minor edits and add citation

Author: ctoney

README.Rmd

@@ -24,11 +24,11 @@ The Forest Inventory and Analysis Program ([FIA](https://research.fs.usda.gov/pr
 
 **FIAstemmap** is an R package for mapping tree stem locations on FIA plots, modeling individual crown dimensions, and generating plot-level estimates of fractional tree canopy cover. Several stand height metrics can be calculated. Spatial analysis of tree point pattern is facilitated for the standard FIA four-point cluster plot design. Efficient data processing supports national applications. The package provides an updated implementation of the software originally described by Toney et al. 2009 [[1]](#references). The original implementation for modeling plot canopy cover from individual tree measurements has supported several applications of FIA data, including:
 
-* reference data for classifying vegetation types and mapping tree canopy cover in the LANDFIRE Program [[2, 3, 4, 5]](#references)
-* National Land Cover Database (NLCD) Tree Canopy Cover (TCC) science and development [[6]](#references)
-* wildlife habitat analyses [[7, 8, 9]](#references)
-* mapping erosion risk in rangelands [[10]](#references)
-* comparative assessments of tree canopy cover estimation methods [[11, 12]](#references)
+* vegetation type classification and tree canopy cover mapping in the LANDFIRE Program [[2, 3, 4, 5]](#references)
+* National Land Cover Database (NLCD) Tree Canopy Cover science and development [[6, 7]](#references)
+* wildlife habitat analysis [[8, 9, 10]](#references)
+* mapping erosion risk [[11]](#references)
+* assessment of tree canopy cover estimation methods [[12, 13]](#references)
 
 ## Installation
 
@@ -56,21 +56,23 @@ library(FIAstemmap)
 
 [3] Moore, Annabelle; La Puma, Inga; Dillon, Greg; Smail, Tobin; Schleeweis, Karen; Toney, Chris; Menakis, Jim; Bastian, Henry; Picotte, Josh; Dockter, Daryn; Tolk, Brian. 2024. Twenty years of science and management with LANDFIRE. Connected Science, October 2024. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 2 p. Available: https://research.fs.usda.gov/treesearch/68397.
 
-[4] Vogelmann, Jim & Kost, Jay & Tolk, Brian & Howard, Stephen & Short, Karen & Chen, Xuexia & Huang, Chengquan & Pabst, Kari & Rollins, Matthew. (2011). Monitoring Landscape Change for LANDFIRE Using Multi-Temporal Satellite Imagery and Ancillary Data. _Selected Topics in Applied Earth Observations and Remote Sensing, IEEE Journal of_. 4. 252 - 264. 10. https://doi.org/10.1109/JSTARS.2010.2044478.
+[4] Vogelmann, Jim & Kost, Jay & Tolk, Brian & Howard, Stephen & Short, Karen & Chen, Xuexia & Huang, Chengquan & Pabst, Kari & Rollins, Matthew. (2011). Monitoring Landscape Change for LANDFIRE Using Multi-Temporal Satellite Imagery and Ancillary Data. _Selected Topics in Applied Earth Observations and Remote Sensing, IEEE Journal of_. 4. 252-264. 10. https://doi.org/10.1109/JSTARS.2010.2044478.
 
-[5] Nelson, K.J., Connot, J., Peterson, B. et al. 2013. The LANDFIRE Refresh Strategy: Updating the National Dataset. _Fire Ecology_, 9, 80–101. https://doi.org/10.4996/fireecology.0902080.
+[5] Nelson, K.J., Connot, J., Peterson, B. et al. 2013. The LANDFIRE Refresh Strategy: Updating the National Dataset. _Fire Ecology_, 9, 80-101, https://doi.org/10.4996/fireecology.0902080.
 
 [6] Toney, Chris; Liknes, Greg; Lister, Andy; Meneguzzo, Dacia. 2012. Assessing alternative measures of tree canopy cover: Photo-interpreted NAIP and ground-based estimates. In: McWilliams, Will; Roesch, Francis A. eds. 2012. _Monitoring Across Borders: 2010 Joint Meeting of the Forest Inventory and Analysis (FIA) Symposium and the Southern Mensurationists_. e-Gen. Tech. Rep. SRS-157. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station. 209-215. Available: https://research.fs.usda.gov/treesearch/41009.
 
-[7] Tavernia, B., Nelson, M., Goerndt, M., Walters, B., & Toney, C. (2013). Changes in forest habitat classes under alternative climate and land-use change scenarios in the northeast and midwest, USA. _Mathematical and Computational Forestry & Natural-Resource Sciences_ (MCFNS), **5**:2, 135-150(15). Retrieved from https://www.mcfns.com/index.php/Journal/article/view/MCFNS_165.
+[7] Derwin, J.M., Thomas, V.A., Wynne, R.H., Coulston, J.W., Liknes, G.C., Bender, S., Blinn, C.E., Brooks, E.B., Ruefenacht, B., Benton, R. and Finco, M.V., 2020. Estimating tree canopy cover using harmonic regression coefficients derived from multitemporal Landsat data. _International Journal of Applied Earth Observation and Geoinformation_, 86, 101985, https://doi.org/10.1016/j.jag.2019.101985.
 
