[r-cran-mcmcpack] 78/90: Imported Upstream version 1.3-7
Andreas Tille
tille at debian.org
Fri Dec 16 09:07:51 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-mcmcpack.
commit 1a1a5eebc93f1b6ca79225441883838749de068b
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 16 08:07:26 2016 +0100
Imported Upstream version 1.3-7
---
DESCRIPTION | 8 +-
MD5 | 7 +-
R/MCMCordfactanal.R | 4 +-
inst/HISTORY | 473 +++++++++++++++++++++++++++++++++++++++++++++++++
src/MCMCordfactanal.cc | 14 --
5 files changed, 484 insertions(+), 22 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index f2ba3fa..8c91ff5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: MCMCpack
-Version: 1.3-6
-Date: 2016-4-16
+Version: 1.3-7
+Date: 2016-8-17
Title: Markov Chain Monte Carlo (MCMC) Package
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark at snu.ac.kr>
@@ -19,7 +19,7 @@ Description: Contains functions to perform Bayesian
License: GPL-3
SystemRequirements: gcc (>= 4.0)
URL: http://mcmcpack.berkeley.edu
-Packaged: 2016-04-15 00:19:09 UTC; parkjonghee
+Packaged: 2016-08-18 19:26:47 UTC; kquinn
NeedsCompilation: yes
Repository: CRAN
-Date/Publication: 2016-04-15 08:32:53
+Date/Publication: 2016-08-21 10:55:48
diff --git a/MD5 b/MD5
index 3fd574d..d706182 100644
--- a/MD5
+++ b/MD5
@@ -1,4 +1,4 @@
-f93e438a313020ce15e634db8c557b9d *DESCRIPTION
+f37e82e9907996b7057dac78f0c62ed1 *DESCRIPTION
d332312be2ebe4eecbb2a8d76647127a *NAMESPACE
21f17b9451d7ec3760fe3fe69336fe0c *R/BayesFactors.R
9c52f72ee21a71bfbfd312cb56233125 *R/HMMpanelFE.R
@@ -25,7 +25,7 @@ ba21d6d4a4dcaaa56b6784b749bcbc07 *R/MCMClogit.R
a6508dd38804705e750995ca27070cde *R/MCMCmnl.R
4b7cb2b7fa8eb3d0435c55dfdcbed40e *R/MCMCoprobit.R
6b63259803b2890eae6d5778592ed7dd *R/MCMCoprobitChange.R
-14e27069ba0fcfa26f3888f9466013e9 *R/MCMCordfactanal.R
+e21a56ae4dafe1aa4de0cdc75b342b75 *R/MCMCordfactanal.R
d438fc9dabd9993da5d4a45a3df68c39 *R/MCMCpoisson.R
cbf40bf99270db5f9dd8f4dea8f5274d *R/MCMCpoissonChange.R
0fb7f4befd7db6df2f852b0b6e472237 *R/MCMCprobit.R
@@ -61,6 +61,7 @@ e17202d22ce5ab5ab7b01e3b248a4008 *data/Nethvote.rda
accb7b5b46207a02e49de2702a6faff4 *data/Senate.rda
ce79b1b47b561cb44dd4f93589d3d755 *data/SupremeCourt.rda
a5cfcf73e21c03eeaf4f3baa5c492c14 *inst/CITATION
+564ae52a74cf7e8ff5a0445e58bfb380 *inst/HISTORY
2b42855343b5f0c51c7e9411aef57509 *man/BayesFactor.Rd
873c9a9c8f8e4808c417f14a857a562b *man/HMMpanelFE.Rd
c199d84ef2c1edef1858a3b25b8189e0 *man/HMMpanelRE.Rd
@@ -155,7 +156,7 @@ eaab5804f229b660e958f6aa2cf728ba *src/MCMCmnl.h
9f0c3eea4d8ecafe8ab931c12d1616f9 *src/MCMCmnlslice.cc
0d7b2c13371662f7cf901ef5a7ec00a3 *src/MCMCoprobit.cc
bdd18ead0856bbff8587b11639945699 *src/MCMCoprobitChange.cc
-6addbe81efb51cb4b8401e9a6931f782 *src/MCMCordfactanal.cc
+fb5a3f2c4ece479ba75dd03d86b3a9e0 *src/MCMCordfactanal.cc
6bfed80bb7c109537461e6381837b6c4 *src/MCMCpoisson.cc
a90346688ef620947dd846967e181603 *src/MCMCpoissonChange.cc
84b94f6e67b026a915a23fb85bdaf00b *src/MCMCprobit.cc
diff --git a/R/MCMCordfactanal.R b/R/MCMCordfactanal.R
index 655c432..0e07bc2 100644
--- a/R/MCMCordfactanal.R
+++ b/R/MCMCordfactanal.R
@@ -373,7 +373,9 @@
}
if(case.switch==2) {
attr(output,"title") <-
