diff --git a/joss.06366/10.21105.joss.06366.crossref.xml b/joss.06366/10.21105.joss.06366.crossref.xml
new file mode 100644
index 0000000000..6e07ca2965
--- /dev/null
+++ b/joss.06366/10.21105.joss.06366.crossref.xml
@@ -0,0 +1,264 @@
+
+
+
+ 20240423T131339-85b26985be3e04ece05b13d8f535093416473d8e
+ 20240423131339
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 04
+ 2024
+
+
+ 9
+
+ 96
+
+
+
+ The fqar package: R tools for analyzing floristic
+quality assessment data
+
+
+
+ Andrew
+ Gard
+ https://orcid.org/0000-0003-4434-0755
+
+
+ Alexia
+ Myers
+
+
+ Irene
+ Luwabelwa
+
+
+
+ 04
+ 23
+ 2024
+
+
+ 6366
+
+
+ 10.21105/joss.06366
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.11002086
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/6366
+
+
+
+ 10.21105/joss.06366
+ https://joss.theoj.org/papers/10.21105/joss.06366
+
+
+ https://joss.theoj.org/papers/10.21105/joss.06366.pdf
+
+
+
+
+
+ fqadata: Contains regional floristic quality
+assessment databases
+ Foxfoot
+ 2023
+ Foxfoot, I. (2023). fqadata: Contains
+regional floristic quality assessment databases.
+https://CRAN.R-project.org/package=fqadata
+
+
+ fqacalc: Calculate floristic quality
+assessment metrics
+ Foxfoot
+ 2023
+ Foxfoot, I. (2023). fqacalc:
+Calculate floristic quality assessment metrics.
+https://CRAN.R-project.org/package=fqacalc
+
+
+ Tidy data
+ Wickham
+ Journal of Statistical
+Software
+ 10
+ 59
+ 10.18637/jss.v059.i10
+ 2014
+ Wickham, H. (2014). Tidy data.
+Journal of Statistical Software, 59(10), 1–23.
+https://doi.org/10.18637/jss.v059.i10
+
+
+ A null model test of floristic quality
+assessment: Are plant species’ coefficients of conservatism
+valid?
+ Matthews
+ Ecological Indicators
+ 52
+ 10.1016/j.ecolind.2014.11.017
+ 2015
+ Matthews, J. W., Spyreas, G., &
+Long, C. M. (2015). A null model test of floristic quality assessment:
+Are plant species’ coefficients of conservatism valid? Ecological
+Indicators, 52, 1–7.
+https://doi.org/10.1016/j.ecolind.2014.11.017
+
+
+ Properties and performance of the floristic
+quality index in Great Lakes coastal wetlands
+ Bourdaghs
+ Wetlands
+ 3
+ 26
+ 10.1672/0277-5212(2006)26[718:papotf]2.0.co;2
+ 2006
+ Bourdaghs, M., Johnston, C. A., &
+Regal, R. R. (2006). Properties and performance of the floristic quality
+index in Great Lakes coastal wetlands. Wetlands, 26(3), 718–735.
+https://doi.org/10.1672/0277-5212(2006)26[718:papotf]2.0.co;2
+
+
+ Testing the efficacy of species richness and
+floristic quality assessment of quality, temporal change, and fire
+effects in tallgrass prairie natural areas
+ Bowles
+ Natural Areas Journal
+ 1
+ 26
+ 10.3375/0885-8608(2006)26[17:tteosr]2.0.co;2
+ 2006
+ Bowles, M., & Jones, M. (2006).
+Testing the efficacy of species richness and floristic quality
+assessment of quality, temporal change, and fire effects in tallgrass
+prairie natural areas. Natural Areas Journal, 26(1), 17–30.
+https://doi.org/10.3375/0885-8608(2006)26[17:tteosr]2.0.co;2
+
+
+ Ecology of floristic quality assessment:
+Testing for correlations between coefficients of conservatism, species
+traits and mycorrhizal responsiveness
+ Bauer
+ AoB PLANTS
+ 10
+ 10.1093/aobpla/plx073
+ 2018
+ Bauer, K., J. (2018). Ecology of
+floristic quality assessment: Testing for correlations between
+coefficients of conservatism, species traits and mycorrhizal
+responsiveness. AoB PLANTS, 10.
