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(this page)| 2024-11-12 15:35:29 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-mvtnorm) Updated 1.3.1 to 1.3.2
Changes in Version 1.3-2 (2024-11-04):
Features:
* Explain and illustrate that omitting data dimensions
produces marginal log-likelihoods in Chapter 7.
* Add low-level functionality for reduced rank covariances in
new Chapter 8.
Bugfixes:
* 'invcholD' and 'Dchol' avoided very small diagonals; now
they also avoid very large diagonals (such that inverting
the result doesn't give too small diagonals).
* Fix partial argument matches, reported by KH.
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| 2024-11-06 14:05:02 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-mvtnorm) Updated 1.2.5 to 1.3.1
Changes in Version 1.3-1 (2024-09-02):
Bugfixes:
* Challenging numeric test of score function at ML estimate
failed on Mac M1.
Changes in Version 1.2-6 (2024-08-17):
Features:
* Add 'logdet()' function for computing log-determinants from
lower triangular matrices.
* Speed up 'solve(<ltMatrices>, ...)'.
Bugfixes:
* Avoid unnecessary copying of large data objects.
* -1/2 -> -1 for det(C) in lmvnorm_src vignette; spotted by
Kurt Hornik
* Use 'M\_PI'.
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| 2024-06-08 16:49:19 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-mvtnorm) Updated 1.2.4 to 1.2.5
R CMD Rdconv -t txt mvtnorm/inst/NEWS.Rd
NEWS file for the 'mvtnorm' package
Changes in Version 1.2-5 (2024-05-18):
Features:
* Update the 'Using mvtnorm' package vignette and references
therein.
* Speed up 'Mult(<ltMatrices>, transpose = TRUE)'.
* Speed up 'ldmvnorm()'.
* Add constructor 'syMatrices' for multiple symmetric matrices
and 'as.syMatrices' for coercion from 'ltMatrices'.
Bugfixes:
* Fix segmentation fault or unnecessary error or warning +
approximation for 'algorithm = Miwa()' or 'TVPACK()', in
case dimension reduction to one-dimensional is possible,
e.g., for
pmvnorm(lower = rep(-Inf,3), upper = c(-1, Inf, Inf),
sigma = diag(3), algorithm = Miwa())
# or
pmvnorm(lower = c(-Inf,-Inf),
upper = c(- 1, Inf), sigma=diag(2), algorithm = TVPACK())
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| 2024-02-03 12:13:21 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-mvtnorm) Udated 1.2.2 to 1.2.4
Changes in Version 1.2-4 (2023-11-27):
Bugfixes:
* Remove empty print statement from 'miwa.c'
Changes in Version 1.2-3 (2023-08-17):
Features:
* Allow to change 'rnorm' in 'rmvnorm', feature request by
Ralf Stubner.
Bugfixes:
* Fix variable declarations in 'tvpack.f' as reported by Intel
compilers icx/ipcx/ifx from oneAPI 2023.2.0 and oneMKL
2023.2.0, thanks to BDR
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| 2023-06-11 05:47:33 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-mvtnorm) Updated 1.3.1 to 1.2.2
Changes in Version 1.2-2 (2023-06-05):
Bugfixes:
* Fix overflow problem reported by ASAN.
Documentation:
* Be even more careful inverting / computing Cholesky factors
for hessians (M1 and macos-arm64).
Changes in Version 1.2-1 (2023-06-02):
Bugfixes:
* Avoid attempts to allocate zero length arrays for
one-dimensional problems.
Documentation:
* Catch M1mac problems with inverting hessians.
Changes in Version 1.2-0 (2023-06-02):
* New 'lpmvnorm' function for computing multivariate normal
log-likelihoods for interval-censored observations.
* New 'slpmvnorm' function for computing the corresponding
score function for interval-censored observations.
* New 'ldmvnorm' function for computing multivariate normal
log-likelihoods for exact observations.
* New 'sldmvnorm' function for computing the corresponding
score function for exact observations.
