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+%% This BibTeX bibliography file was created using BibDesk.
+%% https://bibdesk.sourceforge.io/
+
+%% Created for Andrew Gard at 2023-08-10 14:35:11 -0500 
+
+
+%% Saved with string encoding Unicode (UTF-8) 
+
+
+
+@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{oldham1995floristic,
+	author = {Oldham, MJ and Bakowsky, WD and Sutherland, DA},
+	date-added = {2022-08-30 10:59:12 -0500},
+	date-modified = {2022-08-30 10:59:12 -0500},
+	journal = {Ontario. Natural Heritage Information Center Report, Ministry of Natural Resources, Peterborough, Ontario, Canada},
+	title = {Floristic Quality Assessment System},
+	year = {1995},
+	bdsk-url-1 = {http://dx.doi.org/10.13140/RG.2.2.35685.91360}}
+
+@article{freeman2012coefficients,
+	author = {Freeman, Craig C},
+	date-added = {2022-08-30 10:23:15 -0500},
+	date-modified = {2022-08-30 10:23:15 -0500},
+	journal = {Kansas Biological Survey \& RL McGregor Herbarium http://ksnhi. ku. edu/resources/plants},
+	title = {Coefficients of conservatism for Kansas vascular plants (2012) and selected life history attributes},
+	year = {2012}}
+
+@article{bowles2006testing,
+	author = {Bowles, Marlin and Jones, Michael},
+	date-added = {2022-08-30 10:07:03 -0500},
+	date-modified = {2022-08-31 17:49:04 -0500},
+	journal = {Natural Areas Journal},
+	number = {1},
+	pages = {17--30},
+	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},
+	volume = {26},
+	year = {2006},
+	bdsk-url-1 = {https://doi.org/10.3375/0885-8608(2006)26%5B17:TTEOSR%5D2.0.CO;2}}
+
+@article{bauer,
+	author = {Bauer, J., Koziol, L., & Bever, J.},
+	date-added = {2022-08-30 09:42:59 -0500},
+	date-modified = {2022-08-30 09:42:59 -0500},
+	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},
+	volume = 10,
+	year = 2018,
+	bdsk-url-1 = {https://doi.org/10.1093/aobpla/plx073}}
+
+@article{zinnen,
+	author = {Zinnen, J., Spyreas, Zaya, D., Matthews, J.},
+	date-added = {2022-08-30 09:42:52 -0500},
+	date-modified = {2022-08-30 10:16:57 -0500},
+	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},
+	volume = 121,
+	year = 2021,
+	bdsk-url-1 = {https://doi.org/10.1016/j.ecolind.2020.107078}}
+
+@webpage{naturecite,
+	date-added = {2022-08-25 13:21:07 -0500},
+	date-modified = {2022-08-25 13:22:08 -0500},
+	url = {https://www.naturecite.org/},
+	bdsk-url-1 = {https://www.naturecite.org/}}
+
+@manual{rcore,
+	address = {Vienna, Austria},
+	author = {{R Core Team}},
+	date-added = {2022-08-25 13:07:50 -0500},
+	date-modified = {2022-08-25 13:07:58 -0500},
+	organization = {R Foundation for Statistical Computing},
+	title = {R: A Language and Environment for Statistical Computing},
+	url = {https://www.R-project.org/},
+	year = {2022},
+	bdsk-url-1 = {https://www.R-project.org/}}
+
+@book{rericha,
+	author = {Gerould Wilhelm and Laura 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},
+	year = {2017}}
+
+@article{ladd2015ecological,
+	author = {Ladd, Douglas and Thomas, Justin R},
+	date-added = {2022-08-25 12:40:17 -0500},
+	date-modified = {2022-08-31 17:58:47 -0500},
+	journal = {Phytoneuron},
+	number = {1},
+	pages = {1--274},
+	title = {Ecological checklist of the Missouri flora for floristic quality assessment},
+	url = {https://www.biodiversitylibrary.org/part/175050},
+	volume = {12},
+	year = {2015},
+	bdsk-url-1 = {https://www.biodiversitylibrary.org/part/175050}}
+
+@manual{Wickham:2022vf,
+	author = {Hadley Wickham and Romain Fran{\c c}ois and Lionel Henry and Kirill M{\"u}ller},
+	date-added = {2022-08-25 12:36:12 -0500},
+	date-modified = {2022-08-25 12:36:12 -0500},
+	note = {R package version 1.0.9},
+	title = {dplyr: A Grammar of Data Manipulation},
+	url = {https://CRAN.R-project.org/package=dplyr},
+	year = {2022},
+	bdsk-url-1 = {https://CRAN.R-project.org/package=dplyr}}
+
+@article{JSSv059i10,
