prcurve {analogue}  R Documentation 
A principal curve is a nonparametric generalisation of the principal component and is a curve that passes through the middle of a cloud of data points for a certain definition of ‘middle’.
prcurve(X, method = c("ca", "pca", "random", "user"), start = NULL, smoother = smoothSpline, complexity, vary = FALSE, maxComp, finalCV = FALSE, axis = 1, rank = FALSE, stretch = 2, maxit = 10, trace = FALSE, thresh = 0.001, plotit = FALSE, ...) initCurve(X, method = c("ca", "pca", "random", "user"), rank = FALSE, axis = 1, start)
X 
a matrixlike object containing the variables to which the principal curve is to be fitted. 
method 
character; method to use when initialising the principal
curve. 
start 
numeric vector specifying the initial curve when

smoother 
function; the choice of smoother used to fit the
principal curve. Currently, the only options are

complexity 
numeric; the complexity of the fitted smooth functions. The function passed as argument 
vary 
logical; should the complexity of the smoother fitted to
each variable in 
maxComp 
numeric; the upper limt on the allowed complexity. 
finalCV 
logial; should a final fit of the smooth function be performed using cross validation? 
axis 
numeric; the ordinaion axis to use as the initial curve. 
rank 
logical; should rank position on the gradient be used? Not yet implemented. 
stretch 
numeric; a factor by which the curve can be extrapolated when points are projected. Default is 2 (times the last segment length). 
maxit 
numeric; the maximum number of iterations. 
trace 
logical; print progress on the iterations be printed to the console? 
thresh 
numeric; convergence threshold on shortest distances to
the curve. The algorithm is considered to have converged when the
latest iteration produces a total residual distance to the curve
that is within 
plotit 
logical; should the fitting process be plotted? If

... 
additional arguments are passed solely on to the function

An object of class "prcurve"
with the following components:
s 
a matrix corresponding to 
tag 
an index, such that 
lambda 
for each point, its arclength from the beginning of the curve. 
dist 
the sumofsquared distances from the points to their projections. 
converged 
logical; did the algorithm converge? 
iter 
numeric; the number of iterations performed. 
totalDist 
numeric; total sumofsquared distances. 
complexity 
numeric vector; the complexity of the smoother
fitted to each variable in 
call 
the matched call. 
ordination 
an object of class 
data 
a copy of the data used to fit the principal curve. 
The fitting function uses function
project_to_curve
in package princurve
to find the projection of the data on to the fitted curve.
Gavin L. Simpson
smoothGAM
and smoothSpline
for the
wrappers fitting smooth functions to each variable.
## Load Abernethy Forest data set data(abernethy) ## Remove the Depth and Age variables abernethy2 < abernethy[, (37:38)] ## Fit the principal curve using the median complexity over ## all species aber.pc < prcurve(abernethy2, method = "ca", trace = TRUE, vary = FALSE, penalty = 1.4) ## Extract fitted values fit < fitted(aber.pc) ## locations on curve abun < fitted(aber.pc, type = "smooths") ## fitted response ## Fit the principal curve using varying complexity of smoothers ## for each species aber.pc2 < prcurve(abernethy2, method = "ca", trace = TRUE, vary = TRUE, penalty = 1.4) ## Predict new locations take < abernethy2[1:10, ] pred < predict(aber.pc2, take) ## Not run: ## Fit principal curve using a GAM  currently slow ~10secs aber.pc3 < prcurve(abernethy2 / 100, method = "ca", trace = TRUE, vary = TRUE, smoother = smoothGAM, bs = "cr", family = mgcv::betar()) ## End(Not run)