIPTION b/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 +36,14 @@ Imports:
     knitr,
     knitcitations,
     leaflet,
+    mapview,
+    palmerpenguins,
+    parallel,
     parsedate,
     pdftools,
     pins,
-    plyt,
+    quanteda,
+    plyr,
     qualtRics,
     readr,
     reshape2,
@@ -44,13 +54,14 @@ Imports:
     solrium,
     stringi,
     stringr,
+    tidycensus,
     tidyr,
     tidytext,
+    tigris,
     textdata,
     wordcloud,
     viridis,
-    xml
-
+    XML
 Remotes: 
     rstudio/bookdown
 License: Apache License (>= 2)
diff --git a/materials/_quarto.yml b/materials/_quarto.yml
@@ -23,7 +23,7 @@ book:
       - icon: twitter
         href: https://twitter.com/ucsb_nceas
       - icon: github
-        href: https://github.com/NCEAS/nceas-training/tree/2023-08-usgs
+        href: https://github.com/NCEAS/nceas-training/tree/2023-09-ucsb-faculty
 
   chapters:
     - index.qmd # preface
@@ -39,7 +39,6 @@ book:
     - session_10.qmd # clean wrangle data
     - session_11.qmd # collab `Git` & GitHub
     - session_12.qmd # appendix: RStudio server setup + Git & GitHub setup
-
 
 bibliography: book.bib
 

diff --git a/materials/book.bib b/materials/book.bib
@@ -273,3 +273,178 @@ @article{michener2015
     number = {10},
 
