merit.function: Compute the chi2 merit function for template fitting
In oczoske/slacR: R-package to measure v and sigma from VIMOS IFU cubes

Description Usage Arguments Details Value Note Author(s) See Also

This function computes the noise weighted chi2 merit function for template fitting. The model is a stellar template spectrum convolved with a Gaussian or Gauss-Hermitian LOSVD. It is matched to a galaxy spectrum. The galaxy spectrum, the model spectrum and the residuals can be plotted.

merit.function(p, galaxy, template, LOSVD=c("gauss", "gh",
               "gauss-hermite"), mask = TRUE, noise = NULL,
               plot = FALSE, verbose = FALSE, return.fit = FALSE,
               sigma.max = 1000, ...)

`p`	a two-component `vector` containing the parameters for the template fit: velocity `v` and velocity dispersion `sigma`, both in km/s.
`galaxy`	an object of class `spectrum` containing the galaxy spectrum that is to be fitted
`template`	an object of class `spectrum` containing the stellar template spectrum
`LOSVD`	Shape of the LOSVD to be fit to the spectrum. Defaults to Gaussian but can also be set to a Gauss-Hermite series, to order 4.
`mask`	a data.frame with two columns `x1` and `x2` giving the left and right limits of wavelength regions that are to be masked; or, the name of a file containing such a data.frame; or, a logical vector along `galaxy$lambda`, with `TRUE` for pixels that shall be included in the fit
`noise`	a vector along `galaxy$lambda` containing an estimate of the noise for each pixel; or, a single number giving the average noise value. If missing, the merit function will be unnormalized.
`plot`	`logical`. If `TRUE`, the galaxy spectrum will be plotted along with the model and residuals.
`verbose`	`logical`. If `TRUE`, informative messages will be printed
`return.fit`	`logical`. If `FALSE`, only the value of the merit function will be returned, otherwise a list (see below).
`sigma.max`	the maximum allowed value for `sigma`. If `sigma` is larger than `sigma.max`, the function will return `NA`.
`...`	Parameters to be passed to `build.model`, in particular the orders of the multiplicative and additive polynomials

The value returned by this function does not seem to be a proper chi2 yet.

If return.fit is FALSE, only the value of the merit function is returned. This should be the setting for optimising over the parameters. If return.fit is TRUE, a list is returned with the components

`L, M`	the coordinates of `galaxy`
`gof`	the value of the merit function
`v, sigma, h3, h4`	the kinematic parameters used in the computation of the merit function
`lambda, model, residual`	the model spectrum and the residuals on the wavelength vector of `galaxy`
`mask, noise`	the mask and noise vectors
`lm.fit`	the linear fit for the coefficients of the multiplicative and additive polynomials