southeastern database names updated

ifoxfoot · Jul 10, 2023 · 715b352 · 715b352
1 parent dfda0c5
commit 715b352
Show file tree

Hide file tree

Showing 5 changed files with 22 additions and 11 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
 # fqadata 1.0.0.9000
 
-* Added a `NEWS.md` file to track changes to the package.
+## Breaking Changes
+
+-   Southeastern regional databases were renamed to more closely match their names in other tools and publications. The changes are as follows:
+    -   southeastern_mountains_2014 -\> appalachian_mountains_2013
+    -   southeastern_plain_2014 -\> coastal_plain_southeast_2013
+    -   southeastern_interior_plateau_2014 -\> interior_plateau_2013
+    -   southeastern_piedmont_2014 -\> southeastern_piedmont_2013
+    -   southeastern_southern_coastal_plain_2014 -\> southern_coastal_plain_2013
+
+## Misc Changes
+
+-   Added a `NEWS.md` file to track changes to the package.
diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R
@@ -321,7 +321,7 @@ southern_coastal_plain <- southeastern_cols %>%
   select(ID, accepted_scientific_name, scientific_name, name_origin, family, acronym,
          ave_c_value_southern_coastal_plain, physiognomy,
          duration, common_name, nwpl_cstl_plain, native) %>%
-  mutate(fqa_db = "southeastern_southern_coastal_plain_2014") %>%
+  mutate(fqa_db = "southern_coastal_plain_2013") %>%
   rename(c = ave_c_value_southern_coastal_plain) %>%
   rename(w = nwpl_cstl_plain) %>%
   filter(!c == "NA") %>%
@@ -332,7 +332,7 @@ southeastern_plain <- southeastern_cols %>%
   select(ID, accepted_scientific_name, scientific_name, name_origin, family, acronym,
          ave_c_value_plains, physiognomy,
          duration, common_name, nwpl_cstl_plain, native) %>%
-  mutate(fqa_db = "southeastern_plain_2014") %>%
+  mutate(fqa_db = "coastal_plain_southeast_2013") %>%
   rename(c = ave_c_value_plains) %>%
   rename(w = nwpl_cstl_plain) %>%
   filter(!c == "NA") %>%
@@ -344,7 +344,7 @@ southeastern_piedmont <- southeastern_cols %>%
   select(ID, accepted_scientific_name, scientific_name, name_origin, family, acronym,
          ave_c_value_piedmont, physiognomy,
          duration, common_name, nwpl_e_mtns, native) %>%
-  mutate(fqa_db = "southeastern_piedmont_2014") %>%
+  mutate(fqa_db = "southeastern_piedmont_2013") %>%
   rename(c = ave_c_value_piedmont) %>%
   rename(w = nwpl_e_mtns) %>%
   filter(!c == "NA") %>%
@@ -355,7 +355,7 @@ southeastern_mountains <- southeastern_cols %>%
   select(ID, accepted_scientific_name, scientific_name, name_origin, family, acronym,
          ave_c_value_mountains, physiognomy,
          duration, common_name, nwpl_e_mtns, native) %>%
-  mutate(fqa_db = "southeastern_mountains_2014") %>%
+  mutate(fqa_db = "appalachian_mountains_2013") %>%
   rename(c = ave_c_value_mountains) %>%
   rename(w = nwpl_e_mtns) %>%
   filter(!c == "NA") %>%
@@ -366,7 +366,7 @@ southeastern_plateau <- southeastern_cols %>%
   select(ID, accepted_scientific_name, scientific_name, name_origin, family, acronym,
          ave_c_value_interior_plateau, physiognomy,
          duration, common_name, nwpl_e_mtns, native) %>%
-  mutate(fqa_db = "southeastern_interior_plateau_2014") %>%
+  mutate(fqa_db = "interior_plateau_2013") %>%
   rename(c = ave_c_value_interior_plateau) %>%
   rename(w = nwpl_e_mtns) %>%
   filter(!c == "NA") %>%

