diff --git a/man/simInitAnd.Rd b/man/simInitAnd.Rd index 43b03ec..966f965 100644 --- a/man/simInitAnd.Rd +++ b/man/simInitAnd.Rd @@ -114,7 +114,21 @@ of \code{beginCluster()}, to use parallelism for this function, allowing for more control over cluster use.} \item{...}{An alternative way to pass \code{objects}, i.e., they can just be named -arguments rather than in a \code{objects = list(...)}} +arguments rather than in a \code{objects = list(...)}. It can also be any +\code{options} that begins with \code{spades}, \code{reproducible} or \code{Require}, i.e., +those identified in \code{spadesOptions()}, +\code{reproducibleOptions()} or \code{RequireOptions()}. +These will be assigned to the equivalent option \emph{during} the \code{simInit} and \code{spades} +calls only, i.e., they will revert after the \code{simInit} or \code{spades} calls +are complete. NOTE: these are not passed to the \code{simList} per se, i.e., they are +not be available in the \code{simList} during either +the \code{simInit} or \code{spades} calls via \code{sim$xxx}, though they will be returned to the \code{simList} +at the end of each of these calls (so that the next call to e.g., \code{spades} can +see them). For convenience, these can be supplied without their package prefix, +e.g., \code{lowMemory} can be specified instead of \code{spades.lowMemory}. In cases that +share option name (\code{reproducible.verbose} and \code{Require.verbose} both exist), +passing \code{verbose = FALSE} will set both. Obviously this may cause unexpected +problems if a module is also expecting a value.} } \description{ Run \code{simInit} and \code{Experiment} in one step