fitTwoRateReachModel: Fit the Two-Rate Model To a Dataset.
In thartbm/RateRate: Evaluate and Fit the Two-Rate Model of Motor Learning

Description Usage Arguments Details Value See Also Examples

View source: R/TwoRateModel.R

Fit Smith et al's (2006) Two-Rate Model to a set of reach deviations and a perturbation schedule.

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fitTwoRateReachModel(reaches, schedule, oneTwoRates = 2, verbose = FALSE,
  grid = "uniform", gridsteps = 7, checkStability = TRUE, method = "NM",
  fnscale = 1)

`reaches`	A sequence of reach deviations.
`schedule`	A sequence of feedback manipulations.
`oneTwoRates`	How many processes to fit? (1 or 2)
`verbose`	Should detailed information be outputted during the fitting?
`grid`	How are parameters values for grid search distributed in [0,1]? One of 'uniform' (default), 'restricted' or 'skewed'.
`gridsteps`	How many values of each parameter are used in grid search?
`checkStability`	Use additional stability constraints? (default=TRUE)
`method`	Fitting method, currently one of "Nelder-Mead" (default and very robust, also 'NM', a linear optimization method) or "BFGS" (a quasi-Newton, non-linear method, also 'QN' or 'Quasi-Newton'). See `optim` for details.
`fnscale`	Fitting is done on function/fnscale, where fnscale is already multiplied by -1 to make it an optimization where appropriate. By default it is set to 1. To make different schedules more comparable, use the largest deviation from zero in the schedule; fnscale=max(abs(schedule), na.rm=T). See `optim` for details.

This function runs a grid search first, and picks the best 5 are fit with least square optimization after which the best fit is returned. Mean squared error, as given by twoRateReachModelErrors is used to determine quality of fit.

The sequences of reaches and the schedule should have the same length. NAs in the reaches will be ignored, but in the schedule they indicate error-clamp trials.

The model prediction base on the parameters can be retrieved by evaluating them, based on the perturbation schedule, with twoRateReachModel.

In the Two-Rate Model of motor learning, the motor output X on a trial t, is the sum of the output of a slow and fast process:

X(t) = Xs(t) + Xf(t)

And each of these two processes retain part of their previous learning and learn from previous errors:

Xs(t) = Rs . Xs(t-1) + Ls . E(t-1)

Xf(t) = Rf . Xf(t-1) + Lf . E(t-1)

The four parameters Rs, Ls, Rf and Lf are returned, except when a one-process fit is requested, in which case only Rs and Ls are fit.

The set of parameters that minimizes the difference between model output and the reaches given the perturbation schedule.

twoRateReachModelErrors and twoRateReachModel

Smith MA, Ghazizadeh A, Shadmehr R (2006). Interacting Adaptive Processes with Different Timescales Underlie Short-Term Motor Learning. PLoS Biol. 2006 Jun;4(6):e179. https://doi.org/10.1371/journal.pbio.0040179

data("RotAdapt")
param <- fitTwoRateReachModel(RotAdapt$reaches,RotAdapt$schedule, method='BFGS')
param

tworatemodel <- twoRateReachModel(param, RotAdapt$schedule)
str(tworatemodel)

plot(RotAdapt$reaches, ylim=c(-35,35), col='gray')
lines(tworatemodel$total)
lines(tworatemodel$slow, col='blue')
lines(tworatemodel$fast, col='red')