crossValFit: Cross Validation for Model Fits

In metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

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

metabCombiner documentation built on Dec. 10, 2020, 2 a.m.