modelHD: Fitting height-diameter models

In BIOMASS: Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

Fitting height-diameter models

Description

This function fits and compares (optional) height-diameter models.

Usage

modelHD(D, H, method = NULL, useWeight = FALSE, drawGraph = FALSE, plot = NULL)

Arguments

D	Vector with diameter measurements (in cm). NA values are accepted but a minimum of 10 valid entries (i.e. having a corresponding height in H) is required.
H	Vector with total height measurements (in m). NA values are accepted but a minimum of 10 valid entries (i.e. having a corresponding diameter in D) is required.
method	Method used to fit the relationship. To be chosen between: log1, log2 log 1: (log(H) = a+ b*log(D)) (equivalent to a power model) log 2: (log(H) = a+ b*log(D) + c*log(D)^2) weibull: H = a*(1-exp(-(D/b)^c)) michaelis: H = (A * D)/(B + D) If NULL, all the methods will be compared.
useWeight	If weight is TRUE, model weights will be (D^2)*H (i.e. weights are proportional to tree volume, so that larger trees have a stronger influence during the construction of the model).
drawGraph	If TRUE, a graphic will illustrate the relationship between H and D. Only if argument plot is null.
plot	(optional) Plot ID, must be either one value, or a vector of the same length as D. This argument is used to build stand-specific HD models.

Details

All the back transformations for log-log models are done using the Baskerville correction (0.5 * RSE^2, where RSE is the Residual Standard Error).

Value

If plot is NULL or has a single value, a single list is returned. If there is more than one plot, multiple embedded lists are returned with plots as the list names.

If model is not null (model comparison), returns a list :

• input: list of the data used to construct the model (list(H, D))

• model: outputs of the model (same outputs as given by stats::lm(), stats::nls())

• RSE: Residual Standard Error of the model

• RSElog: Residual Standard Error of the log model (NULL if other model)

• residuals: Residuals of the model

• coefficients: Coefficients of the model

• R.squared: R^2 of the model

• formula: Formula of the model

• method: Name of the method used to construct the model

• predicted: Predicted height values

• fitPlot: a ggplot object containing the model fitting plot

If the parameter model is null, the function return a plot with all the methods for comparison, the function also returns a data.frame with:

• method: The method that had been used to construct the plot

• RSE: Residual Standard Error of the model

• RSElog: Residual Standard Error of the log model (NULL if other model)

• Average_bias: The average bias for the model

Author(s)

Maxime REJOU-MECHAIN, Arthur PERE, Ariane TANGUY, Arthur Bailly

See Also

retrieveH()

Examples

# Load a data set
data(NouraguesHD)

# Fit H-D models for the Nouragues dataset

HDmodel <- modelHD(D = NouraguesHD$D, H = NouraguesHD$H, drawGraph = TRUE)


# For a chosen model
HDmodel <- modelHD(D = NouraguesHD$D, H = NouraguesHD$H,
method = "log2", drawGraph = TRUE)

# Using weights
HDmodel <- modelHD(
  D = NouraguesHD$D, H = NouraguesHD$H,
  method = "log2", useWeight = TRUE,
  drawGraph = TRUE)

# With multiple stands (plots)
HDmodel <- modelHD(
  D = NouraguesHD$D, H = NouraguesHD$H,
  method = "log2", useWeight = TRUE, 
  plot = NouraguesHD$plotId, drawGraph = TRUE)

BIOMASS documentation built on April 3, 2025, 6:09 p.m.