initialize_tau {gemini} | R Documentation

## initialize_tau

### Description

Initialize all tau values based on the observed replicate variance.

### Usage

    initialize_tau(Model, CONSTANT = 32, prior_shape = 0.5,
      window = NULL, monotonize = FALSE, verbose = FALSE)

### Arguments

`Model` | an object of class gemini.model
`CONSTANT` | a numeric indicating a constant value that shifts counts to reduce outliers (default = 32).
`prior_shape` | shape parameter of Gamma distribution used to model the variation in the data in `Input`. If single numeric value, then shape parameters for all samples are assumed equal. Otherwise, a named numeric vector of shape parameters the same length as the number of samples (excluding early time point).
`window` | numeric if window smoothing should be done on initialized tau values, otherwise NULL (default) for no window smoothing
`monotonize` | logical specifying whether the variance should be monotonically increasing (default FALSE)
`verbose` | default FALSE

### Value

a Model object of class gemini.model including new slots for alpha and beta values

### Examples

    data("Model", package = "gemini")
    Model <- initialize_tau(Model, CONSTANT = 32, prior_shape = 0.5)

[Package gemini version 1.2.0 Index]