fit.models: Fit all models to data
In Stickbreaker: Fits Stickbreaking, Multiplicative and Additive Models to Data

Description Usage Arguments Details Value See Also Examples

View source: R/model_fitting_functions.R

Fit all models using fit.models. Used as a wrapper to combine outputs from estimate.d.MLE, estimate.d.RDB, estimate.d.sequential, fit.stick.model.given.d, fit.mult.model, fit.add.model, and summarize.fits.for.posterior.calc.

1	fit.models(data, d.range, d.adj.max = 1.1, wts = c(2, 1))

`data`	(Required). A list containing fitness values for allele combinations. See examples in `data` or in the vignette.
`d.range`	(Required). Range of realistic fitness changes from WT. "d" is the difference between maximal fitness and WT fitness. For example, WT fitness for the virus phix174 is about 20, but values up to about 25 have been observed, so d.range was set to: d.range <- c(0.1,10).
`d.adj.max`	(Optional). Default 1.1. When the estimation of d fails in `estimate.d.MLE`, `estimate.d.RDB`, or `estimate.d.sequential` then d becomes 1.1*WT fitness so that models can be fit.
`wts`	(Optional). Default c(2,1).

Function is a wrapper that fits the data to all three models. First, it estimates $d$ and, using this estimate, fits the stickbreaking model. Then it fits the multiplicative and additive models.

List:
[[1]] fit.smry contains the R^2 and P values for all models coefficients
[[2]] fit.stick contains stickbreaking model details like the intercept, slope, and predicted fitness values for the given allele combinations.
[[2]] fit.mult contains multiplicative model details like the intercept, slope, and predicted fitness values for the given allele combinations.
[[2]] fit.stick contains additive model details like the intercept, slope, and predicted fitness values for the given allele combinations.

estimate.d.MLE, estimate.d.RDB, estimate.d.sequential, fit.stick.model.given.d, fit.mult.model, fit.add.model, summarize.fits.for.posterior.calc, estimate.d.MLE, estimate.d.RDB, estimate.d.sequential