* New 'ldpmvnorm' function for computing multivariate normal
log-likelihoods for a mix of exact and interval-censored
observations.
* New 'sldpmvnorm' function for computing the corresponding
score function for a mix of exact and interval-censored
observations.
* New class 'ltMatrices' representing multiple lower triangular
matrices, with some useful methods.
* New package vignette 'lmvnorm_src' describing these new
features.
* 'pmvnorm', 'qmvnorm', 'pmvt', and 'qmvt' gain a 'seed'
argument.
* Regression tests were improved.
* Internal standardization is described better in the docs,
suggested by Chris Wymant.
* New 'NEWS' file, the old file containing information up to
version 1.1-3 is available as 'NEWS.old'.
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| 2022-05-22 14:35:27 by Makoto Fujiwara | Files touched by this commit (2) |
Log message: (math/R-mvtnorm) Updated 1.1.2 to 1.1.3 (test passes) (from: inst/NEWS) Changes in version 1.1-3 (2021-10-05) o fix diffs reported on M1mac |
| 2021-10-26 12:56:13 by Nia Alarie | Files touched by this commit (458) |
Log message: math: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes |
| 2021-10-07 16:28:36 by Nia Alarie | Files touched by this commit (458) |
Log message: math: Remove SHA1 hashes for distfiles |
| 2021-09-14 09:59:13 by Jonathan Perkin | Files touched by this commit (1) |
Log message: R-mvtnorm: gfortran.mk should not be directly included. |
2021-09-11 16:24:00 by Makoto Fujiwara | Files touched by this commit (2) |  |
Log message:
(math/R-mvtnorm) Updated 1.0.11 to 1.1.2
Changes in version 1.1-2 (2021-06-07)
o Miwa(n) now also works for non-zero mean|delta; n <= 4097, not 4098 \
(from C code);
optional 'checkCorr=' argument; documentation, one NOTE less.
Minimal C code cleanup.
mvt() <-> probval() simplification.
Handles +/-Inf as +/-maxval for non-orthrant probabilities (with a warning).
o TVPACK() now also works when some (but not all) bounds are (-Inf, Inf).
o mvtnorm() and mvt() now also return an attribute "algorithm" and \
gain optional
argument 'keepAttr' to allow returning bare numbers.
Changes in version 1.1-1 (2020-06-09)
o allow to turn-off symmetry checks (patch contributed by Feng Li \
<feng.li_at_cufe.edu.cn>
Changes in version 1.1-0 (2020-02-24)
o replace MVPHI and MVPHNV by calls to R's {p,q}norm5, following
a suggestion by Benjamin Christoffersen <boennecd_at_gmail.com>
Changes in version 1.0-12 (2020-01-06)
o fix Rdiff issues
Changes in version 1.0-11 (2019-06-19)
o improve documentation and error messages
Changes in version 1.0-10 (2019-03-04)
o eliminate warning when calling qmvt with arg sigma = 1
Changes in version 1.0-9 (2019-02-28)
o adapt to recent changes in r-devel
Changes in version 1.0-8 (2018-05-31)
o pmvt(..., sigma = ) was ignored in the univariate case
(reported by Alec Stephenson)
o documentation updates
Changes in version 1.0-7 (2018-01-25)
o pmvt(..., df = ) is scalar only
Changes in version 1.0-6 (2017-03-01)
o use registered C routines
Changes in version 1.0-5 (2016-02-02)
o improvements in quantile estimation
Changes in version 1.0-4 (2016-01-19)
o a new algorithm for quantile estimation, again. Quantiles are
now computed by a stochastic root finding algorithm. Note
that f.quantile in the output of qmv{t,norm} is now (again)
the squared difference between the cdf evaluated at the
quantile and the level. The \code{interval} argument to the
quantile functions is used as a starting value for the
root finder when available.
o clean-ups in C and R code and documentation
Changes in version 1.0-3 (2015-07-21)
o new algorithm for quantile estimation. Quantiles are
now computed by minimising the squared distance between the
distribution function and the probability whereas previous versions
used uniroot(). The procedure is now performed multiple times with
difference random seeds in order to stabilise the results. The
\code{interval} argument to the quantile functions is IGNORED now.
