Defines functions zigControl

Documented in zigControl

#' Settings for the fitZig function
#' @param tol The tolerance for the difference in negative log likelihood estimates for a feature to remain active.
#' @param maxit The maximum number of iterations for the expectation-maximization algorithm.
#' @param verbose Whether to display iterative step summary statistics or not.
#' @param dfMethod Either 'default' or 'modified' (by responsibilities).
#' @param pvalMethod Either 'default' or 'bootstrap'.
#' @return The value for the tolerance, maximum no. of iterations, and the verbose warning.
#' @note \code{\link{fitZig}} makes use of zigControl.
#' @name zigControl
#' @aliases settings2
#' @seealso \code{\link{fitZig}} \code{\link{cumNorm}} \code{\link{plotOTU}}
#' @examples
#' control =  zigControl(tol=1e-10,maxit=10,verbose=FALSE)
zigControl <-function(tol=1e-4,maxit=10,verbose=TRUE,dfMethod="modified",pvalMethod="default"){
	# to do: add stop if not
	DFMETHODS <- c("default", "modified")
	PMETHODS  <- c("default", "bootstrap")
	dfMethod  <- DFMETHODS[pmatch(dfMethod, DFMETHODS)]
	pvalMethod<- PMETHODS[pmatch(pvalMethod,PMETHODS)]


	set <-list(tol=tol,maxit=maxit,verbose=verbose,dfMethod=dfMethod,pvalMethod=pvalMethod);

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metagenomeSeq documentation built on May 2, 2018, 2:35 a.m.