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Analyze the spatial pattern of trees on an FIA plot

Source: R/spatstat_helpers.R
spatstat_helpers.Rd

Functions that facilitate point pattern analysis of FIA tree data using the spatstat library.

Usage

create_fia_owin(linear_unit = "ft", macroplot = FALSE, npoly = 360)

create_fia_ppp(
  tree_list,
  live_trees = TRUE,
  min_dia = 5,
  linear_unit = "ft",
  macroplot = FALSE,
  window = NULL,
  mark_cols = NULL,
  mark_as_factor = NULL
)

Arguments

linear_unit

An optional character string specifying the linear distance unit. Defaults to the native FIA unit of "ft", but may be set to "m" instead (or "meter" / "metre").

macroplot

An optional logical value. The default is FALSE, which defines the FIA plot footprint in terms of the standard four-subplot configuration with subplot radius of 24 ft (7.3152 m). By default, "macroplot trees" having DIST outside the subplot boundary are not included. This argument may be set to TRUE in which case the observation window will be defined using the FIA optional "macroplot" configuration instead (58.9 ft or 18.227 m radius, used only in certain areas of the Pacific Northwest FIA region).

npoly

Integer value giving the number of edges to use for polygon approximation. Defaults to 360.

tree_list

A data frame containing a set of tree records for one FIA plot (see Details).

live_trees

A logical value, TRUE to include live trees only (the default, i.e., STATUSCD == 1).

min_dia

A numeric value specifying the minimum diameter threshold for included trees. The default is 5.0. Trees less than 5-in. diameter but greater than or equal to 1.0-in. diameter, denoted as "saplings", are only recorded in FIA microplots so cannot be stem-mapped across the full 4-subplot footprint.

window

An optional object of class "owin" defining the observation window of an FIA plot in the 2-D plane. Defaults to create_fia_owin(linear_unit, macroplot).

mark_cols

An optional character vector of column names in tree_list to designate as spatstat marks which carry additional information for each data point in a point pattern object.

mark_as_factor

An optional subset of mark_cols to be treated as factor marks. If not already factor, these will be coerced as such upon input. factor marks are those that take only a finite number of possible values (e.g. colors or types).

Details

create_fia_owin() returns an object of class "owin" from the spatstat library. This object represents the generic 2-D observation window for the nationally standard FIA plot design which is a four-point cluster of subplots. Used when creating a spatstat point pattern object for an FIA tree list.

create_fia_ppp() returns an object of class "ppp" representing the point pattern of an FIA tree list in the 2-D plane. A point pattern object defines the dataset for using a stem-mapped FIA plot with functions of the spatstat library.

The standard set of columns for tree list data in FIAstemmap is given below, along with the status of each column as required or optional for create_fia_ppp():

  • PLT_CN: optional, create_fia_ppp() assumes input is for one plot

  • SUBP: required subplot number

  • TREE: required tree number within a subplot

  • AZIMUTH: required horizontal angle from subplot center

  • DIST: required distance from subplot center

  • STATUSCD: required tree status code (1 = live, 2 = dead)

  • SPCD: optional FIA species code

  • SPGRPCD: optional FIA species group code

  • DIA: optional tree diameter

  • HT: optional tree height

  • ACTUALHT: optional tree actual height (accounts for broken top)

  • CCLCD: optional crown class code

  • TPA_UNADJ: optional tree expansion factor (per acre)

  • CRWIDTH: optional crown width (may be computed with TODO)

References

Baddeley A, Rubak E, Turner R (2015). Spatial Point Patterns: Methodology and Applications with R. Chapman and Hall/CRC Press, London. ISBN 9781482210200, https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/p/book/9781482210200/.

Ripley, B.D. (1977) Modelling spatial patterns. Journal of the Royal Statistical Society: Series B (Methodological), 39:2, 172–192. https://doi.org/10.1111/j.2517-6161.1977.tb01615.x.

See also

spatstat package: https://cran.r-project.org/package=spatstat

Examples

# observation window for the standard FIA plot design
w <- create_fia_owin()
summary(w)
#> Window: polygonal boundary
#> 4 separate polygons (no holes)
#>            vertices    area relative.area
#> polygon 1       360 1809.62          0.25
#> polygon 2       360 1809.62          0.25
#> polygon 3       360 1809.62          0.25
#> polygon 4       360 1809.62          0.25
#> enclosing rectangle: [-127.921, 127.921] x [-84.001, 144.001] feet
#>                      (255.8 x 228 feet)
#> Window area = 7238.47 square feet
#> Unit of length: 1 foot
#> Fraction of frame area: 0.124

# or using metric units
w <- create_fia_owin("m")
summary(w)
#> Window: polygonal boundary
#> 4 separate polygons (no holes)
#>            vertices    area relative.area
#> polygon 1       360 168.119          0.25
#> polygon 2       360 168.119          0.25
#> polygon 3       360 168.119          0.25
#> polygon 4       360 168.119          0.25
#> enclosing rectangle: [-38.99032, 38.99032] x [-25.6035, 43.8915] meters
#>                      (77.98 x 69.5 meters)
#> Window area = 672.475 square meters
#> Unit of length: 1 meter
#> Fraction of frame area: 0.124

plot(w, main = "FIA standard four-subplot design")


# point pattern object for the plantation example data
X <- create_fia_ppp(plantation)
summary(X)
#> Planar point pattern:  89 points
#> Average intensity 0.01229542 points per square foot
#> 
#> Coordinates are given to 16 decimal places
#> 
#> Window: polygonal boundary
#> 4 separate polygons (no holes)
#>            vertices    area relative.area
#> polygon 1       360 1809.62          0.25
#> polygon 2       360 1809.62          0.25
#> polygon 3       360 1809.62          0.25
#> polygon 4       360 1809.62          0.25
#> enclosing rectangle: [-127.921, 127.921] x [-84.001, 144.001] feet
#>                      (255.8 x 228 feet)
#> Window area = 7238.47 square feet
#> Unit of length: 1 foot
#> Fraction of frame area: 0.124

plot(X, pch = 16, main = "Loblolly pine plantation")


# plot trees as trees :)
X <- create_fia_ppp(plantation, mark_cols = "SPCD")
plot(X, main = "Loblolly pine plantation",
     shape = "arrows", direction = 90, size = 12, cols = "darkgreen",
     background = "gray90", legend = FALSE)


# Ripley's K-function
K <- spatstat.explore::Kest(X, rmax = 12)
plot(K, main = "Ripley's K-function for the plantation trees")