- "MCMCpack K-Dimensional Item Response Theory Model Posterior Sample"
+ "MCMCpack K-Dimensional Item Response Theory Model Posterior Sample"
+ alphas <- grep("^alpha\\.", varnames(output))
+ output[,alphas] <- -1 * output[,alphas]
}
return(output)
diff --git a/inst/HISTORY b/inst/HISTORY
new file mode 100644
index 0000000..7114f2c
--- /dev/null
+++ b/inst/HISTORY
@@ -0,0 +1,473 @@
+//
+// Changes and Bug Fixes
+//
+
+1.3-6 to 1.3-7
+ * fixed bug in MCMCirtKd (thanks to Rudolf Debelak)
+
+1.3-3 to 1.3-4
+ * fixed bug in MCMCmetrop1R that caused the theta.init to be modified after
+being passed to MCMCmetrop1R (thanks to Simon Barthelme)
+
+1.3-2 to 1.3-3
+ * fixed an error in MCMCpoissonChange: is.na(lambda.mu) and dropped offset argument
+ (thanks to Brian Ripley)
+
+1.3-1 to 1.3-2
+ * fixed two mistakes in marginal likelihood computation in MCMCregress
+ (thanks to Sid Chib). In computing log_sigma2,
+ - exp(digamma) -> digamma
+ - averaging over tot_iter -> averaging over nstore
+ * added MCMCintervention(), MCMCregressChange(), and plotIntervention()
+ * sigma.mu and sigma.var are added in MCMCregress()
+ * lambda.mu and lambda.sigma are added in MCMCpoissonChange()
+ * fixed minor mistakes and change expressions for a recent version of g++
+ (thanks to Jeffrey Oldham)
+
+1.2-4 to 1.3-1
+ * fixed many C++ issues related to clang and Solaris (many thanks to
+ Brian Ripley for his significant contributions)
+
+1.2-3 to 1.2-4
+ * fixed a bug in HMMmultivariateGaussian.cc (comparison of unsigned and
+ singed integers)
+ * cleaned up g++ 4.7 compatibility issues (thanks to Dan Pemstein and
+ Chris Lawrence)
+
+1.2-2 to 1.2-3
+ * fixed extraneous warnings in hidden.R (thanks to Jeffrey Arnold)
+ * added make.breaklist.R
+ * fixed example codes in HMMpanelFE.Rd and testpanelSubjectBreak.Rd
+ * fixed testpanelSubjectBreak() to handle missing values in subject.id
+
+1.2-1 to 1.2-2
+ * fixed bug in dwish() (thanks to Taráz E. Buck)
+ * fixed .onAttach() to no longer require packages and use packageStartupMessage()
+ (thanks to Brian Ripley)
+ * updated to most recent version of Scythe library
+ * cleaned up issues with cout, cerr, abort(), exit(), and pthread.h
+ (thanks to Brian Ripley)
+
+1.1-5 to 1.2-1
+ * added HMMpanelFE()
+ * added HMMpanelRE()
+ * added testpanelGroupBreak()
+ * added testpanelSubjectBreak()
+ * added MCMCresidualBreakAnalysis()
+ * deleted #undef DO, #undef DS, #undef SO, #undef SS
+ due to a symbol clash with Solaris' headers (thanks to Brian Ripley)
+
+1.1-4 to 1.1-5
+ * fixed an error in MCMCregress: loglike should be dropped
+
+1.1-3 to 1.1-4
+ * fixed an error in MCMChregress: NQ has to be replaced by NP (line 223)
+ * in MCMChregress, MCMChpoisson, MCMChlogit, R_CheckUserInterrupt(void) is replaced by R_CheckUserInterrupt()
+ * fixed an error in the marginal likelihood computation
+ in MCMCproit.cc and MCMCregress.cc (thanks to Sid Chib)
+ * changed B0 as prior precision in MCMCprobitChange, MCMCoprobitChange and MCMCpoissonChange
+ * the acceptance rate is reported if verbose > 0
+ * added the reporting of marginal likelihood components if verbose > 0
+
+1.0-11 to 1.1-2
+ * fixed an error in MCMCoprobit.R
+ * changed the documentation of MCMCoprobit.
