fitgamParam: List fit_gam Defaults

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

List fit_gam Defaults

Description

List of default parameters for GAM fitting step of main package workflow, which can be used as input for the wrapper functions. See help(fit_gam) or ?fit_gam for more details.

Usage

fitgamParam(
  useID = FALSE,
  k = seq(10, 20, 2),
  iterFilter = 2,
  outlier = "MAD",
  coef = 2,
  prop = 0.5,
  weights = 1,
  bs = "bs",
  family = "scat",
  m = c(3, 2),
  method = "REML",
  rtx = c("min", "max"),
  rty = c("min", "max"),
  optimizer = "newton",
  message = TRUE
)

Arguments

useID	choice of preserving identity-based anchors; default: FALSE
k	values for GAM basis dimension k
iterFilter	number of outlier filtering iterations; default: 2
outlier	outlier filtering method (either "MAD" (mean absolute deviation) or "boxplot"); default: "MAD"
coef	outlier filtering coefficient; default: 2
prop	minimum proportion of fits in which a point can be a flagged outlier; default: 0.5
weights	optional supplied weights to individual points; default: 1
bs	choice of spline type ("bs" or "ps"); default: "bs"
family	choice of family ("scat" or "gaussian"); default: "scat"
m	basis and penalty order; default: c(3,2)
method	smoothing parameter estimation method; default: "REML"
rtx	ordered pair of endpoints for rtx; default: ("min", "max")
rty	ordered pair of endpoints for rty; default: ("min", "max")
optimizer	numerical optimization for GAM; default: "newton"
message	option to print progress message; default: TRUE

Value

list of fit_gam parameters

See Also

fit_gam, metabCombine

Examples

fitParam <- fitgamParam(k = c(12,14,18,20), iterFilter = 1, bs = "ps",
                        family = "gaussian", method = "GCV.Cp")

hhabra/metabCombiner documentation built on Jan. 26, 2024, 12:23 p.m.