+	abstract = {A huge amount of effort is spent cleaning data to get it ready for analysis, but there has been little research on how to make data cleaning as easy and effective as possible. This paper tackles a small, but important, component of data cleaning: data tidying. Tidy datasets are easy to manipulate, model and visualize, and have a specific structure: each variable is a column, each observation is a row, and each type of observational unit is a table. This framework makes it easy to tidy messy datasets because only a small set of tools are needed to deal with a wide range of un-tidy datasets. This structure also makes it easier to develop tidy tools for data analysis, tools that both input and output tidy datasets. The advantages of a consistent data structure and matching tools are demonstrated with a case study free from mundane data manipulation chores.},
+	author = {Wickham, Hadley},
+	date-added = {2022-08-25 09:29:48 -0500},
+	date-modified = {2022-08-25 09:29:48 -0500},
+	doi = {10.18637/jss.v059.i10},
+	journal = {Journal of Statistical Software},
+	number = {10},
+	pages = {1--23},
+	title = {Tidy Data},
+	url = {https://www.jstatsoft.org/index.php/jss/article/view/v059i10},
+	volume = {59},
+	year = {2014},
+	bdsk-url-1 = {https://www.jstatsoft.org/index.php/jss/article/view/v059i10},
+	bdsk-url-2 = {https://doi.org/10.18637/jss.v059.i10}}
+
+@techreport{wilhelm1977,
+	author = {Gerould Wilhelm},
+	date-added = {2022-08-25 09:15:42 -0500},
+	date-modified = {2022-08-25 09:17:19 -0500},
+	institution = {Kane county urban development division},
+	title = {Ecological assessment of open land areas in Kane County, Illinois},
+	year = {1977}}
+
+@inproceedings{swink1994plants,
+	author = {Swink, Floyd and Wilhelm, Gerould and others},
+	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},
+	year = {1994}}
+
+@inproceedings{spyreas2015users,
+	author = {Spyreas, Greg},
+	booktitle = {Wild Things Conference 2015},
+	date-added = {2022-08-18 13:59:15 -0500},
+	date-modified = {2022-08-31 19:41:34 -0500},
+	title = {A Users Guide to Floristic Quality Assessment (FQI and Mean C)},
+	url = {http://www.wildthingscommunity.org/wild-things-conferences/wild-things-2015},
+	year = {2015},
+	bdsk-url-1 = {http://www.wildthingscommunity.org/wild-things-conferences/wild-things-2015}}
+
+@article{spyreas2019floristic,
+	author = {Spyreas, Greg},
+	date-added = {2022-08-18 13:58:45 -0500},
+	date-modified = {2022-08-18 13:58:45 -0500},
+	journal = {Ecosphere},
+	number = {8},
+	pages = {e02825},
+	publisher = {Wiley Online Library},
+	title = {Floristic Quality Assessment: a critique, a defense, and a primer},
+	volume = {10},
+	year = {2019}}
+
+@article{freyman2016universal,
+	author = {Freyman, William A and Masters, Linda A and Packard, Stephen},
+	date-added = {2022-08-18 13:57:10 -0500},
+	date-modified = {2022-08-31 17:54:26 -0500},
+	journal = {Methods in Ecology and Evolution},
+	number = {3},
+	pages = {380--383},
+	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},
+	volume = {7},
+	year = {2016},
+	bdsk-url-1 = {https://doi.org/10.1111/2041-210X.12491}}

paper/paper.md

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+---
+title: 'fqar: An R package for analyzing floristic quality assessment data'
+tags:
+  - R
+  - ecology
+  - floristic quality assessment
+authors:
+  - name: Andrew Gard
+    orcid: 0000-0003-4434-0755
+    equal-contrib: false
+    affiliation: 1
+    corresponding: true 
+  - name: Alexia Myers
+    equal-contrib: false 
+    affiliation: 1
+affiliations:
+ - name: Lake Forest College, Lake Forest IL, USA
+   index: 1
+date: 18 August 2022
+bibliography: fqar_refs.bib
+
+---
+
+# Summary
+
+Floristic Quality Assessment (FQA) is a standardized method for rating the ecological value of natural areas based on the plant species found within them [@spyreas2015users]. Each species considered native to a particular region is assigned a *coefficient of conservatism*, C, on a scale of 0-10 by experts in local flora. Larger values of C correspond to species that tend to be found in undegraded sites, while lower values indicate species that are more tolerant to human impacts. An inventory of the site in question is conducted, and the average of the C-values found there is computed. This *native mean-C value*, sometimes weighted by the total number of plant species identified to give the so-called *floristic quality index* [@bowles2006testing], is frequently used by land managers and other agents to quantify an area's state of conservancy [@zinnen]. 