-[8] Rowland, M.M.; Vojta, C.D.; tech. eds. 2013. A technical guide for monitoring wildlife habitat. Gen. Tech. Rep. WO-89. Washington, DC: U.S. Department of Agriculture, Forest Service: 400 p. Available: https://doi.org/10.2737/WO-GTR-89.
+[8] Tavernia, B., Nelson, M., Goerndt, M., Walters, B., & Toney, C. (2013). Changes in forest habitat classes under alternative climate and land-use change scenarios in the northeast and midwest, USA. _Mathematical and Computational Forestry & Natural-Resource Sciences_ (MCFNS), 5:2, 135-150. Retrieved from https://www.mcfns.com/index.php/Journal/article/view/MCFNS_165.
 
-[9] Michael C. McGrann, Bradley Wagner, Matthew Klauer, Kasia Kaphan, Erik Meyer, Brett J. Furnas. 2022. Using an acoustic complexity index to help monitor climate change effects on avian diversity.
+[9] Rowland, M.M.; Vojta, C.D.; tech. eds. 2013. A technical guide for monitoring wildlife habitat. Gen. Tech. Rep. WO-89. Washington, DC: U.S. Department of Agriculture, Forest Service: 400 p. Available: https://doi.org/10.2737/WO-GTR-89.
+
+[10] Michael C. McGrann, Bradley Wagner, Matthew Klauer, Kasia Kaphan, Erik Meyer, Brett J. Furnas. 2022. Using an acoustic complexity index to help monitor climate change effects on avian diversity.
 _Ecological Indicators_, Volume 142, 109271, https://doi.org/10.1016/j.ecolind.2022.109271.
 
-[10] McGwire KC, Weltz MA, Nouwakpo S, Spaeth K, Founds M, Cadaret E. 2020. Mapping erosion risk for saline rangelands of the Mancos Shale using the rangeland hydrology erosion model. _Land Degradation & Development_. 31: 2552-2564. https://doi.org/10.1002/ldr.3620.
+[11] McGwire KC, Weltz MA, Nouwakpo S, Spaeth K, Founds M, Cadaret E. 2020. Mapping erosion risk for saline rangelands of the Mancos Shale using the rangeland hydrology erosion model. _Land Degradation & Development_. 31: 2552-2564, https://doi.org/10.1002/ldr.3620.
 
-[11] Riemann, R., Liknes, G., O'Neil-Dunne, J., Toney, C., Lister, T. (2016). Comparative assessment of methods for estimating tree canopy cover across a rural-to-urban gradient in the mid-Atlantic region of the USA. _Environmental Monitoring and Assessment_ **188**:297. https://doi.org/10.1007/s10661-016-5281-8.
+[12] Riemann, R., Liknes, G., O'Neil-Dunne, J., Toney, C., Lister, T. (2016). Comparative assessment of methods for estimating tree canopy cover across a rural-to-urban gradient in the mid-Atlantic region of the USA. _Environmental Monitoring and Assessment_, 188, 297, https://doi.org/10.1007/s10661-016-5281-8.
 
-[12] Andrew N. Gray, Anne C.S. McIntosh, Steven L. Garman, Michael A. Shettles. 2021. Predicting canopy cover of diverse forest types from individual tree measurements. _Forest Ecology and Management_, Volume 501, 119682, ISSN 0378-1127, https://doi.org/10.1016/j.foreco.2021.119682.
+[13] Andrew N. Gray, Anne C.S. McIntosh, Steven L. Garman, Michael A. Shettles. 2021. Predicting canopy cover of diverse forest types from individual tree measurements. _Forest Ecology and Management_, Volume 501, 119682, ISSN 0378-1127, https://doi.org/10.1016/j.foreco.2021.119682.

README.md

@@ -25,14 +25,14 @@ al. 2009 [\[1\]](#references). The original implementation for modeling
 plot canopy cover from individual tree measurements has supported
 several applications of FIA data, including:
 
-- reference data for classifying vegetation types and mapping tree
-  canopy cover in the LANDFIRE Program [\[2, 3, 4, 5\]](#references)
-- National Land Cover Database (NLCD) Tree Canopy Cover (TCC) science
-  and development [\[6\]](#references)
-- wildlife habitat analyses [\[7, 8, 9\]](#references)
-- mapping erosion risk in rangelands [\[10\]](#references)
-- comparative assessments of tree canopy cover estimation methods [\[11,
-  12\]](#references)
+- vegetation type classification and tree canopy cover mapping in the
+  LANDFIRE Program [\[2, 3, 4, 5\]](#references)
+- National Land Cover Database (NLCD) Tree Canopy Cover science and
+  development [\[6, 7\]](#references)
+- wildlife habitat analysis [\[8, 9, 10\]](#references)
+- mapping erosion risk [\[11\]](#references)
+- assessment of tree canopy cover estimation methods [\[12,
+  13\]](#references)
 
 ## Installation
 
@@ -82,11 +82,11 @@ Short, Karen & Chen, Xuexia & Huang, Chengquan & Pabst, Kari & Rollins,
 Matthew. (2011). Monitoring Landscape Change for LANDFIRE Using
 Multi-Temporal Satellite Imagery and Ancillary Data. *Selected Topics in
 Applied Earth Observations and Remote Sensing, IEEE Journal of*. 4.
-252 - 264. 10. <https://doi.org/10.1109/JSTARS.2010.2044478>.
+252-264. 10. <https://doi.org/10.1109/JSTARS.2010.2044478>.
 
 \[5\] Nelson, K.J., Connot, J., Peterson, B. et al. 2013. The LANDFIRE
 Refresh Strategy: Updating the National Dataset. *Fire Ecology*, 9,
-80–101. <https://doi.org/10.4996/fireecology.0902080>.
+80-101, <https://doi.org/10.4996/fireecology.0902080>.
 
 \[6\] Toney, Chris; Liknes, Greg; Lister, Andy; Meneguzzo, Dacia. 2012.
 Assessing alternative measures of tree canopy cover: Photo-interpreted
@@ -97,36 +97,43 @@ Mensurationists*. e-Gen. Tech. Rep. SRS-157. Asheville, NC: U.S.
 Department of Agriculture, Forest Service, Southern Research Station.
 209-215. Available: <https://research.fs.usda.gov/treesearch/41009>.
 
-\[7\] Tavernia, B., Nelson, M., Goerndt, M., Walters, B., & Toney, C.
+\[7\] Derwin, J.M., Thomas, V.A., Wynne, R.H., Coulston, J.W., Liknes,
+G.C., Bender, S., Blinn, C.E., Brooks, E.B., Ruefenacht, B., Benton, R.
+and Finco, M.V., 2020. Estimating tree canopy cover using harmonic
+regression coefficients derived from multitemporal Landsat data.
+*International Journal of Applied Earth Observation and Geoinformation*,
+86, 101985, <https://doi.org/10.1016/j.jag.2019.101985>.
+
+\[8\] Tavernia, B., Nelson, M., Goerndt, M., Walters, B., & Toney, C.
 (2013). Changes in forest habitat classes under alternative climate and
 land-use change scenarios in the northeast and midwest, USA.
 *Mathematical and Computational Forestry & Natural-Resource Sciences*
-(MCFNS), **5**:2, 135-150(15). Retrieved from
+(MCFNS), 5:2, 135-150. Retrieved from
 <https://www.mcfns.com/index.php/Journal/article/view/MCFNS_165>.
 
-\[8\] Rowland, M.M.; Vojta, C.D.; tech. eds. 2013. A technical guide for
+\[9\] Rowland, M.M.; Vojta, C.D.; tech. eds. 2013. A technical guide for
 monitoring wildlife habitat. Gen. Tech. Rep. WO-89. Washington, DC: U.S.
 Department of Agriculture, Forest Service: 400 p. Available:
 <https://doi.org/10.2737/WO-GTR-89>.
 
-\[9\] Michael C. McGrann, Bradley Wagner, Matthew Klauer, Kasia Kaphan,
+\[10\] Michael C. McGrann, Bradley Wagner, Matthew Klauer, Kasia Kaphan,
 Erik Meyer, Brett J. Furnas. 2022. Using an acoustic complexity index to
 help monitor climate change effects on avian diversity. *Ecological
 Indicators*, Volume 142, 109271,
 <https://doi.org/10.1016/j.ecolind.2022.109271>.
 
-\[10\] McGwire KC, Weltz MA, Nouwakpo S, Spaeth K, Founds M, Cadaret E.
+\[11\] McGwire KC, Weltz MA, Nouwakpo S, Spaeth K, Founds M, Cadaret E.
 2020. Mapping erosion risk for saline rangelands of the Mancos Shale
 using the rangeland hydrology erosion model. *Land Degradation &
-Development*. 31: 2552-2564. <https://doi.org/10.1002/ldr.3620>.
+Development*. 31: 2552-2564, <https://doi.org/10.1002/ldr.3620>.
 
-\[11\] Riemann, R., Liknes, G., O’Neil-Dunne, J., Toney, C., Lister, T.
+\[12\] Riemann, R., Liknes, G., O’Neil-Dunne, J., Toney, C., Lister, T.
 (2016). Comparative assessment of methods for estimating tree canopy
 cover across a rural-to-urban gradient in the mid-Atlantic region of the
-USA. *Environmental Monitoring and Assessment* **188**:297.
+USA. *Environmental Monitoring and Assessment*, 188, 297,
 <https://doi.org/10.1007/s10661-016-5281-8>.
 
-\[12\] Andrew N. Gray, Anne C.S. McIntosh, Steven L. Garman, Michael A.
+\[13\] Andrew N. Gray, Anne C.S. McIntosh, Steven L. Garman, Michael A.
 Shettles. 2021. Predicting canopy cover of diverse forest types from
 individual tree measurements. *Forest Ecology and Management*, Volume
 501, 119682, ISSN 0378-1127,