venelin / PCMBase
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#' 0-length branches.}
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#' \item{\code{PCMBase.Tolerance.Symmetric }}{A double specifying the tolerance in tests
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#' for symmetric matrices. Default 1e-8; see also \code{\link{isSymmetric}}.}
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#' \item{\code{PCMBase.Lmr.mode }}{An integer code specifying the parallel likelihood calculation mode.}
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#' \item{\code{PCMBase.ParamValue.LowerLimit}}{Default lower limit value for parameters, default setting is -10.0.}
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#' \item{\code{PCMBase.ParamValue.LowerLimit.NonNegativeDiagonal}}{Default lower limit value for parameters corresponding to non-negative diagonal elements of matrices, default setting is 0.0.}
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#' \item{\code{PCMBase.Lmr.mode} }{An integer code specifying the parallel likelihood calculation mode.}
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#' \item{\code{PCMBase.ParamValue.LowerLimit} }{Default lower limit value for parameters, default setting is -10.0.}
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#' \item{\code{PCMBase.ParamValue.LowerLimit.NonNegativeDiagonal} }{Default lower limit value for parameters corresponding to non-negative diagonal elements of matrices, default setting is 0.0.}
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#' \item{\code{PCMBase.ParamValue.UpperLimit} }{Default upper limit value for parameters, default setting is 10.0.}
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#' \item{\code{PCMBase.Transpose.Sigma_x} }{Should upper diagonal factors for variance-covariance 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.}
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#' \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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Project Totals (16 files) 36.01%
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