+
+Although floristic quality assessment dates back to the  1970s [@wilhelm1977], its use has expanded significantly in recent years, in part due to the creation of a central data repository, [universalfqa.org](https://universalfqa.org/) [@freyman2016universal], where practitioners can easily upload site inventories, select appropriate species databases, and receive quantitative assessments in .csv format. The site provides access to thousands of public assessments from dozens of public databases, covering much of the continental United States and parts of Canada. For instance, see [@oldham1995floristic] for Ontario, Canada flora and [@rericha] for flora of the Chicago, USA region.
+
+The `fqar` packages provides tools for downloading and analyzing floristic quality assessment data using R [@rcore].
+
+# Statement of need
+
+The [universalfqa.org](https://universalfqa.org/) website is calibrated for practitioners in the field rather than data analysts at their desks. It facilitates the recording, storing, and publicizing of individual floristic quality assessments and performs calculations of the statistical measures most often cited by land managers and conservation organizations in their reporting, including native mean-C. Still, the reports it generates are poorly-suited for data analysis for a number of technical reasons, including the following:
+
+- Exported .csv files include multiple sorts of observations, including assessment-level data like location and weather, raw species inventories, and summary statistics like mean C, all in a single spreadsheet.
+- Descriptors for the various sorts of observations sometimes appear as cell entries, sometimes as header rows, and sometimes not at all.
+- Individual cells are formatted inconsistently.
+
+The `fqar` package addresses these and other difficulties. 
+
+# Typical workflow
+
+Available databases of plant species and their associated C-values can be viewed and downloaded using a family of indexing functions. For instance, the following code produces a data frame listing all public assessments that draw on the 2015 Missouri database [@ladd2015ecological]:
+
+```r 
+library(fqar)
+missouri_assessments_available <- index_fqa_assessments(database_id = 63)
+```
+
+A summary of the `database_id` numbers assigned by  [universalfqa.org](https://universalfqa.org/) can be obtained with the `index_fqa_databases()` function.
+
+An analyst can download all available assessments in a given database or specify a narrower subset by practitioner, site, date, or other criteria using `dplyr` [@Wickham:2022vf] syntax. For instance, the following code downloads all assessments done by Justin Thomas using the Missouri database.
+
+```r
+thomas_fqas <- download_assessment_list(database_id = 63,
+                                        practitioner == "Justin Thomas")
+```
+
+The output of this commands is a list of data frames in the raw format provided by [universalfqa.org](https://universalfqa.org/). Summary data can be obtained in tidy format [@JSSv059i10] with `assessment_list_glance()`:
+
+```r
+thomas_tidy <- assessment_list_glance(thomas_fqas)
+```
+
+Species inventories for individual assessments can be extracted (again in tidy format) with `fqar::assessment_inventory()`.
+
+# Availability
+
+The `fqar` package is freely available via the Comprehensive R Archive Network (CRAN). 
+
+`install.packages("fqar")`
+
+Alternatively, the latest developmental version can be installed directly from GitHub:
+
+`devtools::install_github("equitable-equations/fqar")`
+
+Thorough documentation is provided. A long-form vignette gives a birds-eye overview of the package's functionality while help files for individual functions provide guidance on particular data analysis tasks. 
+
+# Acknowledgements
+
+The authors wish to thanks Glenn Adelson, Ph.D  (Lake Forest College) and Justin Thomas, M.Sc ([NatureCITE](https://www.naturecite.org/)) for their insight into floristic quality assessment. 
+
+# References
+