Cleaning up the repo with new pubs and some markdown changes.

Added a set of publications to paper.bib and added DOIs where neccessary. Fixed those references in the paper.md file.
Added affiliations for researchers in the md file.
Removed LICENSE to keep the LICENSE.md file.

.github/workflows/draft-pdf.yml

@@ -1,5 +1,4 @@
 on: [push]
-
 jobs:
   paper:
     runs-on: ubuntu-latest

paper.bib

@@ -1,31 +1,79 @@
 @article{goring2015neotoma,
-  title={Neotoma: A programmatic interface to the Neotoma Paleoecological Database},
-  author={Goring, Simon and Dawson, Andria and Simpson, Gavin and Ram, Karthik and Graham, Russ and Grimm, Eric and Williams, John},
+  title={{neotoma}: A programmatic interface to the Neotoma Paleoecological Database},
+  author={Goring, Simon and Dawson, Andria and Simpson, Gavin and Ram, Karthik and Graham, Russ and Grimm, Eric and Williams, John W.},
   journal={Open Quaternary},
   volume={1},
   number={1},
   year={2015},
-  publisher={Ubiquity Press}
+  publisher={Ubiquity Press},
+  doi={10.5334/oq.ab}
+}
+
+@article{byun2021extensive,
+title={Extensive wetland development in mid-latitude North America during the B{\o}lling--Aller{\o}d},
+author={Byun, Eunji and Sato, Hiromitsu and Cowling, Sharon A and Finkelstein, Sarah A},
+journal={Nature Geoscience},
+volume={14},
+number={1},
+pages={30--35},
+year={2021},
+publisher={Nature Publishing Group UK London},
+doi={10.1038/s41561-020-00670-4}
+}
+
+@article{kujawa2016effects,
+title={The effects of anthropogenic land cover change on pollen-vegetation relationships in the American Midwest},
+author={Kujawa, Ellen Ruth and Goring, Simon and Dawson, Andria and Calcote, Randy and Grimm, Eric C and Hotchkiss, Sara C and Jackson, Stephen T and Lynch, Elizabeth A and McLachlan, Jason and St-Jacques, Jeannine-Marie and {Umbanhowar Jr.}, Charles and Williams, John W.},
+journal={Anthropocene},
+volume={15},
+pages={60--71},
+year={2016},
+publisher={Elsevier},
+doi={10.1016/j.ancene.2016.09.005}
+}
+
+@article{wang2023plants,
+title={Plants maintain climate fidelity in the face of dynamic climate change},
+author={Wang, Yue and Pineda-Munoz, Silvia and McGuire, Jenny L},
+journal={Proceedings of the National Academy of Sciences},
+volume={120},
+number={7},
+pages={e2201946119},
+year={2023},
+publisher={National Acad Sciences},
+doi={10.1073/pnas.2201946119}
 }
 
 @article{williams2018neotoma,
   title={The Neotoma Paleoecology Database, a multiproxy, international, community-curated data resource},
-  author={Williams, John W and Grimm, Eric C and Blois, Jessica L and Charles, Donald F and Davis, Edward B and Goring, Simon J and Graham, Russell W and Smith, Alison J and Anderson, Michael and Arroyo-Cabrales, Joaquin and others},
+  author={Williams, John W and Grimm, Eric C and Blois, Jessica L and Charles, Donald F and 
+  Davis, Edward B and Goring, Simon J and Graham, Russell W and Smith, Alison J and
+  Anderson, Michael and Arroyo-Cabrales, Joaquin and Ashworth, Allan C. and Betancourt, Julio L. and
+  Bills, Brian W. and Booth, Robert K. and
+  Buckland, Philip I. and
+  Curry, B. Brandon and
+  Giesecke, Thomas and
+  Jackson, Stephen T. and
+  Latorre, Claudio and
+  Nichols, Jonathan and Purdum, Timshel and Roth, Robert E. and Stryker, Michael and Takahara, Hikaru},
   journal={Quaternary Research},
   volume={89},
   number={1},
   pages={156--177},
   year={2018},
-  publisher={Cambridge University Press}
+  publisher={Cambridge University Press},
+  doi={10.1017/qua.2017.105}
 }
 
-@InBook{Goring2018a,
-title         = {The {N}eotoma {P}aleoecology {D}atabase: A research-outreach nexus.},
-year          = {2018},
-author        = {Goring, S. J. and Graham, R. and Loeffler, S. and Myrbo, A. and Ormand, C. J. and Oliver, James S., III and Williams, J. W.},
-type          = {Book Section},
-__markedentry = {[simon:6]},
-booktitle     = {Paleobiology Short Course},
+  @book{goring2018nexus,
+    place={Cambridge},
+    series={Elements of Paleontology},
+    title={The Neotoma Paleoecology Database: A Research Outreach Nexus},
+    doi={10.1017/9781108681582},
+    publisher={Cambridge University Press},
+    author={Goring, Simon James and Graham, Russell and Loeffler, Shane and Myrbo, Amy and Oliver, James S. and Ormond, Carol and Williams, John W.},
+    year={2018},
+    collection={Elements of Paleontology}
 }
 
