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doc: various updates and add spelling word list
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‎DESCRIPTION‎

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Title: Stand structure analysis of US national forest inventory plots
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Version: 0.0.0.9000
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Authors@R:
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person("Chris", "Toney", , "chris.toney@usda.gov", role = c("aut", "cre"))
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person("Chris", "Toney", email = "jctoney@gmail.com",
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role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5734-6510"))
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Description: Maps individual tree stem locations on field plots of the Forest
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Inventory and Analysis (FIA) Program of USDA Forest Service. Stem locations
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are mapped in cartesian coordinate space based on distance and azimuth
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License: MIT + file LICENSE
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Depends: R (>= 4.1.0)
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Imports: gdalraster, methods, spatstat.geom
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Suggests: spatstat.explore, testthat (>= 3.0.0)
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Suggests:
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spatstat.explore,
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spelling,
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testthat (>= 3.0.0)
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URL: https://ctoney.github.io/FIAstemmap/
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Config/testthat/edition: 3
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Encoding: UTF-8
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.3
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Language: en-US

‎R/spatstat_helpers.R‎

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#' Helper functions for spatial point pattern analysis of FIA plots
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#' Analyze tree spatial pattern on FIA plots
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#'
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#' Functions that facilitate analysis of FIA tree data using the \pkg{spatstat}
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#' library.
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#' Functions that facilitate point pattern analysis of FIA tree data using the
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#' \pkg{spatstat} library.
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#'
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#' @name spatstat_helpers
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#' @details
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#' @param npoly Integer value giving the number of edges to use for polygon
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#' approximation. Defaults to `360`.
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#' @param tree_list A data frame containing a set of tree records for one FIA
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#' plot (see Deatils).
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#' plot (see Details).
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#' @param live_trees A logical value, `TRUE` to include live trees only (the
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#' default, i.e., `STATUSCD == 1`).
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#' @param min_dia A numeric value specifying the minimum diameter threshold
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#' to designate as \pkg{spatstat} `marks` which carry additional information for
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#' each data point in a point pattern object.
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#' @param mark_as_factor An optional subset of `mark_cols` to be treated as
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#' `factor` marks. If not already `factor`, these will be corced as such upon
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#' `factor` marks. If not already `factor`, these will be coerced as such upon
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#' input. `factor` marks are those that take only a finite number of possible
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#' values (e.g. colors or types).
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#'
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#'
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#' plot(w, main = "FIA standard four-subplot design")
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#'
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#' # point pattern object for the plantation example dataset
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#' # point pattern object for the plantation example data
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#' X <- create_fia_ppp(plantation)
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#' summary(X)
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#'
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#' plot(X, main = "Pine plantation stem map")
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#' plot(X, pch = 16, main = "Loblolly pine plantation")
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#'
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#' # plot trees as trees :)
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#' X <- create_fia_ppp(plantation, mark_cols = "SPCD")
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#' plot(X, main = "Pine plantation stem map",
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#' plot(X, main = "Loblolly pine plantation",
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#' shape = "arrows", direction = 90, size = 12, cols = "darkgreen",
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#' background = "gray90", legend = FALSE)
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#'

‎README.Rmd‎

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)
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```
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# FIA stem map
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<!-- badges: start -->
2019
<!-- badges: end -->
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**This is an implementation update, currently in-development**
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## NOTE: this repo is an implementation update currently in-development
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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:
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The Forest Inventory and Analysis Program ([FIA](https://research.fs.usda.gov/programs/nfi)) 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:
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* reference data for classifying vegetation types and mapping tree canopy cover in the LANDFIRE Program [[2, 3, 4, 5]](#References)
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* National Land Cover Database (NLCD) Tree Canopy Cover (TCC) science and development [[6]](#References)
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[1] Toney, Chris; Shaw, John D.; Nelson, Mark D. 2009. A stem-map model for predicting tree canopy cover of Forest Inventory and Analysis (FIA) plots. In: McWilliams, Will; Moisen, Gretchen; Czaplewski, Ray, comps. _Forest Inventory and Analysis (FIA) Symposium 2008_; October 21-23, 2008; Park City, UT. Proc. RMRS-P-56CD. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 19 p. Available: https://research.fs.usda.gov/treesearch/33381.
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[2] LANDFIRE: LANDFIRE Existing Vegetation Cover layer. (LF2024 version releasd 2025 - last update). U.S. Department of Interior, Geological Survey, and U.S. Department of Agriculture. [Online]. Available: https://landfire.gov/vegetation/evc [accessed 2026, Feb 24].
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[2] LANDFIRE: LANDFIRE Existing Vegetation Cover layer. (LF2024 version released 2025 - last update). U.S. Department of Interior, Geological Survey, and U.S. Department of Agriculture. [Online]. Available: https://landfire.gov/vegetation/evc [accessed 2026, Feb 24].
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[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.
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‎README.md‎

