LR_nb: Get the value of the log-likelihood ratio of alpha

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

Description

Get the value of the log-likelihood ratio of alpha

Usage

LR_nb(
  Alpha,
  X,
  CC,
  responseFun = c("linear", "quadratic", "nonparametric", "dynamic"),
  muMarg,
  psi,
  nleqslv.control = list(trace = FALSE),
  n,
  NB_params,
  NB_params_noLab,
  thetaMat,
  ncols,
  nonParamRespFun,
  envGradEst,
  ...
)

Arguments

Alpha	a vector of length d, the environmental gradient
X	the n-by-p count matrix
CC	the n-by-d covariate matrix
responseFun	a character string indicating the type of response function
muMarg	an n-by-p offset matrix
psi	a scalar, an importance parameter
nleqslv.control	the control list for the nleqslv() function
n	number of samples
NB_params	Starting values for the NB_params
NB_params_noLab	Starting values for the NB_params without label
thetaMat	a matrix of size n-by-p with estimated dispersion parameters
ncols	a scalar, the number of columns of X
nonParamRespFun	A list, the result of the estNPresp() function
envGradEst	a character string, indicating how the environmental gradient should be fitted. 'LR' using the likelihood-ratio criterion, or 'ML' a full maximum likelihood solution
...	Further arguments passed on to other functions DON'T USE 'p' as variable name, partial matching in the grad-function in the numDeriv package

Value

: a scalar, the evaluation of the log-likelihood ratio at the given alpha

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