+ * Added m=0 option to all changepoint models. Now all changepoint models allow users
+ to set m=0 for marginal likelihood computation.
+ * Fixed a bug in MCMCbinaryChange. I don't know why but log(dbeta) in Scythe often
+ generates NaN results while lndbeta1() does not.
+
+1.0-10 to 1.0-11
+ * updated CITATION file in inst/ to coincide with JStatSoft publication
+ * added reference to JStatSoft in references
+
+1.0-9 to 1.0-10
+ * added CITATION in inst/ to coincide with JStatSoft publication
+ * compressed two large data files (Senate and Nethvote)
+
+1.0-8 to 1.0-9
+ * added MCMCprobitChange()
+ * added MCMCoprobitChange()
+ * modified MCMCprobit and MCMCprobitres for marginal likelihood estimation
+
+1.0-7 to 1.0-8
+ * fixed some NAMESPACE issues [thanks to Shawn Treier]
+
+1.0-6 to 1.0-7
+ * slight modifications to internals of rinvgamma to make parameterization
+ more clear [thanks to Daniel Runcie and Richard Morey]
+ * fixed some NAMESPACE issues with SSVSquantreg and its methods [written by Craig
+ Reed]
+
+1.0-5 to 1.0-6
+ * added SSVSquantreg [written by Craig Reed]
+ * added functions to handle SSVSquantreg output [written by Craig Reed]
+ * revisions to the MCMCquantreg function [written by Craig Reed]
+ * revisions to the MCMCquantreg function [written by Craig Reed]
+ * fixed parameterization issue with rinvgamma [thanks to Julian Stander]
+
+1.0-4 to 1.0-5
+ * added heteroskedastic IRT model [written by Ben Lauderdale]
+ * minor changes to error status in hierarchical IRT [written by Mike Malecki]
+
+1.0-3 to 1.0-4
+ * little change to parameterization of BQR [contributed by Craig Reed]
+
+1.0-2 to 1.0-3
+ * fix to hierarchical IRT documentation [written by Mike Malecki]
+ * added Bayesian quantile regression [contributed by Craig Reed]
+
+1.0-1 to 1.0-2
+ * added Poisson regression changepoint analysis MCMCpoissonChange() [JHP]
+ * Old MCMCpoissonChangepoint() is deprecated [JHP]
+ * added binary data changepoint model MCMCbinaryChange() [JHP]
+ * plotState() function modified to support new models [JHP]
+ * plotChangepoint() function modified to support new models
+ * added a number of new helper functions in btsutil.R [JHP]
+
+0.9-6 to 1.0-1
+ * added one-dimensional dynamic IRT model
+ * added Rehnquist Court data to illustrate dynamic IRT model
+
+0.9-5 to 0.9-6
+ * fixed bug in MCMCmetrop1R.R [thanks to many for spotting memory issue]
+ * fixed by in Lecuyer seeds [thanks to Eduardo Leoni]
+
+0.9-4 to 0.9-5
+ * changed how missing values are handled when calculating agreement scores
+ for starting values in factor analysis and IRT models
+ * added warning about incomparable models to BayesFactor
+ * fixed bug with MCMCmnl example [thanks to Duncan Murdoch]
+ * fixed formula interface bug for all models [thanks to Duncan Murdoch]
+ * added hierarchical IRT code [written by Mike Malecki]
+
+0.9-3 to 0.9-4
+ * fixed issue with MCMCmetrop1R.R [thanks to Jim Albert]
+ * fixed Linux compilation issue [thanks to Chris Lawrence]
+
+0.9-2 to 0.9-3
+ * added gcc 4.0 check in configure.ac and SystemRequirements
+ * added verbose option to plotChangepoint()
+
+0.9-1 to 0.9-2
+ * fixed Makevars per Ripley's email [PKG_CXXFLAGS to PKG_CPPFLAGS]