Changes in version 1.0-2 (2014-12-16)
o start providing C interfaces to the underlying algorithms.
mvtnorm_C_mvtdst() directly calls Alan's FORTRAN code and
can be used in other packages via LinkingTo. See
mvtnorm/inst/C_API_Example for an example very much inspired
by the example provided in package xts.
o provide .C interfaces to the FORTRAN routines and allow switching
on/off of R' RNG.
Changes in version 1.0-1 (2014-11-11)
o replace internal MVCHNV FORTRAN FUNCTION with
R's sqrt(qchisq(p, n, FALSE, FALSE). This fixes a
problem where NaN was returned as reported by
David Charles Airey <airey_david_charles_at_lilly.com>
Changes in version 1.0-0 (2014-07-08)
o After 14 years, we now feel safe enough to publish mvtnorm 1.0-0.
Many packages depend, import, or suggest mvtnorm, so this version
change also indicates that the package is now stable and, to a very
large extent, the API is frozen. We will of course continue to fix
bugs or other problems but new features are unlikely to go into this
package.
o use Authors@R in DESCRIPTION
o switch to standard NEWS format
Changes in version 0.9-99992 (2014-05-03)
o cleanups by MM
Changes in version 0.9-99991 (2014-04-25)
o version 0.9-9999 introduced new bug in dmvnorm
Changes in version 0.9-9999 (2014-04-17)
o dmvnorm (again) returns NaN in case sigma is not decomposable
Changes in version 0.9-9998 (2014-03-21)
o faster code for dmvnorm by Matteo Fasiolo <mf364 at bath.ac.uk>
Changes in version 0.9-9997 (2014-01-17)
o T. Miwa fixed a runtime error in miwa.c reported by UB sanitizer
Changes in version 0.9-9996 (2013-09-16)
o documentation updates/corrections/examples by Marius Hofert
o df = Inf
o rmvt(): argument 'mean' not allowed anymore (prone to misuse)
o pmvnorm(lower=c(-Inf, 0, 0), upper=c(0, Inf, Inf),
mean=c(0, 0, 0), sigma=S, algorithm = Miwa())
returned NaN, fixed by Xuefei Mi
Changes in version 0.9-9995 (2013-05-29)
o update to version 2013-06-29 of mvtdst.f from Alan's website
(fixed a bug for 2-dim pmvt)
Changes in version 0.9-9994 (2012-12-06)
o set.seed(29)
rmvnorm(10, ...)
produces the same first ten rows as
set.seed(29)
rmvnorm(100, ...)
o as suggested by Paul Johnson <pauljohn_at_ku.edu>. There is a new
argument pre0.9_9993 for changing back to the `old' output. This
_DOES NOT_ apply to rmvt.
Changes in version 0.9-9993 (2012-10-22)
o sigma is called `scale' matrix of {dpq}mvt, thanks to
Richard Boys <Richard.Boys_at_ncl.ac.uk> for the hint
Changes in version 0.9-9992 (2012-01-19)
o qmvt(..., df = 0, ...) gave NaN
o R CMD check works on x64 with GCC 4.6.2 (Debian 4.6.2-11)
Changes in version 0.9-9991 (2011-06-10)
o tvpack wasn't working on 64bit machines. The reason
was that the wrapper SUBROUTINEs around the original
FUNCTIONs didn't return the appropriate double precision
for unknown reasons. Redefining TVTL and BVTL as FUNCTIONs
fixed the problem.
Changes in version 0.9-999 (2011-04-26)
o still problems in fix approx_interval (when !is.null(sigma));
disable for the time being
Changes in version 0.9-99 (2011-04-21)
o fix bug in approx_interval spotted by Ravi Varadhan
<rvaradhan_at_jhmi.edu>
Changes in version 0.9-98 (2011-04-19)
o allow ... to pass arguments to rmvnorm in rmvt
Changes in version 0.9-97 (2011-01-31)
o use check.attributes = FALSE in isSymmetric calls
(requested by Nick Sabbe <nick.sabbe_at_ugent.be>)
Changes in version 0.9-96 (2011-01-28)
o use fixed interval when sigma is specified in qmvt
Changes in version 0.9-95 (2010-11-18)
o q{mvt,mvnorm} shall always return a list, not a vector
checks for correlation matrices are less picky now
Changes in version 0.9-94 (2010-11-16)
o allow for two different noncentral t distributions (via type
argument)
o add support for one-dimensional quantiles (requested by Jerry Lewis
<jerry.lewis_at_biogenidec.com>)
o documentation fixes for problems spotted by
Jerry Lewis <jerry.lewis_at_biogenidec.com>
o interface to Alan's TVPACK algorithms for 2- and 3-d
probabilities by Bjoern Bornkamp added.
Changes in version 0.9-92 (2010-07-06)
o update to new mvtdstpack.f (7/10) by Alan. Fixes
potential bias problem in higher dimension.
Changes in version 0.9-91 (2010-04-13)
o better search interval for uniroot in qmv{t,norm} speeds up
quantile estimation; suggestion by Björn Bornkamp
<bornkamp_at_statistik.tu-dortmund.de>
Changes in version 0.9-9 (2010-01-27)
o document ... in pmvt.Rd
Changes in version 0.9-8 (2009-10-27)
o add citation entry
Changes in version 0.9-7 (2009-05-22)
o make sure `error' is not NA
Changes in version 0.9-6 (2009-03-25)
o update Alan's FORTRAN code
Changes in version 0.9-5 (2009-03-17)
o fix FORTRAN bug spotted by Alex Lenkoski
<lenkoski_at_stat.washington.edu>
Changes in version 0.9-3 (2008-12-22)
o update meta data
Changes in version 0.9-2 (2008-07-08)
o be a little more liberal (tol = sqrt(.Machine$double.eps))
when testing for symmetry of covariance matrices
(and make R CMD CHECK monomvn happy again)
Changes in version 0.9-1 (2008-07-02)
o better check for covariance matrices, suggested by
James Rogers <James.A.Rogers_at_pfizer.com>
Changes in version 0.9-0 (2008-04-01)
o add support for the multivariate normal distributions in small
dimensions by Miwa's method thanks to Tetsuhisa Miwa and Xuefei Mi;
both have been added as `authors'.
o new argument `algorithm' defaulting to `GenzBretz()' with
`Miwa()' being the alternative. Those two functions are now used
to specify hyper parameters such as `abseps'.
o internal function `mvt' is no longer exported.
Changes in version 0.8-3 (2008-02-19)
o make sure rmvnorm(1, sigma = matrix(0.5, 1, 1)) works
(reported by Kurt Hornik)
Changes in version 0.8-2 (2008-02-10)
o rmvnorm() now issues a warning for non-symmetric sigma and uses
the eigenvalue decomposition as default.
o make gfortran 4.3 happy
Changes in version 0.8-1 (2007-07-24)
o Orion Poplawski <orion_at_cora.nwra.com> spotted a meaningless check in
the regression tests
Changes in version 0.8-0 (2007-07-23)
o upgrade to 7/7 version of MVTDST (includes better support for
dimensions > 100). Thanks to Karen Conneely <conneely_at_umich.edu>
for motivating the update and for checking the new version.
o rmvnorm() now can also use a Cholesky decomposition to compute
the root of sigma (thanks to Fabian Scheipl)
Changes in version 0.7-5 (2006-09-15)
o fix problem reported by valgrind
Changes in version 0.7-4 (2006-09-08)
o add long requested `dmvt'
o call RNG functions only one time
o make sure unifrnd is double precision
Changes in version 0.7-3 (2006-08-23)
o make sure pmvnorm(lo=c(-Inf,-Inf), up=c(Inf,Inf), mean=c(0,0) == 0
Changes in version 0.7-2 (2005-08-29)
o make gfortran happy (a warning about unused variable NF remains)
Changes in version 0.7-1 (2004-11-18)
o use #!/bin/sh
Changes in version 0.7-0 (2004-10-14)
o a coding session with Frank produced `qmv{t,norm}'.
try to check if the support specified by `lower' and `upper' is
empty (problem spotted by Peter Thomson <peter_at_statsresearch.co.nz>)
Alan's fix prevents negative values to be returned.
o some cosmetics
Changes in version 0.6-8 (2004-06-03)
o EXIT statements are not supported by `f2c', Alan added GOTO
statements to `MVCHNC'
Changes in version 0.6-7 (2004-05-27)
o Alan's fix to MVCHNC solves problems with large degree of freedom
Changes in version 0.6-6 (2004-01-22)
o `La.eigen' is deprecated and `eigen' replaces it in R-1.9.0
Changes in version 0.6-5 (2003-11-14)
o check if covariance matrix is pd in rmvnorm (by Fritz Leisch)
Changes in version 0.6-4 (2003-10-06)
o use new base function `cov2cor'
Changes in version 0.6-3 (2003-07-21)
o Alans changes were restricted to N <= 100, now N <= 1000
are possible again
Changes in version 0.6-2 (2003-06-25)
o Alan's recent changes to `mvt.f' make `g77 -pedantic -Wall'
happy
Changes in version 0.6-1 (2003-06-18)
o pmvt(..., df = 0, ...) will return normal probabilities for both
the univariate and multvariate problem
Changes in version 0.6-0 (2003-06-17)
o Fortran code in `mvt.f' updated to recent version by Alan and Frank.
This fixes problems with `pmvt' and large degrees of freedom.
Changes in version 0.5-15 (2003-06-16)
o a note on one-sided probabilities in `pmvt'
correlation matrices in cats example a little bit nicer
Changes in version 0.5-14 (2003-05-06)
o the package owns a vignette based on the paper in RNews 1(2)
Changes in version 0.5-12 (2003-05-08)
o allow df=0 for pmvt
Changes in version 0.5-11 (2003-04-29)
o package npmc trys to use 'mvt' which is internal: export it anyway
Changes in version 0.5-10 (2003-04-23)
o mvtnorm is now in a NAMESPACE
Changes in version 0.5-9 (2003-02-13)
o log argument added to dmvnorm, thanks to
Jerome Asselin <jerome_at_hivnet.ubc.ca>
Changes in version 0.5-8 (2003-01-21)
o fixed bugreport PR#2478: sigma for univariate probabilities
Changes in version 0.5-7 (2002-11-27)
o use R's random number generator in the FORTRAN code:
set.seed has now has the desired impact.
Changes in version 0.5-6 (2002-10-07)
o rmvt added
Changes in version 0.5-5 (2002-07-03)
o use .Fortran(..., PACKAGE="mvtnorm")
Changes in version 0.5-4 (2002-04-09)
o correlation matrices for sigma with unequal variances incorrectly
computed, added `sig2corr' for that propose, tol argument removed,
fix by Alan to mvt.f
Changes in version 0.5-2 (2002-03-22)
o Frank added `tol' argument to MVTDST, now in mvtnorm
Changes in version 0.5-1 (2002-01-24)
o pmvt(0,1) works now
Changes in version 0.5-0 (2001-12-10)
o release for R-1.4.0
Changes in version 0.4-4 (2001-12-06)
o bugfix
Changes in version 0.4-3 (2001-12-05)
o the length of lower, upper and mean (delta) is now recycled to the
length of the largest, i.e. it is possible to say
pmvnorm(lower=-Inf, upper=1, mean=rep(1,10), corr=diag(10))
Changes in version 0.4-2 (2001-12-04)
o several typos, man-pages improved
Changes in version 0.4-1 (2001-12-04)
o interface changed: sigma (covariance matrix) can be specified as
well
o {rd}mvnorm added from package e1071 (thanks to Fritz!)
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