aRchi (version 2.1.3)

add_leaves: Generate foliage to a QSM or skeleton with segmented annual shoots.

Description

Generate foliage to a QSM or skeleton with segmented annual shoots.

Usage

add_leaves(
  aRchi,
  aArea = 73.027,
  bArea = 0.826,
  aNl = 2.563,
  bNl = 0.4402,
  aNin = 2.1337,
  bNin = 0.3818,
  elev = c(17, 45),
  elev_error = 5,
  az_err = 20,
  phyllo = "opposite_decussate",
  simple = T,
  petiole = 0.5
)
# S4 method for aRchi
add_leaves(
  aRchi,
  aArea = 73.027,
  bArea = 0.826,
  aNl = 2.563,
  bNl = 0.4402,
  aNin = 2.1337,
  bNin = 0.3818,
  elev = c(17, 45),
  elev_error = 5,
  az_err = 20,
  phyllo = "opposite_decussate",
  simple = T,
  petiole = 0.5
)

Value

The aRchi file now including the reconstructed foliage.

Arguments

aRchi

a file of class aRchi.

aArea

numeric. Allometric coefficient (a) for leaf area per annual shoot.

bArea

numeric. Allometric coefficient (b) for leaf area per annual shoot.

aNl

numeric. Allometric coefficient (a) for the number of leaves per annual shoot.

bNl

numeric. Allometric coefficient (b) for the number of leaves per annual shoot.

aNin

numeric. Allometric coefficient (a) for the number of internodes per annual shoot.

bNin

numeric. Allometric coefficient (b) for the number of internodes per annual shoot.

elev

numeric. A single value or a vector of length 2 giving the leaves elevation angles.

elev_error

numeric. A random error added to leaves elevation angle.

az_err

numeric. A random error added to leaves azimuth.

phyllo

character. The phyllotaxy used to insert the leaves along the annual shoot. Accepted values: "alternate", "spiral", "opposite", "opposite_decussate".

simple

logical. Bypass the allometry for the number of leaves per annual shoot to insert the leaves on each internode.

petiole

numeric. The petiole length given as a multiplier of the leaf length.

Details

Allometries for the leaf area, number of leaves and number of internodes are computed at the annual shoot level and are of the form X = a*AS_length^b. The leaves elevation angle is constant if a single value is provided for elev or is linearly interpolated based of the leaf relative height within the tree crown if two values are provided.

References

Lecigne, B., Delagrange, S., Lauri, P. É., & Messier, C. (2022). Trimming influences tree light interception and space exploration: contrasted responses of two cultivars of Fraxinus pennsylvanica at various scales of their architecture. Trees, 1-17. https://doi.org/10.1007/s00468-022-02273-5

Examples

# \donttest{
# import aRchi file
aRchi=system.file("extdata","Tree_2.aRchi",package = "aRchi")
aRchi = aRchi::read_aRchi(aRchi)

# smooth skeleton
aRchi = smooth_skeleton(aRchi)

# segment annual shoots
aRchi = aRchi::segment_annual_shoots(aRchi,tree_age = 13)

# add physiological ages
aRchi = aRchi::add_physiological_ages(aRchi)

# add leaves
aRchi = aRchi::add_leaves(aRchi)

plot(aRchi,leaves=TRUE,bg="white",color="chocolate4")
# }