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<!-- badges: end -->
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**This is an implementation update, currently in-development**
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The Forest Inventory and Analysis (FIA) Program of USDA Forest Service
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provide tree-level measurements from a systematic grid of field plots
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across all forest ownerships and land uses in the US. **FIAstemmap** is
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an R package for mapping tree stem locations on FIA plots, modeling
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individual crown dimensions, and generating plot-level estimates of
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fractional tree canopy cover. Several stand height metrics can be
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calculated. Spatial analysis of tree point pattern is facilitated for
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the standard FIA four-point cluster plot design. Efficient data
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## NOTE: this repo is an implementation update currently in-development
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The Forest Inventory and Analysis Program
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([FIA](https://research.fs.usda.gov/programs/nfi)) of USDA Forest
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Service provide tree-level measurements from a systematic grid of field
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plots across all forest ownerships and land uses in the US.
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**FIAstemmap** is an R package for mapping tree stem locations on FIA
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plots, modeling individual crown dimensions, and generating plot-level
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estimates of fractional tree canopy cover. Several stand height metrics
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can be calculated. Spatial analysis of tree point pattern is facilitated
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for the standard FIA four-point cluster plot design. Efficient data
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processing supports national applications. The package provides an
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updated implementation of the software originally described by Toney et
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al. 2009 [\[1\]](#References). The original implementation for modeling
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<https://research.fs.usda.gov/treesearch/33381>.
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\[2\] LANDFIRE: LANDFIRE Existing Vegetation Cover layer. (LF2024
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version releasd 2025 - last update). U.S. Department of Interior,
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version released 2025 - last update). U.S. Department of Interior,
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Geological Survey, and U.S. Department of Agriculture. \[Online\].
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Available: <https://landfire.gov/vegetation/evc> \[accessed 2026, Feb
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24\].

‎inst/CITATION‎

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bibentry(
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bibtype = "InProceedings",
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title = "A stem-map model for predicting tree canopy cover of Forest Inventory and Analysis (FIA) plots",
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author = c(
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person("Chris", "Toney", role = "aut", comment = c(ORCID = "0000-0001-5734-6510")),
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person(c("John", "D."), "Shaw", role = "aut"),
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person(c("Mark", "D."), "Nelson", role = "aut")),
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year = "2009",
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booktitle = "Forest Inventory and Analysis (FIA) Symposium 2008",
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editor = as.person("Will McWilliams [com], Gretchen Moisen [com], Ray Czaplewski [com]"),
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month = "October 21-23, 2008",
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address = "Park City, UT",
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number = "RMRS-P-56CD",
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organization = "USDA Forest Service, Rocky Mountain Research Station",
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publisher = "USDA Forest Service, Rocky Mountain Research Station",
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url = "https://research.fs.usda.gov/treesearch/33381"
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)

‎inst/WORDLIST‎

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ACTUALHT
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Asheville
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Bastian
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Bechtold
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Biging
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Cadaret
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Chengquan
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Connot
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Czaplewski
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Dacia
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Daryn
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Dockter
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FIA
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Furnas
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Garman
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Goerndt
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ISSN
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Inga
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Kaphan
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Kasia
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Klauer
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Kost
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LANDFIRE
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LF
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Liknes
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MCFNS
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Mancos
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McGrann
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McGwire
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McWilliams
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Menakis
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Meneguzzo
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Mensurationists
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Moisen
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NAIP
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NLCD
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Nouwakpo
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Picotte
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Proc
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RMRS
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Roesch
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SRS
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Schleeweis
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Shettles
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Smail
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Spaeth
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TCC
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Tavernia
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Tobin
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Tolk
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Vogelmann
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Vojta
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WO
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Weltz
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Xuexia
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al
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allometric
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et
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loblolly
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macroplot
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microplot
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microplots
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midwest
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ownerships
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rangeland
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rangelands
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spatstat

‎man/spatstat_helpers.Rd‎

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‎tests/spelling.R‎

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if(requireNamespace('spelling', quietly = TRUE))
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spelling::spell_check_test(vignettes = TRUE, error = FALSE,
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skip_on_cran = TRUE)

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