 }
+
+
+@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},
+	year = {2023},
+	month = {01},
+	date = {2023-01},
+	journal = {Ecosphere},
+	volume = {14},
+	number = {1},
+	doi = {10.1002/ecs2.4342},
+	url = {http://dx.doi.org/10.1002/ecs2.4342},
+	langid = {en}
+}
+
+@article{dicks2014,
+	title = {Organising evidence for environmental management decisions: a {\textquoteleft}4S{\textquoteright} hierarchy},
+	author = {Dicks, Lynn V. and Walsh, Jessica C. and Sutherland, William J.},
+	year = {2014},
+	month = {11},
+	date = {2014-11},
+	journal = {Trends in Ecology & Evolution},
+	pages = {607--613},
+	volume = {29},
+	number = {11},
+	doi = {10.1016/j.tree.2014.09.004},
+	url = {http://dx.doi.org/10.1016/j.tree.2014.09.004},
+	langid = {en}
+}
+
+@article{hampton2011,
+	title = {Collaboration and Productivity in Scientific Synthesis},
+	author = {Hampton, Stephanie E. and Parker, John N.},
+	year = {2011},
+	month = {11},
+	date = {2011-11},
+	journal = {BioScience},
+	pages = {900--910},
+	volume = {61},
+	number = {11},
+	doi = {10.1525/bio.2011.61.11.9},
+	url = {http://dx.doi.org/10.1525/bio.2011.61.11.9},
+	langid = {en}
+}
+
+@article{carpenter2009,
+	title = {Accelerate Synthesis in Ecology and Environmental Sciences},
+	author = {Carpenter, Stephen R. and Armbrust, E. Virginia and Arzberger, Peter W. and Chapin, F. Stuart and Elser, James J. and Hackett, Edward J. and Ives, Anthony R. and Kareiva, Peter M. and Leibold, Mathew A. and Lundberg, Per and Mangel, Marc and Merchant, Nirav and Murdoch, William W. and Palmer, Margaret A. and Peters, Debra P. C. and Pickett, Steward T. A. and Smith, Kathleen K. and Wall, Diana H. and Zimmerman, Ann S.},
+	year = {2009},
+	month = {09},
+	date = {2009-09},
+	journal = {BioScience},
+	pages = {699--701},
+	volume = {59},
+	number = {8},
+	doi = {10.1525/bio.2009.59.8.11},
+	url = {http://dx.doi.org/10.1525/bio.2009.59.8.11},
+	langid = {en}
+}
+
+@article{wyborn2018,
+	title = {Understanding the Impacts of Research Synthesis},
+	author = {Wyborn, Carina and Louder, Elena and Harrison, Jerry and Montambault, Jensen and Montana, Jasper and Ryan, Melanie and Bednarek, Angela and {Nesshöver}, Carsten and Pullin, Andrew and Reed, Mark and Dellecker, Emilie and Kramer, Jonathan and Boyd, James and Dellecker, Adrian and Hutton, Jonathan},
+	year = {2018},
+	month = {08},
+	date = {2018-08},
+	journal = {Environmental Science & Policy},
+	pages = {72--84},
+	volume = {86},
+	doi = {10.1016/j.envsci.2018.04.013},
+	url = {http://dx.doi.org/10.1016/j.envsci.2018.04.013},
+	langid = {en}
+}
+
+@article{rodrigo2013,
+	title = {Science Incubators: Synthesis Centers and Their Role in the Research Ecosystem},
+	author = {Rodrigo, Allen and Alberts, Susan and Cranston, Karen and Kingsolver, Joel and Lapp, Hilmar and McClain, Craig and Smith, Robin and Vision, Todd and Weintraub, Jory and Wiegmann, Brian},
+	year = {2013},
+	month = {01},
+	date = {2013-01-15},
+	journal = {PLoS Biology},
+	pages = {e1001468},
+	volume = {11},
+	number = {1},
+	doi = {10.1371/journal.pbio.1001468},
+	url = {http://dx.doi.org/10.1371/journal.pbio.1001468},
+	langid = {en}
+}
+
+@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}
+}
+
diff --git a/materials/data/text/dsc-plan-ch8.pdf b/materials/data/text/dsc-plan-ch8.pdf
diff --git a/materials/images/SASAP-logo.jpg b/materials/images/SASAP-logo.jpg
diff --git a/materials/images/allison-horst-why-tidy-data.png b/materials/images/allison-horst-why-tidy-data.png
diff --git a/materials/images/census_geos.png b/materials/images/census_geos.png
diff --git a/materials/images/discovered_token.png b/materials/images/discovered_token.png
diff --git a/materials/images/edi_abstract_example.png b/materials/images/edi_abstract_example.png
diff --git a/materials/images/edi_ezEML_login.png b/materials/images/edi_ezEML_login.png
diff --git a/materials/images/edi_ezEML_menu.png b/materials/images/edi_ezEML_menu.png
diff --git a/materials/images/edi_landing_page.png b/materials/images/edi_landing_page.png
diff --git a/materials/images/edi_new_eml.png b/materials/images/edi_new_eml.png
diff --git a/materials/images/flexdashboard-1.png b/materials/images/flexdashboard-1.png
diff --git a/materials/images/flexdashboard-2.png b/materials/images/flexdashboard-2.png
diff --git a/materials/images/flexdashboard-publish-icon.png b/materials/images/flexdashboard-publish-icon.png
diff --git a/materials/images/furrr-logo.png b/materials/images/furrr-logo.png
diff --git a/materials/images/future-logo.png b/materials/images/future-logo.png
diff --git a/materials/images/get_decennial_message.png b/materials/images/get_decennial_message.png
diff --git a/materials/images/git-index-delta.png b/materials/images/git-index-delta.png
diff --git a/materials/images/git-workflows-merged-branch.png b/materials/images/git-workflows-merged-branch.png
diff --git a/materials/images/git-workflows-two-branches.png b/materials/images/git-workflows-two-branches.png
diff --git a/materials/images/git_sitrep.png b/materials/images/git_sitrep.png
diff --git a/materials/images/intro-to-synthesis-1.png b/materials/images/intro-to-synthesis-1.png
diff --git a/materials/images/intro-to-synthesis-2.png b/materials/images/intro-to-synthesis-2.png
diff --git a/materials/images/jarreaus_2015_goalsandmotivations.png b/materials/images/jarreaus_2015_goalsandmotivations.png
diff --git a/materials/images/knb_landing_2023.png b/materials/images/knb_landing_2023.png
diff --git a/materials/images/knb_submit_form.png b/materials/images/knb_submit_form.png
diff --git a/materials/images/logic-model-template.png b/materials/images/logic-model-template.png
diff --git a/materials/images/ohi-logo.jpg b/materials/images/ohi-logo.jpg
diff --git a/materials/images/penguins-logo.png b/materials/images/penguins-logo.png
diff --git a/materials/images/processor.png b/materials/images/processor.png
diff --git a/materials/images/processors.png b/materials/images/processors.png
diff --git a/materials/images/reproducible-workflows-targets-1.png b/materials/images/reproducible-workflows-targets-1.png
diff --git a/materials/images/reproducible-workflows-targets-2.png b/materials/images/reproducible-workflows-targets-2.png
diff --git a/materials/images/reproducible-workflows-targets-3.png b/materials/images/reproducible-workflows-targets-3.png
diff --git a/materials/images/reproducible-workflows-targets-4.png b/materials/images/reproducible-workflows-targets-4.png
diff --git a/materials/images/schedule.png b/materials/images/schedule.png
diff --git a/materials/images/serial-parallel-exec.png b/materials/images/serial-parallel-exec.png
diff --git a/materials/images/shiny-navbar-dynplot.png b/materials/images/shiny-navbar-dynplot.png
diff --git a/materials/images/shiny-navbar-empty.png b/materials/images/shiny-navbar-empty.png
diff --git a/materials/images/shiny-navbar-tab1.png b/materials/images/shiny-navbar-tab1.png
diff --git a/materials/images/shiny-navbar-tab2.png b/materials/images/shiny-navbar-tab2.png
diff --git a/materials/images/tidycensus_logo.png b/materials/images/tidycensus_logo.png
diff --git a/materials/images/tidytext-barplot.png b/materials/images/tidytext-barplot.png
diff --git a/materials/images/tidytext-logo.png b/materials/images/tidytext-logo.png
diff --git a/materials/images/tidytext-lollipopplot.png b/materials/images/tidytext-lollipopplot.png
diff --git a/materials/images/tidytext-nontidy-workflow.png b/materials/images/tidytext-nontidy-workflow.png
diff --git a/materials/images/tidytext-tidy-workflow.png b/materials/images/tidytext-tidy-workflow.png
diff --git a/materials/images/tigris_sticker.png b/materials/images/tigris_sticker.png
diff --git a/materials/images/unset_token.png b/materials/images/unset_token.png
diff --git a/materials/images/usgs-logo.png b/materials/images/usgs-logo.png
diff --git a/materials/images/vizualization-r-practice-flexdashboard-shiny-1.png b/materials/images/vizualization-r-practice-flexdashboard-shiny-1.png
diff --git a/materials/images/wf-targets-outdated.png b/materials/images/wf-targets-outdated.png
diff --git a/materials/index.qmd b/materials/index.qmd
@@ -5,6 +5,7 @@
 ::: column-margin
 ![](cover.png){width="80%" fig-align="center"}
 