+https://doi.org/10.1093/aobpla/plx073
+
+
+ Niche ecology in floristic quality
+assessment: Are species with higher conservatism more
+specialized?
+ Zinnen
+ Ecological Indicators
+ 121
+ 10.1016/j.ecolind.2020.107078
+ 2021
+ Zinnen, S., J. (2021). Niche ecology
+in floristic quality assessment: Are species with higher conservatism
+more specialized? Ecological Indicators, 121.
+https://doi.org/10.1016/j.ecolind.2020.107078
+
+
+ R: A language and environment for statistical
+computing
+ R Core Team
+ 2022
+ R Core Team. (2022). R: A language
+and environment for statistical computing. R Foundation for Statistical
+Computing. https://www.R-project.org/
+
+
+ Flora of the Chicago region: A floristic and
+ecological synthesis
+ Wilhelm
+ 9781883362157
+ 2017
+ Wilhelm, G., & Rericha, L.
+(2017). Flora of the Chicago region: A floristic and ecological
+synthesis. Indiana Academy of Sciences.
+ISBN: 9781883362157
+
+
+ Plants of the Chicago region
+ Swink
+ 1883362016
+ 1994
+ Swink, F., & Wilhelm, G. (1994).
+Plants of the Chicago region. Indiana Academy of Science.
+ISBN: 1883362016
+
+
+ Floristic quality assessment: A critique, a
+defense, and a primer
+ Spyreas
+ Ecosphere
+ 8
+ 10
+ 10.1002/ecs2.2825
+ 2019
+ Spyreas, G. (2019). Floristic quality
+assessment: A critique, a defense, and a primer. Ecosphere, 10(8),
+e02825. https://doi.org/10.1002/ecs2.2825
+
+
+ The universal floristic quality assessment
+(FQA) calculator: An online tool for ecological assessment and
+monitoring
+ Freyman
+ Methods in Ecology and
+Evolution
+ 3
+ 7
+ 10.1002/ecs2.2825
+ 2016
+ Freyman, W. A., Masters, L. A., &
+Packard, S. (2016). The universal floristic quality assessment (FQA)
+calculator: An online tool for ecological assessment and monitoring.
+Methods in Ecology and Evolution, 7(3), 380–383.
+https://doi.org/10.1002/ecs2.2825
+
+
+
+
+
+
diff --git a/joss.06366/10.21105.joss.06366.jats b/joss.06366/10.21105.joss.06366.jats
new file mode 100644
index 0000000000..b22d30758e
--- /dev/null
+++ b/joss.06366/10.21105.joss.06366.jats
@@ -0,0 +1,472 @@
+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+6366
+10.21105/joss.06366
+
+The fqar package: R tools for analyzing floristic quality
+assessment data
+
+
+
+https://orcid.org/0000-0003-4434-0755
+
+Gard
+Andrew
+
+
+*
+
+
+
+Myers
+Alexia
+
+
+
+
+
+Luwabelwa
+Irene
+
+
+
+
+
+Lake Forest College, Lake Forest IL, USA
+
+
+
+
+* E-mail:
+
+
+18
+8
+2023
+
+9
+96
+6366
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+R
+ecology
+floristic quality assessment
+
+
+
+
+
+ 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
+ (Spyreas,
+ 2019;
+ Swink
+ & Wilhelm, 1994). Each species known to be found in a
+ particular region is assigned a coefficient of
+ conservatism, C, on a scale of 0-10 by experts in local flora
+ (non-native species are generally assigned a zero C-value by default).
+ 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
+ (Bauer,
+ 2018). An inventory of the site 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
+ (Bowles
+ & Jones, 2006), is frequently used by land managers and
+ other agents to quantify an area’s state of conservancy
+ (Zinnen,
+ 2021).
+
In recent years, it has become increasingly standard for
+ practitioners to upload their floristic quality assessments to a
+ central repository,
+ universalfqa.org
+ (Freyman
+ et al., 2016), which already includes tens of thousands of
+ assessments from over one hundred floristic quality databases. This
+ large public data cache represents a potentially invaluable resource
+ for quantitative ecologists, though it has so far gone largely
+ unexplored due to a lack of both technical tools for interacting
+ programmatically with the repository and accessible workflows for
+ analyzing the floristic quality data housed there.