diff --git a/data-raw/Regional_db_notes.csv b/data-raw/Regional_db_notes.csv
@@ -1,9 +1,9 @@
 Regional Name,Year,# Taxa,Score,Recommendation,Notes,Downloaded?,FQA Name in App,Citation,Download Notes,Link,Summary
-"Appalachian Mtn (EPA Ecoregions 66,67,68,69)  2013",2013,3831,5,YES,Wetlands Only,YES-online,southeastern_mountains_2014,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants
+"Appalachian Mtn (EPA Ecoregions 66,67,68,69)  2013",2013,3831,5,YES,Wetlands Only,YES-online,appalachian_mountains_2013,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants
 Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,Reviewed
 Atlantic Coastal Pine Barrens (8.5.4) 2018,2018,2094,4,"Yes, with reservations",NA,YES-Universal FQA,atlantic_coastal_pine_barrens_2018,"Faber-Langendoen, D., Cameron, D., Gilman, A. V., Metzler, K. J., Ring, R. M., & Sneddon, L. (2019). Development of an Ecoregional Floristic Quality Assessment Method for the Northeastern United States. Northeastern Naturalist, 26(3), 593-608.",2021 version on Universal FQA calculator,,Rec with reservations
 Chicago Region USACE 2017,2017,3171,5,YES,NA,YES-Robbie,chicago_region_2017,"Herman, B., Sliwinski, R. and S. Whitaker. 2017. Chicago Region FQA (Floristic Quality Assessment) Calculator. U.S. Army Corps of Engineers, Chicago, IL.",,,
-"Coastal Plain of the Southeast (EPA Ecoregions 63,65) 2013",2013,4632,5,YES,Wetlands Only,YES-online,southeastern_plain_2014,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
+"Coastal Plain of the Southeast (EPA Ecoregions 63,65) 2013",2013,4632,5,YES,Wetlands Only,YES-online,coastal_plain_southeast_2013,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
 Colorado Floristic Quality Assessment Indices 2020,2020,3375,5,YES,NA,YES-online,colorado_2020,"Smith, P., G. Doyle, and J. Lemly. 2020. Revision of Colorado’s Floristic Quality Assessment
 Indices. Colorado Natural Heritage Program, Colorado State University, Fort Collins, Colorado.",,https://cnhp.colostate.edu/cwic/tools/calculator/,
 "Dakotas (excluding the Black Hills) 2001, 2017*",2017,1558,1,Previously Certified,NA,YES-Universal FQA,dakotas_excluding_black_hills_2017,"The Northern Great Plains Floristic Quality Assessment Panel. 2001. Coefficients of conservatism for the vascular flora of the Dakotas and adjacent grasslands. U.S. Geological Survey, Biological Resources Division, Information and Technology Report USGS/BRD/ITR-2001-0001, 32 p.",,,
@@ -13,7 +13,7 @@ Florida 2011,2011,850,5,YES,Marsh Habitat,YES-online,florida_2011,"Cohen, M. J.,
 Florida-South 2009,2009,1340,5,YES,Excluding the Keys,YES-online,florida_south_2009,"Mortellaro, S., Barry, M., Gann, G., Zahina, J., Channon, S., Hilsenbeck, C., Scofield, D., Wilder, G., & Wilhem, G. (2009). Coefficients of conservatism values and the floristic quality index for the vascular plants of South Florida. South Florida Ecological Services Field Office, Vero Beach, Florida, pp78.",,,
 "Illinois 1997, 2020",2020,3040,5,YES,NA,YES-Universal FQA,illinois_2020,"Taft, J. B., Wilhelm, G. S., Ladd, D. M., & Masters, L. A. 1997. Floristic quality assessment for vegetation in Illinois, a method for assessing vegetation integrity. Westville: Illinois Native Plant Society.",Downloaded 2020 version only,,
 "Indiana 2004, 2019",2019,2821,5,YES,NA,YES-Universal FQA,indiana_2019,"Rothrock, P.E. 2004. Floristic quality assessment in Indiana: The concept,use, and development of coefficients of conservatism. Final Report for ARN A305-4-53, EPAWetland Program Development Grant CD975586-01.",downloaded 2019 version only,,
-"Interior Plateau (EPA Ecoregions 70,71,72) 2013",2013,3473,5,YES,Wetlands Only,YES-online,southeastern_interior_plateau_2014,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
+"Interior Plateau (EPA Ecoregions 70,71,72) 2013",2013,3473,5,YES,Wetlands Only,YES-online,interior_plateau_2013,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
 Iowa 2001 ,2001,1963,5,YES,NA,YES-Universal FQA,iowa_2001,"McMullen, C. M., & Farrar, D. (2004). Floristic Quality Assessment and Mitigation Recommendations, Worle Creek Riparian Corridor, 500 th St. to State Ave., Ames, IA. Draft Report to Stanley Consultants 100 Court Ave.",,,