+
 ![](images/logo-ucsb-office-research.png){width="80%" fig-align="center"}
 
 ![](images/logo-ucsb-library.jpg){width="80%" fig-align="center"}
@@ -15,10 +16,12 @@
 
 Hosted by the [National Center for Ecological Anlysis and Synthesis (NCEAS)](https://www.nceas.ucsb.edu/) and in partnership with [UCSB's Office of Research](https://www.research.ucsb.edu/), this seminar series is a training program where participants engage in synthesis research in a small cohort. It will equip participants with data science and team science tools, and provide them with a platform to conduct collaborative synthesis research. The overall aim is to grow cross-departmental relationships and interdisciplinary research outputs.
 
+
 ## NCEAS Expertise
 
 NCEAS, 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.
 
+
 ## Week One: Crafting Your Synthesis Research Question
 
 *September 11 - 15, 2023*
@@ -28,6 +31,7 @@ NCEAS, a research affiliate of UCSB, is a leading expert on interdisciplinary da
 -   Participants will develop research ideas and utilize environmental data science (EDS) skills to test the feasibility of the project and assess the quality of data associated with it
 -   Participants will create a Data Management Plan as a tool for adaptive research, and apply new EDS skills and tools to progress research and synthesis research products
 
+
 ### Schedule
 
 ::: column-page
@@ -36,6 +40,7 @@ NCEAS, a research affiliate of UCSB, is a leading expert on interdisciplinary da
 
 ## Full Schedule
 
+
 +-------------------------------------------------------------------+-----------------------+-----------------+-----------------+
 | Session                                                           | Dates                 | Location        | Time            |
 +===================================================================+=======================+=================+=================+
@@ -66,6 +71,7 @@ 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:** Samantha Csik, Renata Curty, Halina Do-Linh, Seth Erickson, Jon Jablonski, Camila Vargas Poulsen (2023). UCSB Faculty Seminar Series: Grow Your Data & Team Science Skills. NCEAS Learning Hub. URL learning.nceas.ucsb.edu/2023-09-ucsb-faculty.
 
 **Additional contributors:** Ben Bolker, Julien Brun, Amber E. Budden, Jeanette Clark, 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.