+
fqar is an R
+ (R Core
+ Team, 2022) package which facilitates the analysis of
+ occurrence and co-occurrence of plant taxa at the regional level.
+ Pulling data on-demand from
+ universalfqa.org,
+ it provides both organizational tools for handling the disparate sorts
+ of data housed there and statistical ones for drawing novel
+ conclusions from that data.
+
+
+ Statement of need
+
The
+ 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. However, its focus on individual assessments is not
+ well-suited to analyses that might wish to consider multiple
+ assessments simultaneously.
+
This package compliments existing R packages for floristic quality
+ analysis, including fqacalc and
+ fqadata, which support the work of field
+ practitioners wishing to make use of R
+ (Foxfoot,
+ 2023a,
+ 2023b). The
+ fqar package enables analysis with a wider
+ lens, allowing users to consider database-wide records of plant taxa
+ or characteristics. By examining entire collections of assessments
+ simultaneously, ecologists may gain insights into floristic quality
+ assessment as well as the various plant species it tracks. Among the
+ wide range of questions made answerable by fqar
+ are the following:
+
+
+
what is the co-occurrence profile of a given species of
+ interest? What other plants (or types of plants) is it most
+ frequently identified alongside?
+
+
+
which species in a given database might be misclassified based
+ on their co-occurrence profiles? It is to be expected that, on
+ average, 9’s and 10’s will tend to be found among higher
+ conservancy flora than 0’s and 1’s. Species that radically depart
+ from this expectation would be candidates for re-evaluation.
+
+
+
what species are most commonly identified in certain regions?
+ Which have been reported seldom or not at all?
+
+
+
which non-native species have become widespread in particular
+ regions? Which tend to be symptomatic of degraded areas, and which
+ seem to be able to coexist alongside conservative native
+ plants?
+
+
+
There is currently great need in the ecological community to
+ validate and potentially refine the floristic quality assessment
+ methodology
+ (Spyreas,
+ 2019). Because C-values, the metric on which FQA is ultimately
+ based, are assigned based on the experience of small numbers of local
+ experts, there are inevitable inconsistencies and irregularities which
+ only a larger-scale reconsideration can address. Thus far the
+ community has only been able to take preliminary or ad hoc steps in
+ that direction
+ (Bourdaghs
+ et al., 2006;
+ Matthews
+ et al., 2015). The fqar package will
+ allow for a more deep, targeted analysis.
+
+
+ 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
+ (Wilhelm
+ & Rericha, 2017). 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:
The output of the former command is a list of data frames in the
+ original format provided by
+ universalfqa.org.
+ Each of these data frames includes several different sorts of
+ information: species-level observations, summary statistics, and
+ metadata. The second command isolates the species inventories and
+ stores them in a tidy format
+ (Wickham,
+ 2014).
+
Next, extract co-occurrence information from this collection of
+ species inventories:
fqar provides tools for both quantitative
+ and visual descriptions of the co-occurrence profile of given
+ species.
+ species_profile(chicago_invs,
+ species = "Fragaria virginiana",
+ native = TRUE) # a data frame
+species_profile_plot(chicago_invs,
+ species = "Fragaria virginiana",
+ native = TRUE) # a visualization
+
+
+
+
+
Here we see that Fragaria virginiana, the wild
+ strawberry, is listed with C
+
+ =0
+ in the Chicago database but co-occurs with a wide variety of more
+ conservative species. In particular, it has been found with 10’s more
+ frequently than it has with other 0’s.
+
Summary co-occurrence information for the entire database can be
+ extracted with
+ assessment_cooccurrences_summary, which gives a
+ complete listing of all observed species and their co-occurring mean
+ C-values.
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
+
Partial funding for this project was provided by the James Rocco
+ Program. The authors also wish to thanks Glenn Adelson, Ph.D (Lake
+ Forest College) and Justin Thomas, M.Sc (NatureCITE) for their insight
+ into floristic quality assessment.
