free.estimate: Estimate parameters with free approach

Description Usage Arguments Value Author(s)

View source: R/free.estimate.R

Description

Estimate unknown parameters with free approach.

Usage

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

Arguments

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.

Value

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).

Author(s)

Tao Hu, Yihui Zhou


ZIBBSeqDiscovery documentation built on May 2, 2019, 4:21 a.m.