diff --git a/paper.bib b/paper.bib index 498442d..f0f2391 100644 --- a/paper.bib +++ b/paper.bib @@ -1,5 +1,5 @@ @article{goring2015neotoma, - title={{neotoma}: A programmatic interface to the Neotoma Paleoecological Database}, + title={{neotoma}: A programmatic interface to the {N}eotoma {P}aleoecological {D}atabase}, 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}, @@ -10,7 +10,7 @@ @article{goring2015neotoma } @article{byun2021extensive, -title={Extensive wetland development in mid-latitude North America during the B{\o}lling--Aller{\o}d}, +title={Extensive wetland development in mid-latitude {N}orth {A}merica during the {B}{\o}lling--{A}ller{\o}d}, author={Byun, Eunji and Sato, Hiromitsu and Cowling, Sharon A and Finkelstein, Sarah A}, journal={Nature Geoscience}, volume={14}, @@ -22,7 +22,7 @@ @article{byun2021extensive } @article{kujawa2016effects, -title={The effects of anthropogenic land cover change on pollen-vegetation relationships in the American Midwest}, +title={The effects of anthropogenic land cover change on pollen-vegetation relationships in the {A}merican {M}idwest}, 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}, @@ -45,7 +45,7 @@ @article{wang2023plants } @article{uhen2021earthlife, -title={The EarthLife Consortium API: an extensible, open-source service for accessing fossil data and taxonomies from multiple community paleodata resources}, +title={The {E}arth{L}ife {C}onsortium {API}: an extensible, open-source service for accessing fossil data and taxonomies from multiple community paleodata resources}, author={Uhen, Mark D and Buckland, Philip I and Goring, Simon J and Jenkins, Julian P and Williams, John W}, journal={Frontiers of Biogeography}, volume={13}, @@ -63,7 +63,7 @@ @Manual{oksanen2022vegan } @article{williams2018neotoma, - title={The Neotoma Paleoecology Database, a multiproxy, international, community-curated data resource}, + title={The {N}eotoma {P}aleoecology {D}atabase, 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 Ashworth, Allan C. and Betancourt, Julio L. and @@ -86,7 +86,7 @@ @article{williams2018neotoma @book{goring2018nexus, place={Cambridge}, series={Elements of Paleontology}, - title={The Neotoma Paleoecology Database: A Research Outreach Nexus}, + title={The {N}eotoma {P}aleoecology {D}atabase: 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.}, @@ -113,7 +113,7 @@ @Article{wickham2019tidyverse @misc{Goring2023APD, author = {Goring, Simon J and Dominguez Vidaña, Socorro}, -title = {Neotoma Workshops APD Release}, +title = {Neotoma Workshops {APD} Release}, year = {2023}, publisher = {GitHub}, journal = {GitHub repository}, @@ -122,7 +122,7 @@ @misc{Goring2023APD } @article{grimm2008neotoma, - title={Neotoma: an ecosystem database for the Pliocene, Pleistocene, and Holocene}, + title={Neotoma: an ecosystem database for the {P}liocene, {P}leistocene, and {H}olocene}, author={Grimm, EC}, journal={Illinois State Museum Scientific Papers E Series}, volume={1}, @@ -131,7 +131,7 @@ @article{grimm2008neotoma @misc{goring2023api, author = {Goring, Simon J}, -title = {Neotoma Paleoecology Database API}, +title = {{N}eotoma {P}aleoecology {D}atabase API}, year = {2023}, publisher = {GitHub}, journal = {GitHub repository}, diff --git a/paper.md b/paper.md index d46a0d3..c16d812 100644 --- a/paper.md +++ b/paper.md @@ -33,9 +33,9 @@ The `neotoma2` R package has been under dynamic development for over a year, but # Statement of Need -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]. Additionally, the original v1.0 API that was accessed by the `neotoma` pacakge was deprecated in 2020, meaning the `neotoma` package could no longer access data from Neotoma. +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]. Additionally, the original v1.0 API that was accessed by the `neotoma` package was deprecated in 2020, meaning the `neotoma` package could no longer access data from Neotoma. -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 methods and data objects that are suited to piping using the `%>%` (or `|>`) pipe convention and with implementations for filtering and other common `dplyr` methods. The package also now uses "long" `data.frames` and `tibbles` by default, using the `toWide()` function to transform data into "wide" tables for use with common ecological data packages such as `vegan` [@oksanen2022vegan]. Data objects in the `neotoma2` package now more closely resemble the underlying data model within Neotoma (https://open.neotomadb.org/db_schema) than in the previous package. 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. +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. The `neotoma2` package conforms to a `tidyverse` [@wickham2019tidyverse] approach for data management, with methods and data objects that are suited to piping using the `%>%` (or `|>`) pipe convention and with implementations for filtering and other common `dplyr` methods. The package also now uses "long" `data.frames` and `tibbles` by default, using the `toWide()` function to transform data into "wide" tables for use with common ecological data packages such as `vegan` [@oksanen2022vegan]. Data objects in the `neotoma2` package now more closely resemble the underlying data model within Neotoma (https://open.neotomadb.org/dbschema) than in the previous package. 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. Data from the Neotoma Database can be accessed through the public API (https://api.neotomadb.org) or a PostgreSQL database snapshot with a database client [@williams2018neotoma; https://www.neotomadb.org/data/db-snapshots] or through the EarthLife Consortium API [@uhen2021earthlife]. The R package will simplify many of the operations required to assemble and manipulate datasets, and provides functions that support researchers as part of their analytic workflows by linking Neotoma directly to packages within R used for ecological and earth science research, data visualization and statistical analysis.