fitgamParam {metabCombiner} | R Documentation

## 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",
      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"
`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")

[Package metabCombiner version 1.2.2 Index]