paramFromEM: paramFromEM

In lch14forever/BEEM: BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data

paramFromEM

Description

Inferring parameters from BEEM results

Usage

paramFromEM(
  beem.obj,
  counts,
  metadata,
  sparse = TRUE,
  forceBreak = NULL,
  ncpu = 4,
  enforceLogistic = FALSE,
  dev = 0.05,
  forceSkipWarning = FALSE
)

Arguments

beem.obj	BEEM output list
counts	counts data following MDSINE's OTU table
metadata	metadata following MDSINE's metadata format
sparse	use the sparse mode to estimate the parameters (default: TRUE)
forceBreak	force to break the trajectory to handle pulsed perturbation (or species invasion) (default: NULL)
ncpu	maximal number of CPUs used (default:4)
enforceLogistic	re-estimate the self-interaction parameters (enforce to negative values)
dev	tolerance in mse to select iterations for estimating parameters (default: 0.05)
forceSkipWarning	Use with caution! Force to skip model fit check.

lch14forever/BEEM documentation built on April 5, 2025, 11:24 p.m.