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.
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)
lotri(n1+n2~omega)Can convert lotri objects to data-frames similar to the internal
data frame used in nlmixr(); These can then be converted back with
as.lotri()
Added the ability to add estimates to a lotri object. These
estimates are an attached data.frame to the original lotri matrix.
You can extract them or drop them with the function lotriEst()
Allow specifying fixed components in lotri() matrices.
Add cov, cor, sd, var, and chol options for matrix
specification. The final matrix will always be the covariance matrix
Add function lotriMatInv() which takes a symmetric block matrix
and converts it into a list of matrices. An sort of inverse
operation of lotriMat()
Add error for lotri(~c(40))
Added ability to flag fixed and unfixed components in a
matrix. Currently lotri only supports one type.
For the lotriFix objects, ie those created with population types
of estimates and covariance estimates, allow them to be converted to
an equivalent expression with as.expression() for the lotri object
and lotriDataFrameToLotriExpression() for the data.frame
Added lotriIsBlockMat() to check to see if a matrix is in a block
diagonal matrix form.
call.=FALSE or equivalent.rchklotriMat to mix named and unnamed matrices; When mixed, an
unnamed matrix will be returned.$lower and $upper gives default values even if it
wasn't specified.Matrix import and added lotriMat to create banded
matrices (faster than Matrix for now included repeated matrices
with list(matrix, rep)).upper and lower bounds
are specified|; Returns a list of matrices
where each condition is the name of the matrix returned.| id(lower=c(eta1=3))NEWS.md file to track changes to the package.