nonlinear.fit: Fit nonlinear curves to species data

In phylocurve: Phylogenetic Comparative Methods for High-Dimensional Traits

Description

Transforms raw data into regression curves using the drm function in the drc package. The response data can be constrained between minima and maxima (for example, the default sets any negative predicted y value to 0).

Usage

nonlinear.fit(data, x_variable, y_variable, fct = LL2.3(),
  min_x = -Inf, max_x = Inf, min_y = 0, max_y = Inf, eval_length = 30, ...)

Arguments

data	Data frame with function-valued species data along with a column named "species"
x_variable	The name of the column in data corresponding to the predictor (x) variable
y_variable	The name of the column in data corresponding to the response (y) variable
fct	Function type to pass to drm. Use getMeanFunctions for a full list.
min_x	Lower range to remove from raw x data
max_x	Upper range to remove from raw x data
min_y	Lower range to remove from predicted response (for example, for response data in which only positive values are allowed, the min_y can be set to 0 (the default)).
max_y	Upper range to remove from predicted response.
eval_length	How many points to evaluate along the range of x.
...	Optional further arguments to pass to the drm function.

Value

X	X (formatted for phylocurve.generalized)
Y	Y (formatted for phylocurve.generalized)

Examples

x_length <- 50
nspecies <- 25
sim_data <- sim.curves(nspecies = nspecies,x_length = x_length)

# Fit nonlinear curves to raw data
curve_data <- nonlinear.fit(data = sim_data$data,x_variable = "x",y_variable = "y",min_y = 0)

# Align curve data using dynamic time warping
# NOT RUN (takes several minutes)
# P <- phylocurve.generalized(tree = sim_data$tree,X = curve_data$X,Y = curve_data$Y)

phylocurve documentation built on Dec. 16, 2019, 1:35 a.m.