Merge pull request #16 from mikemahoney218/joss_revision

Fix bibtex: add DOIs and ISBNs, remove duplicate entry, cite books

paper/fqar_refs.bib

@@ -51,6 +51,7 @@ @article{matthews2015null
 	publisher = {Elsevier},
 	title = {A null model test of Floristic Quality Assessment: Are plant species' Coefficients of Conservatism valid?},
 	url = {https://doi.org/10.1016/j.ecolind.2014.11.017},
+        doi = {10.1016/j.ecolind.2014.11.017},
 	volume = {52},
 	year = {2015}}
 
@@ -62,19 +63,12 @@ @article{bourdaghs2006properties
 	number = {3},
 	pages = {718--735},
 	publisher = {Springer},
-	title = {Properties and performance of the floristic quality index in Great Lakes coastal wetlands},
+	title = {Properties and performance of the floristic quality index in {Great Lakes} coastal wetlands},
 	url = {https://doi.org/10.1672/0277-5212(2006)26[718:PAPOTF]2.0.CO;2},
+        doi = {10.1672/0277-5212(2006)26[718:papotf]2.0.co;2},
 	volume = {26},
 	year = {2006}}
 
-@inproceedings{wilhelm2017flora,
-	author = {Wilhelm, Gerould and Rericha, Laura},
-	date-added = {2023-08-10 14:34:57 -0500},
-	date-modified = {2023-08-10 14:34:57 -0500},
-	organization = {Indiana Academy of Science Indianapolis},
-	title = {Flora of the Chicago region: A floristic and ecological synthesis},
-	year = {2017}}
-
 @article{bowles2006testing,
 	author = {Bowles, Marlin and Jones, Michael},
 	date-added = {2022-08-30 10:07:03 -0500},
@@ -85,6 +79,7 @@ @article{bowles2006testing
 	publisher = {BioOne},
 	title = {Testing the efficacy of species richness and floristic quality assessment of quality, temporal change, and fire effects in tallgrass prairie natural areas},
 	url = {https://doi.org/10.3375/0885-8608(2006)26[17:TTEOSR]2.0.CO;2},
+        doi = {10.3375/0885-8608(2006)26[17:tteosr]2.0.co;2},
 	volume = {26},
 	year = {2006},
 	bdsk-url-1 = {https://doi.org/10.3375/0885-8608(2006)26%5B17:TTEOSR%5D2.0.CO;2}}
@@ -96,6 +91,7 @@ @article{bauer
 	journal = {AoB PLANTS},
 	title = {Ecology of Floristic Quality Assessment: testing for correlations between coefficients of conservatism, species traits and mycorrhizal responsiveness},
 	url = {https://doi.org/10.1093/aobpla/plx073},
+        doi = {10.1093/aobpla/plx073},
 	volume = 10,
 	year = 2018,
 	bdsk-url-1 = {https://doi.org/10.1093/aobpla/plx073}}
@@ -107,19 +103,11 @@ @article{zinnen
 	journal = {Ecological Indicators},
 	title = {Niche ecology in Floristic Quality Assessment: Are species with higher conservatism more specialized?},
 	url = {https://doi.org/10.1016/j.ecolind.2020.107078},
+        doi = {10.1016/j.ecolind.2020.107078},
 	volume = 121,
 	year = 2021,
 	bdsk-url-1 = {https://doi.org/10.1016/j.ecolind.2020.107078}}
 
-@webpage{naturecite,
-	author = {Thomas, Justin, and Thomas, Dana},
-	date-added = {2022-08-25 13:21:07 -0500},
-	date-modified = {2024-04-20 09:12:37 -0500},
-	lastchecked = {20 April 2024},
-	title = {NatureCite: Center for Integrated Taxonomy and Ecology},
-	url = {https://www.naturecite.org/},
-	bdsk-url-1 = {https://www.naturecite.org/}}
-
 @manual{rcore,
 	address = {Vienna, Austria},
 	author = {{R Core Team}},
@@ -136,15 +124,17 @@ @book{rericha
 	date-added = {2022-08-25 12:52:27 -0500},
 	date-modified = {2022-08-25 12:54:13 -0500},
 	publisher = {Indiana Academy of Sciences},
-	title = {Flora of the Chicago Region: A Floristic and Ecological Synthesis},
+	title = {Flora of the {Chicago} Region: A Floristic and Ecological Synthesis},
+        isbn = {9781883362157},
 	year = {2017}}
 
-@inproceedings{swink1994plants,
-	author = {Swink, Floyd and Wilhelm, Gerould and others},
+@book{swink1994plants,
+	author = {Swink, Floyd and Wilhelm, Gerould},
 	date-added = {2022-08-18 14:00:38 -0500},
 	date-modified = {2022-08-18 14:00:38 -0500},
 	organization = {Indiana Academy of Science},
-	title = {Plants of the Chicago region},
+	title = {Plants of the {Chicago} region},
+        isbn = {1883362016},
 	year = {1994}}
 
 @article{spyreas2019floristic,
@@ -157,6 +147,7 @@ @article{spyreas2019floristic
 	publisher = {Wiley Online Library},
 	title = {Floristic Quality Assessment: a critique, a defense, and a primer},
 	url = {https://doi.org/10.1002/ecs2.2825},
+        doi = {10.1002/ecs2.2825},
 	volume = {10},
 	year = {2019}}
 
@@ -170,6 +161,7 @@ @article{freyman2016universal
 	publisher = {Wiley Online Library},
 	title = {The Universal Floristic Quality Assessment (FQA) Calculator: an online tool for ecological assessment and monitoring},
 	url = {https://doi.org/10.1111/2041-210X.12491},
+        doi = {10.1002/ecs2.2825},
 	volume = {7},
 	year = {2016},
 	bdsk-url-1 = {https://doi.org/10.1111/2041-210X.12491}}

paper/paper.md

@@ -50,7 +50,7 @@ There is currently great need in the ecological community to validate and potent
 
 # Typical workflow
 
-Analysts using `fqar` will typically download and reformat assessments of interest before using functions like `assessment_cooccurrence_summary` to analyze the data. The following workflow does just this for the *Flora of the Chicago Region* database, an updated version of the original floristic quality manual [@wilhelm2017flora]. Depending on the needs of the specific user, such analysis can be restricted to particular practitioners, organizations, or locations, or redirected entirely along the lines described in the previous section.
+Analysts using `fqar` will typically download and reformat assessments of interest before using functions like `assessment_cooccurrence_summary` to analyze the data. The following workflow does just this for the *Flora of the Chicago Region* database, an updated version of the original floristic quality manual [@rericha]. Depending on the needs of the specific user, such analysis can be restricted to particular practitioners, organizations, or locations, or redirected entirely along the lines described in the previous section.
 
 First, download all public assessments in the desired database and reshape them into a standard format: