update references

Author: ctoney

README.Rmd

@@ -23,10 +23,11 @@ knitr::opts_chunk$set(
 
 The Forest Inventory and Analysis (FIA) Program of USDA Forest Service provide tree-level measurements from a systematic grid of field plots across all forest ownerships and land uses in the US. **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]](#References)
-* National Land Cover Database (NLCD) Tree Canopy Cover (TCC) science and development [[4]](#References)
-* wildlife habitat analysis [[5]](#References)
-* comparative assessments of tree canopy cover estimation methods [[6, 7]](#References)
+* 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)
 
 ## Installation
 
@@ -54,10 +55,21 @@ 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] 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.
+[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] 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.
+[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] 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.
+[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] 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.
+[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.
+
+[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.
+
+[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.
+_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] 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.

README.md

@@ -24,12 +24,13 @@ 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 [\[2, 3\]](#References)
+  canopy cover in the LANDFIRE Program [\[2, 3, 4, 5\]](#References)
 - National Land Cover Database (NLCD) Tree Canopy Cover (TCC) science
-  and development [\[4\]](#References)
-- wildlife habitat analysis [\[5\]](#References)
-- comparative assessments of tree canopy cover estimation methods [\[6,
-  7\]](#References)
+  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)
 
 ## Installation
 
@@ -74,7 +75,18 @@ CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain
 Research Station. 2 p. Available:
 <https://research.fs.usda.gov/treesearch/68397>.
 
-\[4\] Toney, Chris; Liknes, Greg; Lister, Andy; Meneguzzo, Dacia. 2012.
+\[4\] 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>.
+
+\[6\] 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
@@ -83,20 +95,36 @@ 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>.
 
-\[5\] Tavernia, B., Nelson, M., Goerndt, M., Walters, B., & Toney, C.
+\[7\] 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>.
 
-\[6\] Riemann, R., Liknes, G., O’Neil-Dunne, J., Toney, C., Lister, T.
+\[8\] 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>.
+
+\[9\] 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. *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>.
+
+\[11\] 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>.
 
-\[7\] Andrew N. Gray, Anne C.S. McIntosh, Steven L. Garman, Michael A.
+\[12\] 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,