crossValFit {metabCombiner}R Documentation

Cross Validation for Model Fits

Description

Helper function for fit_gam() & fit_loess(). Determines optimal value of k basis functions for Generalized Additive Model fits or span for loess fits from among user-defined choices, using a 10-fold cross validation minimizing mean squared error.

Usage

crossValFit(rts, fit, vals, bs, family, m, method, optimizer, loess.pars, ...)

Arguments

rts

data.frame of ordered pair retention times

fit

Either "gam" for GAM fits, or "loess" for loess fits

vals

numeric vector: k values for GAM fits, spans for loess fits. Best value chosen by 10-fold cross validation.

bs

character. Choice of spline method, either "bs" or "ps"

family

character. Choice of mgcv family; see: ?mgcv::family.mgcv

m

integer. Basis and penalty order for GAM; see ?mgcv::s

method

character. Smoothing parameter estimation method; see: ?mgcv::gam

optimizer

character. Method to optimize smoothing parameter; see: ?mgcv::gam

loess.pars

parameters for LOESS fitting; see ?loess.control

...

Other arguments passed to mgcv::gam.

Value

Optimal parameter value as determined by 10-fold cross validation


[Package metabCombiner version 1.0.1 Index]