NORM: NORM

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

NORM

Description

Function to calculate biomass for each sample

Usage

NORM(
  tss,
  gradients,
  perturbInd,
  metadata,
  rmSp,
  params,
  ncpu = 10,
  norder = 3,
  scale = NA,
  smooth = FALSE,
  forceBreak = NULL
)

Arguments

tss	matrix of relative abundances (proportions), variables in rows and sample in columns
gradients	matrix of gradients of addative log (alr) transformed abundances
perturbInd	matrix of perturbation indicator generated by preProcess
rmSp	Speices removed for alr tranformation
params	list(alpha=, beta=) estimated with BLASSO
ncpu	number of CPUs used (default: 10)
norder	order of spline basis (default: 3)
scale	scale the median of all samples
smooth	smooth the biomass after normalization
forceBreak	force to break the trajectory to handle pulsed perturbation (or species invasion) (default: NULL)
meta	metadata

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