cran-comments.md

In nlmixr2/lotri: A Simple Way to Specify Symmetric, Block Diagonal Matrices

• This version will allow 'rxode2' to link to 'lori' without abi linkage (will help CRAN and my maintainence)

• Added a new way of specifying lotri matrices:

Before you could specify matrices as:

m <- lotri({
  a + b ~ c(1,
            0.5, 1)
})

Now you can specify per row as:

m <- lotri({
  a ~ 1
  b ~ c(0.5, 1)
})

This form is now the default when converting from a matrix to a lotri expression. In addition if the matrix is large enough (by default a 5x5 matrix), these would be named when changing them to an expression:

m <- lotri({
  a ~ c(a=1)
  b ~ c(a=0.5, b=1)
  c ~ c(a=0.5, b=0.5, c=1)
  d ~ c(a=0.5, b=0.5, c=0.5, d=1)
  e ~ c(a=0.5, b=0.5, c=0.5, d=1,
        e=1)
})

This way changing to an R parsed expression will be rendered in a more human readable format.

You can change the deparsing options that are used by default with lotri with options(lotri.plusNames=TRUE) which prefers the a+b+c syntax when deparsing. Otherwise, the line format is used by default. The dimension number before naming the values in the line-format can be controlled with options(lotri.nameEst=2) or some other dimension.

• New option of cov added which check for matrix suitability for covariance matrix. When cov=TRUE, off-diagonal elements in covariance matrices may no longer be nonzero if the diagonal value is zero (rxode2#481). This will also check tht the matrix is non-positive definite on the non-diagonal terms. cov can also be a function to allow correction of the matrix to a positive definite matrix automatically.

• New option of rcm; When enabled, and lotriIsBlockMat() is not true, lotri() will permute the matrix to try to get a banded matrix using the Reverse Cuthill McKee algorithm.

• Change internals for lotri so that new rxode2 is no longer required to be binary linked to lotri.

• Add new function rcm() which permutes the matrix to get a band matrix (if possible). This uses the Reverse Reverse Cuthill McKee (RCM) algorithm.

• Moved nmNearPD() to this package and renamed to lotriNearPD(). In addition to moving, this function will now retain the dimension names.

• New exported function lotriAsExpression() which has more fine control than as.expression() and will work without converting the matrix to a lotri form. This by default uses the new line form, but can be changed back to the option(lotri.plusNames=TRUE). Also be default it will name each element in a matrix when the dimension is above 5x5. You can change that number by option(lotri.nameEst=10) to increase it to be named above 10x10. If you do not like the naming you can also disable it with option(lotri.nameEst=TRUE), or if you always want it on you can use `option(lotri.nameEst=FALSE)

• This is a bug-fix release for nlmixr2 piping

nlmixr2/lotri documentation built on Sept. 24, 2024, 6:31 a.m.