Description Usage Arguments Value Author(s)

View source: R/free.estimate.R

Estimate unknown parameters with free approach.

1 2 | ```
free.estimate(m, p, q, n, betastart, bvarstart, psi.start, eta.start,
Y, X, Y.c, ziMatrix)
``` |

`m` |
Number of OTUs. |

`p` |
Number of covariates for count model (e.g., beta-binomial). |

`q` |
Number of covariates for zero model. |

`n` |
Number of samples. |

`betastart` |
Matrix of estimated betas, which are the effects/coefficients for the count model, with dimension p by m. It is used as initial values for the optimization procedure to estimate betas. |

`bvarstart` |
Matrix of variance of estimated betas with dimension p by m. |

`psi.start` |
Estimated vector of logit of overdispersion parameters with length m. And psi.start will be used as initial values for the optimization procedure to estimate psi. |

`eta.start` |
Matrix of estimated etas, which are the effects/coefficients for the zero model, with dimension q by m. It is used as initial values for the optimization procedure to estimate etas. |

`Y` |
Count matrix with dimension n by m. |

`X` |
The design matrix (n by p, p is the number of covariates) for the count model (e.g., beta-binomial), and intercept is included. |

`Y.c` |
Vector of library size with length n. |

`ziMatrix` |
The design matrix (n by q) for the zero model, and intercept is included. |

`betahat` |
Estimation matrix of beta (p by m). |

`bvar` |
Estimation matrix of the variance of estimated betahat (p by m). |

`psi` |
Estimation vector of the logit of the overdispersion parameters (with length m). |

`eta` |
Estimation matrix of eta (q by m). |

Tao Hu, Yihui Zhou

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