fit_gam {metabCombiner} | R Documentation

## Fit RT Projection Model With GAMs

### Description

Fits a (penalized) basis splines curve through a set of ordered pair retention times, modeling one set of retention times (rty) as a function on the other set (rtx). Outlier filtering iterations are performed first, then with the remaining points, the best value of parameter `k` is selected through 10-fold cross validation.

### Usage

    fit_gam(
      object,
      useID = FALSE,
      k = seq(10, 20, 2),
      iterFilter = 2,
      outlier = c("MAD", "boxplot"),
      coef = 2,
      prop = 0.5,
      weights = 1,
      bs = c("bs", "ps"),
      m = c(3, 2),
      family = c("scat", "gaussian"),
      method = "REML",
      optimizer = "newton",
      message = TRUE,
      ...
    )

### Arguments

`object` | a `metabCombiner` object.
`useID` | logical. If set to TRUE, matched ID anchors detected from previous step will never be flagged as outliers.
`k` | integer k values controlling the dimension of the basis of the GAM fit (see: ?mgcv::s). Best value chosen by 10-fold cross validation.
`iterFilter` | integer number of outlier filtering iterations to perform
`outlier` | Thresholding method for outlier dection. If "MAD", the threshold is the mean absolute deviation (MAD) times `coef`; if "boxplot", the threshold is `coef` times IQR plus 3rd quartile of a model's absolute residual values.
`coef` | numeric (> 1) multiplier for determining thresholds for outliers (see `outlier` argument)
`prop` | numeric. A point is excluded if deemed a residual in more than this proportion of fits. Must be between 0 & 1.
`weights` | Optional user supplied weights for each ordered pair. Must be of length equal to number of anchors (n) or a divisor of (n + 2).
`bs` | character. Choice of spline method from mgcv, either "bs" (basis splines) or "ps" (penalized basis splines)
`m` | integer. Basis and penalty order for GAM; see ?mgcv::s
`family` | character. Choice of mgcv family; see: ?mgcv::family.mgcv
`method` | character smoothing parameter estimation method; see: ?mgcv::gam
`optimizer` | character. Method to optimize smoothing parameter; see: ?mgcv::gam
`message` | Option to print message indicating function progress
`...` | Other arguments passed to `mgcv::gam`.

### Details

A set of ordered pair retention times must be previously computed using `selectAnchors()`. The minimum and maximum retention times from both input datasets are included in the set as ordered pairs (min_rtx, min_rty) & (max_rtx, max_rty). The `weights` argument initially determines the contribution of each point to the model fits; they are equally weighed by default, but can be changed using an `n+2` length vector, where n is the number of ordered pairs and the first and last of the weights determines the contribution of the min and max ordered pairs; by default, all weights are initially set to 1 for equal contribution of each point.

The model complexity is determined by `k`. Multiple values of k are allowed, with the best value chosen by 10 fold cross validation. Before this happens, certain ordered pairs are removed based on the model errors. In each iteration, a GAM is fit using each selected value of k. Depending on the `outlier` argument, a point is "removed" from the model (i.e. its corresponding weight set to 0) if its residual is above the threshold for a proportion of fitted models, as determined by `prop`. If an anchor is an "identity" (idx = idy, detected in the `selectAnchors` by setting `useID` to TRUE), then setting `useID` here prevents its removal.

Other arguments, e.g. `family`, `m`, `optimizer`, `bs`, and `method` are GAM specific parameters from the `mgcv` R package. The `family` option is currently limited to the "scat" (scaled t) and "gaussian" families; scat family model fits are more robust to outliers than gaussian fits, but compute much slower. Type of splines are currently limited to basis splines ("bs" or "ps").

### Value

metabCombiner with a fitted GAM model object

### See Also

`selectAnchors`,`fit_loess`,

### Examples

    data(plasma30)
    data(plasma20)

    p30 <- metabData(plasma30, samples = "CHEAR")
    p20 <- metabData(plasma20, samples = "Red", rtmax = 17.25)
    p.comb = metabCombiner(xdata = p30, ydata = p20, binGap = 0.0075)

    p.comb = selectAnchors(p.comb, tolmz = 0.003, tolQ = 0.3, windy = 0.02)
    anchors = getAnchors(p.comb)

    #version 1: using faster, but less robust, gaussian family
    p.comb = fit_gam(p.comb, k = c(10,12,15,17,20), prop = 0.5,
        family = "gaussian", outlier = "MAD", coef = 2)

    #version 2: using slower, but more robust, scat family
    p.comb = fit_gam(p.comb, k = seq(12,20,2), family = "scat",
                         iterFilter = 1, coef = 3, method = "GCV.Cp")

    #version 3 (with identities)
    p.comb = selectAnchors(p.comb, useID = TRUE)
    anchors = getAnchors(p.comb)
    p.comb = fit_gam(p.comb, useID = TRUE, k = seq(12,20,2), iterFilter = 1)

    #version 4 (using identities and weights)
    weights = ifelse(anchors$labels == "I", 2, 1)
    p.comb = fit_gam(p.comb, useID = TRUE, k = seq(12,20,2),
                         iterFilter = 1, weights = weights)

    #version 5 (using boxplot-based outlier detection
    p.comb = fit_gam(p.comb, k = seq(12,20,2), outlier = "boxplot", coef = 1.5)

    #to preview result of fit_gam
    plot(p.comb, pch = 19, outlier = "h", xlab = "CHEAR Plasma (30 min)",
         ylab = "Red-Cross Plasma (20 min)", main = "Example GAM Fit")

[Package metabCombiner version 1.2.2 Index]