func.EM: func.EM

In lch14forever/beem-static: An EM-like algorithm for biomass and microbiome model inference from cross sectional microbial profiling data

Description

Iteratively estimating scaled parameters and biomass

Usage

func.EM(dat, external.perturbation = NULL, ncpu = 1, m.init = NULL,
  scaling = 1000, equil.filter = Inf, model.filter = Inf,
  refresh.iter = 1, lambda.iter = Inf, warm.iter = NULL,
  max.iter = 30, epsilon = 0.001, lambda.choice = 1, alpha = 1,
  debug = FALSE, verbose = TRUE)

Arguments

dat	OTU count/relative abundance matrix (each OTU in one row)
external.perturbation	external perturbation presence matrix (each perturbation in one row, each sample in one column) (Default: NULL)
ncpu	number of CPUs (default: 1)
m.init	initial biomass values (default: use CSS normalization)
scaling	a scaling factor to keep the median of all biomass constant (default: 1000)
equil.filter	threshold for detecting and removing samples not at equilibrium (default: Inf - all the samples will be considered)
model.filter	threshold for detecting and removing samples from different models (default: Inf - all the samples will be considered)
refresh.iter	refresh the removed samples every X iterations (default: 1)
lambda.iter	number of iterations to run before fixing lambda (default: Inf)
warm.iter	number of iterations to run before removing any samples (default: run until convergence and start to remove samples)
max.iter	maximal number of iterations (default 30)
epsilon	convergence threshold (in relative difference): uqn of the relative error in biomass changes (default 1e-3)
lambda.choice	1: use lambda.1se for LASSO, 2: use lambda.min for LASSO, a number between (0, 1): this will select a lambda according to (1-lambda.choice)*lambda.min + lambda.choice*lambda.1se
alpha	the alpha parameter for the Elastic Net model (1-LASSO [default], 0-RIDGE)
debug	output debugging information (default FALSE)
verbose	print out messages

Author(s)

Chenhao Li, Gerald Tan, Niranjan Nagarajan

lch14forever/beem-static documentation built on Aug. 30, 2021, 4:41 p.m.