EMtree: Core computing function

In Rmomal/EMtree: Infers Direct Species Association Networks using Tree Averaging

Core computing function

Description

Core computing function

Usage

EMtree(
  PLN.Cor,
  n = NULL,
  maxIter = 30,
  unlinked = NULL,
  random.init = FALSE,
  cond.tol = 1e-10,
  eps = 0.001,
  verbatim = TRUE,
  plot = FALSE
)

Arguments

PLN.Cor	Either an object resulting from the use of the 'PLN' function from package 'PLNmodels', or an estimation of Gaussian data correlation matrix.
n	Number of samples, required if a correlation matrix is supplied
maxIter	Maximum number of iterations for EMtree
unlinked	An optional vector of nodes which are not linked with each other
random.init	A boolean for trying a random initialization of the EM
cond.tol	Tolerance parameter for the conditioning of psi matrix
eps	Precision parameter controlling the convergence of weights beta
verbatim	Talks if set to TRUE
plot	Plots likelihood if set to TRUE

Value

• edges_prob: p x p matrix of edges probabilities

• edges_weight: p x p matrix of edges weights for any spanning tree

• logpY: vector of log-likelihoods

• maxIter: final number of iterations EMtree has ran

• timeEM: EMtree computation time

• alpha: data signal/noise ratio

Examples

n=30
p=10
Y=data_from_scratch("tree",p=p)$data
PLN_Y = PLNmodels::PLN(Y~1)
EMtree(PLN.Cor=PLN_Y,verbatim=TRUE, plot=TRUE)

Rmomal/EMtree documentation built on Dec. 14, 2024, 8:16 a.m.