fitStd: Fit Standards
In Greenhouse-Lab/lumfit: Luminex Data Processing

Description Usage Arguments Details Value

View source: R/fitStd.R

Fits a specified function to MFI summary of serial dilutions. Optionally an interactive procedure that allows to remove outliers, evaluate resulting fits, perform revisions, and record a message regarding the fit.

fitStd(std, xvar, yvar, model = "sigmoid", Alow = NULL, asym = TRUE,
  interactive = TRUE, monot.prompt = FALSE, rm.before = FALSE,
  rm.after = interactive, maxrm = 2, set.bounds = FALSE,
  overwrite.bounds = FALSE, bg = NULL, smp = NULL,
  optmethod = "Nelder-Mead", maxit = 5000, info = "", ifix = NULL,
  rugcols, ptcol, ...)

`std`	data frame of standard dilutions
`xvar`	character strings for the variables used to fit a standard curve.
`yvar`	character strings for the variables used to fit a standard curve.
`model`	the model to be fit.
`Alow`	lower asymptote for the sigmoid model. If `NULL`, the lower asymptote will be estimated, adding an extra parameter to the model. To fix the asymptote at the level of background, specify `"bg"`. Numeric value of `Alow` will force the asymptote to be fixed at the provided level.
`asym`	if `TRUE`, asymmetry in the fit is allowed, adding an extra parameter to the model.
`interactive`	logical value. If `TRUE`, the user is prompted to evaluate the standards (and/or the fit) and asked to remove outliers if needed. `TRUE` value takes precedence over `rm.before` and `rm.after`: if both are `FALSE`, `rm.after` is reset to `TRUE`.
`monot.prompt`	if `TRUE`, the user is prompted to evaluate the standards and possibly remove outliers if the standards are not monotonic (increasing). `FALSE` value is ignored if `interactive` is `TRUE`.
`rm.before`	logical value indicating if potential outliers should be removed before the model is fitted. Ignored if `interactive` is `FALSE`.
`rm.after`	logical value indicating if potential outliers should be removed after the model is fitted. Ignored if `interactive` is `FALSE`.
`maxrm`	maximum number of outliers to remove.
`set.bounds`	if `TRUE`, the user is given the option to manually set the bound that is not set automatically. In that case, the prompt appears even if `interactive` is `FALSE`.
`overwrite.bounds`	logical value indicating the option to overwrite automatically set bounds. Ignored if `interactive` is `FALSE`.
`bg`	background values
`smp`	sample values
`optmethod`	method to be used in optimization.
`maxit`	maximum number of iterations in optimization.
`info`	information about a particular run for warning messages.
`ifix`	sorted integer vector of length 3 with indices of standards to be used for getting starting values for optimization.
`rugcols`	vector of three colors for the rugplot, which indicates sample values (inside the bounds, between the bounds and extrema, and beyond extrema).
`ptcol`	color of the standard points on the plot.
`...`	further graphical parameters.