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man/PCMOptions.Rd
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87  87  #' 0length branches.} 

88  88  #' \item{\code{PCMBase.Tolerance.Symmetric }}{A double specifying the tolerance in tests 

89  89  #' for symmetric matrices. Default 1e8; see also \code{\link{isSymmetric}}.} 

90    #' \item{\code{PCMBase.Lmr.mode }}{An integer code specifying the parallel likelihood calculation mode.} 

91    #' \item{\code{PCMBase.ParamValue.LowerLimit}}{Default lower limit value for parameters, default setting is 10.0.} 

92    #' \item{\code{PCMBase.ParamValue.LowerLimit.NonNegativeDiagonal}}{Default lower limit value for parameters corresponding to nonnegative diagonal elements of matrices, default setting is 0.0.} 

90  +  #' \item{\code{PCMBase.Lmr.mode} }{An integer code specifying the parallel likelihood calculation mode.} 

91  +  #' \item{\code{PCMBase.ParamValue.LowerLimit} }{Default lower limit value for parameters, default setting is 10.0.} 

92  +  #' \item{\code{PCMBase.ParamValue.LowerLimit.NonNegativeDiagonal} }{Default lower limit value for parameters corresponding to nonnegative diagonal elements of matrices, default setting is 0.0.} 

93  93  #' \item{\code{PCMBase.ParamValue.UpperLimit} }{Default upper limit value for parameters, default setting is 10.0.} 

94  94  #' \item{\code{PCMBase.Transpose.Sigma_x} }{Should upper diagonal factors for variancecovariance rate matrices be transposed, e.g. should Sigma = t(Sigma_x) Sigma_x or, rather Sigma = Sigma_x t(Sigma_x)? Note that the two variants are not equal. The default is FALSE, meaning Sigma = Sigma_x t(Sigma_x). In this case, Sigma_x is not the actual upper Cholesky factor of Sigma, i.e. chol(Sigma) != Sigma_x. See also \code{\link{chol}} and \code{\link{UpperTriFactor}}. This option applies to parameters Sigma_x, Sigmae_x, Sigmaj_x and the measurement errors \code{SE[,,i]} for each measurement i when the argument \code{SE} is specified as a cube.} 

95  95  #' \item{\code{PCMBase.MaxLengthListCladePartitions} }{Maximum number of tree partitions returned by \code{\link{PCMTreeListCladePartitions}}. This option has the goal to interrupt the recursive search for new partitions in the case of calling PCMTreeListCladePartitions on a big tree with a small value of the maxCladeSize argument. By default this is set to Inf.} 
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