+
+
+
+
+
+
+
+ FoxfootIris
+
+ fqadata: Contains regional floristic quality assessment databases
+ 2023
+ https://CRAN.R-project.org/package=fqadata
+
+
+
+
+
+ FoxfootIris
+
+ fqacalc: Calculate floristic quality assessment metrics
+ 2023
+ https://CRAN.R-project.org/package=fqacalc
+
+
+
+
+
+ WickhamHadley
+
+ Tidy data
+ Journal of Statistical Software
+ 2014
+ 59
+ 10
+ https://www.jstatsoft.org/index.php/jss/article/view/v059i10
+ 10.18637/jss.v059.i10
+ 1
+ 23
+
+
+
+
+
+ MatthewsJeffrey W
+ SpyreasGreg
+ LongColleen M
+
+ A null model test of floristic quality assessment: Are plant species’ coefficients of conservatism valid?
+ Ecological Indicators
+ Elsevier
+ 2015
+ 52
+ https://doi.org/10.1016/j.ecolind.2014.11.017
+ 10.1016/j.ecolind.2014.11.017
+ 1
+ 7
+
+
+
+
+
+ BourdaghsMichael
+ JohnstonCarol A
+ RegalRonald R
+
+ Properties and performance of the floristic quality index in Great Lakes coastal wetlands
+ Wetlands
+ Springer
+ 2006
+ 26
+ 3
+ https://doi.org/10.1672/0277-5212(2006)26[718:PAPOTF]2.0.CO;2
+ 10.1672/0277-5212(2006)26[718:papotf]2.0.co;2
+ 718
+ 735
+
+
+
+
+
+ BowlesMarlin
+ JonesMichael
+
+ Testing the efficacy of species richness and floristic quality assessment of quality, temporal change, and fire effects in tallgrass prairie natural areas
+ Natural Areas Journal
+ BioOne
+ 2006
+ 26
+ 1
+ https://doi.org/10.3375/0885-8608(2006)26[17:TTEOSR]2.0.CO;2
+ 10.3375/0885-8608(2006)26[17:tteosr]2.0.co;2
+ 17
+ 30
+
+
+
+
+
+ BauerKoziolJ.
+
+ Ecology of floristic quality assessment: Testing for correlations between coefficients of conservatism, species traits and mycorrhizal responsiveness
+ AoB PLANTS
+ 2018
+ 10
+ https://doi.org/10.1093/aobpla/plx073
+ 10.1093/aobpla/plx073
+
+
+
+
+
+ ZinnenSpyreasJ.
+
+ Niche ecology in floristic quality assessment: Are species with higher conservatism more specialized?
+ Ecological Indicators
+ 2021
+ 121
+ https://doi.org/10.1016/j.ecolind.2020.107078
+ 10.1016/j.ecolind.2020.107078
+
+
+
+
+
+ R Core Team
+
+ R: A language and environment for statistical computing
+ R Foundation for Statistical Computing
+ Vienna, Austria
+ 2022
+ https://www.R-project.org/
+
+
+
+
+
+ WilhelmGerould
+ RerichaLaura
+
+ Flora of the Chicago region: A floristic and ecological synthesis
+ Indiana Academy of Sciences
+ 2017
+ 9781883362157
+
+
+
+
+
+ SwinkFloyd
+ WilhelmGerould
+
+ Plants of the Chicago region
+ Indiana Academy of Science
+ 1994
+ 1883362016
+
+
+
+
+
+ SpyreasGreg
+
+ Floristic quality assessment: A critique, a defense, and a primer
+ Ecosphere
+ Wiley Online Library
+ 2019
+ 10
+ 8
+ https://doi.org/10.1002/ecs2.2825
+ 10.1002/ecs2.2825
+ e02825
+
+
+
+
+
+
+ FreymanWilliam A
+ MastersLinda A
+ PackardStephen
+
+ The universal floristic quality assessment (FQA) calculator: An online tool for ecological assessment and monitoring
+ Methods in Ecology and Evolution
+ Wiley Online Library
+ 2016
+ 7
+ 3
+ https://doi.org/10.1111/2041-210X.12491
+ 10.1002/ecs2.2825
+ 380
+ 383
+
+
+
+
+
diff --git a/joss.06366/10.21105.joss.06366.pdf b/joss.06366/10.21105.joss.06366.pdf
new file mode 100644
index 0000000000..988af53c03
Binary files /dev/null and b/joss.06366/10.21105.joss.06366.pdf differ
diff --git a/joss.06366/media/strawberry_plot.png b/joss.06366/media/strawberry_plot.png
new file mode 100644
index 0000000000..b013384094
Binary files /dev/null and b/joss.06366/media/strawberry_plot.png differ