NBjacobianCol: Jacobian for the estimation of the column scores

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Description

Jacobian for the estimation of the column scores

Usage

NBjacobianCol(
  beta,
  X,
  reg,
  thetas,
  muMarg,
  k,
  n,
  p,
  colWeights,
  nLambda,
  cMatK,
  preFabMat,
  Jac,
  allowMissingness,
  naId
)

Arguments

beta	vector of length p+1+1+(k-1): p row scores, 1 centering, one normalization and (k-1) orhtogonality lagrangian multipliers
X	the nxp data matrix
reg	a nx1 regressor matrix: outer product of rowScores and psis
thetas	nxp matrix with the dispersion parameters (converted to matrix for numeric reasons)
muMarg	the nxp offset
k	an integer, the dimension of the RC solution
n	an integer, the number of samples
p	an integer, the number of taxa
colWeights	the weights used for the restrictions
nLambda	an integer, the number of restrictions
cMatK	the lower dimensions of the colScores
preFabMat	a prefab matrix, (1+X/thetas)
Jac	an empty Jacobian matrix
allowMissingness	A boolean, are missing values present
naId	The numeric index of the missing values in X

Value

A matrix of dimension p+1+1+(k-1) with evaluations of the Jacobian

RCM documentation built on Nov. 8, 2020, 5:22 p.m.