v1.0.0

• 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)

What's Changed

• 17 length of dimnames 1 not equal to array extent by @mattfidler in #18
• Add website to DESCRIPTION by @olivroy in #19
• Update continuous integration by @billdenney in #21
• Off-diagonal values may no longer be nonzero if the diagonal is zero for a covariance matrix by @billdenney in #20
• Feature Request: Remove binary linkages to rxode2 by @mattfidler in #13
• Feature request: reorder to better block matrices by @mattfidler in #22
• Move nearPD here by @mattfidler in #24
• Add rcm to lotri ability by @mattfidler in #26
• Add different way of defining matrices by @mattfidler in #27
• With new engine, dimnames() parser issue by @mattfidler in #28
• Fix known elements in dsl by @mattfidler in #29

New Contributors

• @olivroy made their first contribution in #19

Full Changelog: v0.4.3...v1.0.0

v0.4.3

What's Changed

• More informative error by @mattfidler in #11
• 15 lotriaslotriasdataframelotri by @mattfidler in #16

Full Changelog: v0.4.2...v0.4.3

v0.4.2

lotri 0.4.2

• Bug fix for etas that are inconsistently numbered
• Add case for empty initialization block

What's Changed

• 8 labels a bit off by @mattfidler in #9

New Contributors

• @mattfidler made their first contribution in #9

Full Changelog: v0.4.0...v0.4.2

v0.4.0

lotri 0.4.0

• 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

• Split tests and make them silent by @billdenney in #1

• Update roxygen2 version by @billdenney in #5

New Contributors

• @billdenney made their first contribution in #1

Full Changelog: https://github.com/nlmixr2/lotri/commits/v0.4.0