#' 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)] stopifnot(dfMethod%in%DFMETHODS) stopifnot(pvalMethod%in%PMETHODS) set <-list(tol=tol,maxit=maxit,verbose=verbose,dfMethod=dfMethod,pvalMethod=pvalMethod); return(set) }