 Kansas 2014*,2014,2306,1,Previously Certified,NA,YES-Universal FQA,kansas_2014,"Freeman, Craig C. 2014. Coefficients of conservatism for Kansas vascular plants and selected life history attributed. Kansas Biological Survey and R.L. McGregor Herbarium, University of Kansas.",,,
 Louisiana (Coastal Prairie) 2006 ,2006,591,5,YES,Coastal Marshes Only,YES-Universal FQA,louisiana_coastal_prairie_2006,"Cretini, K. F., Visser, J. M., Krauss, K. W., & Steyer, G. D. (2012). Development and use of a floristic quality index for coastal Louisiana marshes. Environmental monitoring and assessment, 184(4), 2389-2403.",,,
@@ -34,8 +34,8 @@ New Mexico's Middle Rio Grande 2019,2019,612,5,YES,NA,YES-Universal FQA,new_mexi
 "Northeastern Coastal Zone (8.1.7) 2017, 2018",2018,2735,4,YES,NA,YES-Universal FQA,northeastern_coastal_2018,"Faber-Langendoen, D., Cameron, D., Gilman, A. V., Metzler, K. J., Ring, R. M., & Sneddon, L. (2019). Development of an Ecoregional Floristic Quality Assessment Method for the Northeastern United States. Northeastern Naturalist, 26(3), 593-608.",,,
 "Northern Appalachian and Atlantic Maritime Highlands (5.3.1) 2017, 2018",2018,2999,5,YES,NA,YES-Universal FQA,northern_appalachian_atlantic_maritime_highlands_2018,"Faber-Langendoen, D., Cameron, D., Gilman, A. V., Metzler, K. J., Ring, R. M., & Sneddon, L. (2019). Development of an Ecoregional Floristic Quality Assessment Method for the Northeastern United States. Northeastern Naturalist, 26(3), 593-608.",,,
 "Pennsylvania Piedmont 2006, 2013",2013,3419,5,YES,NA,YES-Universal FQA,pennsylvania_piedmont_2013,"Chamberlain, S. J., & Ingram, H. M. (2012). Developing coefficients of conservatism to advance floristic quality assessment in the Mid-Atlantic region. The Journal of the Torrey Botanical Society, 139(4), 416-427.",,,
-Piedmont region (EAP Ecoregion 45) 2013,2013,2029,5,YES,Wetlands Only,YES-online,southeastern_piedmont_2014,"Gianopulos, K. (2014). Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeastern United States. North Carolina Dept. of Environment & Natural Resources, Division of Water Resources: Wetlands Branch. Report to the EPA, Region, 4.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
-Southern Coastal Plain (EPA Ecoregion 75) 2013,2013,4603,5,YES,Wetlands Only,YES-Universal FQA,southeastern_southern_coastal_plain_2014,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
+Piedmont region (EAP Ecoregion 45) 2013,2013,2029,5,YES,Wetlands Only,YES-online,southeastern_piedmont_2013,"Gianopulos, K. (2014). Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeastern United States. North Carolina Dept. of Environment & Natural Resources, Division of Water Resources: Wetlands Branch. Report to the EPA, Region, 4.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
+Southern Coastal Plain (EPA Ecoregion 75) 2013,2013,4603,5,YES,Wetlands Only,YES-Universal FQA,southern_coastal_plain_2013,"Gianopulos, K. 2014. Coefficient of Conservatism Database Development for Wetland Plants Occurring in the Southeast United States. NC Dept. of Envir. Quality, Div. of Water Resources: Wetlands Branch. Report to the EPA.",https://www.ncwetlands.org/project/coefficient_conservatism/,,
 Texas Blackland Prairies 2019,2019,492,5,YES,NA,YES-Universal FQA,texas_blackland_prairie_2019,"Reemts, C. M., & Eidson, J. A. (2019). Choosing Plant Diversity Metrics: A Tallgrass Prairie Case Study. Ecological Restoration, 37(4), 233-245. (include supplemental information)",,,"Map not explixit, used bioregion"
 WA - Eastern Washington State (Columbia Basin) 2013,2013,2734,5,YES,NA,YES-Universal FQA,eastern_washington_columbia_basin_2013,"F. J. Rocchio and R. C. Crawford. 2013. Floristic Quality Assessment for Washington Vegetation. Washington Natural Heritage Program, Washington Department of Natural Resources, Olympia, Washington. Baseline nomenclature: USDA PLANTS",,,Based on eastern Wa counties and ecoregion level 3
 WA - Eastern Washington State (Mountains) 2013,2013,2734,5,YES,NA,YES-Universal FQA,eastern_washington_mountains_2013,"F. J. Rocchio and R. C. Crawford. 2013. Floristic Quality Assessment for Washington Vegetation. Washington Natural Heritage Program, Washington Department of Natural Resources, Olympia, Washington. Baseline nomenclature: USDA PLANTS",,,Based on eastern Wa counties and ecoregion level 3

diff --git a/data/fqa_citations.rda b/data/fqa_citations.rda
diff --git a/data/fqa_db.rda b/data/fqa_db.rda