tprDiameter: Functions to extract diameters from Taper curve

In TapeS: Tree Taper Curves and Sorting Based on 'TapeR'

Functions to extract diameters from Taper curve

Description

Function evaluates TapeR taper curve models for given trees according to species, required height and optionally substracts double bark thickness.

Usage

tprDiameter(
  obj,
  Hx,
  bark = TRUE,
  interval = "none",
  cp = TRUE,
  mono = TRUE,
  Rfn = NULL
)

## S4 method for signature 'tprTrees'
tprDiameter(
  obj,
  Hx,
  bark = TRUE,
  interval = "none",
  cp = TRUE,
  mono = TRUE,
  Rfn = NULL
)

Arguments

obj	object of class 'tprTrees'
Hx	vector of heights for which diameter w/ or w/0 bark are required
bark	should diameter over or under bark be returned?
interval	indicator about whether 'confidence' or 'prediction' intervals are required (defaults to 'none'), optionally function returns the mean squared error of the mean and predictions ('MSE').
cp	cartesian product, i.e. apply all Hx to all trees, defaults to TRUE
mono	logical, defaults to true. If calibrated taper curve is non-monotonic at stem base, a support diameter is added.
Rfn	Rfn setting for residuals error matrix, defaults to list(fn="sig2"), see resVar.

Details

Function evaluates taper curves at required height Hx. By default (cp==TRUE), the taper curve is evaluated at Hx for each tree. If cp==FALSE, each tree is evaluated at exactly one Hx (recycled if necessary). This feature is intended for situations where diameter in relative heights are required. Then, the recycling of one height Hx (e.g. 1.3m) is not possible, since relative heights depend on absolute tree height, which might be different for each tree. Hence a call like tprDiameter(obj, Hx=0.3*Ht(obj), cp=FALSE) is necessary.

Value

a matrix or data.frame depending on value of interval. If 'none' (the default), a matrix of size [length(obj@Ht), length(Hx)] is returned, otherwise a data.frame of size [length(obj@Ht) * length(Hx), 5]. The five columns hold a tree identifier, Hx, lower confidence/prediction interval, the estimated diameter and the upper confidence/prediction interval. In case 'interval=MSE' the returned columns contain a tree identifier, Hx, the estimated diameter and mean squared error (MSE) of the mean and of the prediction. Estimates and intervals include bark or not, depending on bark.

Methods (by class)

• tprDiameter(tprTrees): method for class 'tprTrees'

See Also

tprDiameterCpp for a faster implementation if no confidence or prediction information are required and tprBark for the applied bark reduction.

Examples

## prediction for new tree using implemented 'TapeR' taper curve model
obj <- tprTrees(spp=c(1, 3),
                Hm=list(c(1.3, 5), c(1.3, 5)),
                Dm=list(c(27, 25), c(27, 25)),
                Ht=c(27, 27))
hx <- c(1.3, 5, 7)
## by default, Hx applied on each tree, i.e. result is a 2x3 matrix
tprDiameter(obj, Hx = hx)

## if cp=FALSE, each tree only 'sees' one Hx, i.e. results is a vector
## (obs: length of Hx must be identical to length of obj)
tprDiameter(obj, Hx = c(1.3, 5), cp=FALSE)
tprDiameter(obj, Hx = hx, bark = FALSE)
tprDiameter(obj, Hx = hx, interval = "confidence")
tprDiameter(obj, Hx = hx, bark = FALSE, interval = "prediction")
tprDiameter(obj, Hx = hx, interval = "MSE")
tprDiameter(obj, Hx = hx, bark=FALSE, interval = "MSE")

## here same behaviour, if cp=FALSE
tprDiameter(obj, Hx = c(1.3, 5), bark = FALSE,
            interval = "prediction", cp=FALSE)
## using Cpp-implementation
## faster, but no intervals available
tprDiameterCpp(obj, Hx = hx)
tprDiameterCpp(obj, Hx = c(1.3, 5), cp=FALSE)

## prediction for objects of class 'datBDAT':
if(require(rBDAT)){
  tree <- rBDAT::buildTree(list(spp=1, D1=20:30, H1=1.3, H2=50, H=20:30))
  tree <- bdat_as_tprtrees(tree)
  tprDiameter(tree, Hx = 1.3)
}

TapeS documentation built on March 31, 2023, 7:19 p.m.