 @Article{wickham2019tidyverse,
@@ -43,4 +91,32 @@ @Article{wickham2019tidyverse
 number = {43},
 pages = {1686},
 doi = {10.21105/joss.01686},
+}
+
+@misc{Goring2023APD,
+author = {Goring, Simon J and Dominguez Vidaña, Socorro},
+title = {Neotoma Workshops APD Release},
+year = {2023},
+publisher = {GitHub},
+journal = {GitHub repository},
+url = {https://github.com/NeotomaDB/Workshops/},
+doi = {10.5281/zenodo.7849972}
+}
+
+@article{grimm2008neotoma,
+  title={Neotoma: an ecosystem database for the Pliocene, Pleistocene, and Holocene},
+  author={Grimm, EC},
+  journal={Illinois State Museum Scientific Papers E Series},
+  volume={1},
+  year={2008}
+}
+
+@misc{goring2023api,
+author = {Goring, Simon J},
+title = {Neotoma Paleoecology Database API},
+year = {2023},
+publisher = {GitHub},
+journal = {GitHub repository},
+url = {https://github.com/NeotomaDB/api_nodetest},
+doi = {10.5281/zenodo.7893836}
 }

paper.md

@@ -8,33 +8,35 @@ tags:
   - Holocene
   - Pleistocene
 authors:
-  - name: Socorro Dominguez Vidana
+  - name: Socorro Dominguez Vidaña
     orcid: 0000-0002-7926-4935
     affiliation: 1
   - name: Simon J Goring
     orcid: 0000-0002-2700-4605
-    affiliation: 2
+    affiliation: [2, 3]
 affiliations:
-  - name: Independent Researcher
+  - name: HT Data
     index: 1
-  - name: Department of Geography; University of Wisconsin -- Madison
+  - name: Department of Geography, University of Wisconsin -- Madison
     index: 2
+  - name: Center for Climatic Research, University of Wisconsin -- Madison
+    index: 3
 date: 22 February 2022
 bibliography: paper.bib
 ---
 
 # Summary
 
-The `neotoma2` R package is a tool to access and manipulate data from the Neotoma Paleoecology Database [https://www.neotomadb.org; @williams2018neotoma] within the R environment. Neotoma is a community curated paleoecological data resource, containing over 8 million unique observations, with global coverage, from 37 constituent databases. The package uses the Neotoma API v2.0 [@goringapi] as a tool to import records from the Neotoma database, allowing researchers to examine taxonomic, spatial and temporal patterns across space and time over the last 5.4 million years. The R package allows researchers to both download, and create new records using `get_` (e.g., `get_sites()`) and `set_` functions (e.g., `set_sites()`) respectively. This provides researchers with the opportunity to develop dynamic workflows that include data generated locally, not yet uploaded to Neotoma.
+The `neotoma2` R package is a tool to access and manipulate data from the Neotoma Paleoecology Database (https://www.neotomadb.org) within the R environment. Neotoma is a community curated paleoecological data resource [@williams2018neotoma], containing nearly 9 million unique observations of paleoecological proxies with global coverage from 37 constituent databases. The package uses the Neotoma API v2.0 [@goring2023api] as a tool to import records from the Neotoma database, allowing researchers to examine taxonomic, spatial and temporal patterns across space and time over the last 5.4 million years. The R package allows researchers to download, and create new records using `get_*()` (e.g., `get_sites()`) and `set_*()` functions (e.g., `set_sites()`) respectively. This provides researchers with the opportunity to develop dynamic workflows that include data generated locally, and not yet submitted to the Neotoma database.
 
-The `neotoma2` R package has been under dynamic development for over a year, but has been used for teaching and training [@EPDref2022]. This release of the `neotoma2` R package is intended to act as a clean release of the package, with all of the core features provided.
+The `neotoma2` R package has been under dynamic development for over a year, but has been used for teaching and training [@Goring2023APD]. This release of the `neotoma2` R package is a clean release of the package, with all of the core features provided and extensive test coverage implemented.
 
 # Statement of Need
 
-The `neotoma` R package [@goring2015neotoma] leveraged the Neotoma Paleoeocology Database v1.0 API.  Changes to the underlying database requires new data objects within the R package, to more closely align to the Neotoma data model [@grimm2018]. The broad user community for Neotoma [@Williams2018a;@Goring2018a] requires a toolset that can access and manage data for each of the more than 40 dataset types within Neotoma. This package conforms to a `tidyverse` [@wickham2019tidyverse] approach for data management, with data objects that more closely resemble the underlying data model within Neotoma (https://open.neotomadb.org/db_schema).
+The `neotoma` R package [@goring2015neotoma] leveraged the Neotoma Paleoeocology Database v1.0 API and had been one of the primary tools for researchers working with data from Neotoma [@wang2023plants;@kujawa2016effects; @byun2021extensive]. Changes to the underlying database and a rebuilding of the API required new data objects within the R package to more closely align to the Neotoma data model [@grimm2008neotoma]. The broad user community for Neotoma [@williams2018neotoma; @goring2018nexus] requires a toolset that can access and manage data for each of the more than 40 dataset types within Neotoma and so extensive metadata must be accessed for each record. This package conforms to a `tidyverse` [@wickham2019tidyverse] approach for data management, with data objects that more closely resemble the underlying data model within Neotoma (https://open.neotomadb.org/db_schema). Most importantly the `neotoma2` package provides a toolset for paleoecologists, ecologists, conservation ecologists, archaeologists, and others, to access and examine the broad range of fossil data contained within the Neotoma Paleoecology Database.
 
 # Acknowledgements
 
 We acknowledge contributions from the Neotoma Paleoecology Community, the participants of our workshops for the European Pollen Database, American Quaternary Association and the International Association of Limnologists/International Paleolimnology Association, and members of the EarthCube community. This work was funded through a grant to SJG from the National Science Foundation (NSF-1948926).
 
-# References
+# References