Description Usage Arguments Value Examples
Transforms raw data into regression curves using the GP_fit
function in the GPfit
package. The response data can be constrained between minima and maxima (for example, the default sets any negative predicted y value to 0).
1 2 |
data |
Data frame with function-valued species data along with a column named "species" |
x_variable |
The name of the column in |
y_variable |
The name of the column in |
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 GP_fit function. |
X |
X (formatted for phylocurve.generalized) |
Y |
Y (formatted for phylocurve.generalized) |
1 2 3 4 5 6 7 8 9 10 | x_length <- 50
nspecies <- 25
sim_data <- sim.curves(nspecies = nspecies,x_length = x_length)
# Fit nonlinear curves to raw data
# NOT RUN (takes several minutes)
#curve_data <- GP.fit(data = sim_data$data,x_variable = "x",y_variable = "y",min_y = 0)
# Align curve data using dynamic time warping
# P <- phylocurve.generalized(tree = sim_data$tree,X = curve_data$X,Y = curve_data$Y)
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