bmdd.nlopt: NLopt C++ Implementation of BMDD

In MicrobiomeStat: Statistical Methods for Microbiome Compositional Data

NLopt C++ Implementation of BMDD

Description

High-performance implementation using NLopt L-BFGS-B optimizer in C++. Provides 50-90x speedup over R implementation for cases without covariates. This is a low-level function; most users should use bmdd() instead.

Usage

bmdd.nlopt(W, type = c("count", "proportion"),
           para.alp.init = NULL, para.pi.init = NULL, gam.init = NULL,
           iterlim = 500, tol = 1e-6, trace = FALSE,
           inner.loop = TRUE, inner.iterlim = 20, inner.tol = 1e-6,
           alp.iterlim = 100, alp.tol = 1e-6,
           alp.min = 1e-3, alp.max = 1e3)

Arguments

W	Matrix of observed data (m taxa × n samples)
type	Data type: "count" or "proportion"
para.alp.init	Initial alpha values
para.pi.init	Initial pi values
gam.init	Initial gamma values
iterlim	Maximum iterations (default 500)
tol	Convergence tolerance (default 1e-6)
trace	Print progress (default FALSE)
inner.loop	Use inner loop optimization (default TRUE)
inner.iterlim	Inner loop max iterations (default 20)
inner.tol	Inner loop tolerance (default 1e-6)
alp.iterlim	Alpha optimization iterations (default 100)
alp.tol	Alpha tolerance (default 1e-6)
alp.min	Minimum alpha (default 1e-3)
alp.max	Maximum alpha (default 1e3)

Details

This function provides direct access to the NLopt C++ implementation. Most users should use bmdd() instead, which automatically selects the optimal implementation.

Does not support covariates. For covariate modeling, use bmdd() with method="R".

Value

A list containing estimated parameters (same as bmdd)

References

Zhou, H., Chen, J., & Zhang, X. (2025). BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data. PLoOS Computational Biology, 21(10), e1013124.

See Also

bmdd for the main user interface

Examples

## Not run: 
# Simulate data
m <- 100
n <- 50
W <- matrix(rpois(m*n, 100), m, n)

# Direct NLopt usage (advanced)
result <- bmdd.nlopt(W, type = "count")

# Recommended: use bmdd() instead
result <- bmdd(W, type = "count")  # auto-selects NLopt

## End(Not run)

MicrobiomeStat documentation built on Jan. 9, 2026, 1:07 a.m.