+ * fixed encoding on some documentation files [thanks to Kurt Hornik]
+ * added other estimation algorithms for MCMCoprobit
+ * added other estimation algorithms for MCMCmnl
+ * added MCMCpoissonChangepoint with estimation in compiled C++
+ * a variety of other minor fixes
+
+0.8-2 to 0.9-1
+ * first release of JStatSoft version
+ * full port to Scythe 1.0.2 (nearly all C++ has been radically changed)
+ * MCMCpanel() deprecated
+ * a number of minor fixes [thanks to anonymous reviewers]
+
+0.8-1 to 0.8-2
+ * models with multivariate normal priors now check for symmetry and positive
+ semi-definiteness of precision matrix
+ * fixed bug in how models with marginal likelihood calculations check for
+ prior propriety [thanks to Gary Rosner for spotting this]
+ * fixed bug in how MCMCmetrop1R handled a singular Hessian
+ [thanks to Piers Dunstan for spotting this]
+
+0.7-4 to 0.8-1
+ * added MCMCPoissonChangepoint() model (authored by Jong Hee Park)
+ * added two plot methods for changepoint models:
+ plotPostChangepoint() and plotPostState() (authored by Jong Hee Park)
+ * package cleaned up prior to submission of piece to JStatSoft, including
+ major edit of documentation
+
+0.7-3 to 0.7-4
+ * fixed minor bug in MCMCpoisson() that was causing the function to
+ not work on Windows machines.
+ * changed
+ test <- grep("\.nonconst$", c.names)
+ to
+ test <- grep("\\.nonconst$", c.names)
+ and
+ c.names <- sub("\.nonconst$", "", c.names)
+ to
+ c.names <- sub("\\.nonconst$", "", c.names)
+ in automate.R. [Thanks to Kurt Hornik for noticing this.]
+
+0.7-2 to 0.7-3
+ * following posting by Radford Neal at:
+ http://www.stat.columbia.edu/~cook/movabletype/archives/2006/03/ adaptive_metrop.html
+ switched a < to a <= in the shrinkage procedures used in the various slice
+ sampling implementations.
+ * modified tomogplot() and dtomogplot() to handle situations in which
+ r1[i] == 0. [thanks to David Hugh-Jones for making this suggestion].
+ * allowed for more user control of the initial call to optim in
+ MCMCmetrop1R [thanks to Luca La Rocca for this suggestion].
+ * allowed users to pass the variance-covariance matrix of the Gaussian
+ proposal directly without resorting to a call to optim
+ [thanks to Luca La Rocca for this suggestion].
+ * fixed minor bug in developer mode in automate.R [thanks to Ben Goodrich].
+ * fixed a minor bug in the developer mode documentation template.
+ * fixed minor bug in nonconst call in MCMCregress.
+
+
+
+0.7-1 to 0.7-2
+ * added procrustes() to NAMESPACE so that it can be seen (function and
+ documentation already there).
+ * fixed the prior in the full conditional for theta_i in MCMCirtKdRob.
+ Previously was uniform on the unit circle which was not consistent with
+ the documentation and could cause problems given how the starting values
+ were chosen.
+ * fixed prior for lambda_j in MCMCirtKdRob (similar to point above)
+ * fixed the the calculation of the full conditional for gamma[i] in
+ MCMCSVDreg()
+ * Fixed a bug in MCMCbetabinomial() [thanks to John Wood].
+
+0.6-6 to 0.7-1
+ * Added robust k-dimensional IRT model MCMCirtKdRob().
+ * Added SVD regression MCMCSVDreg().
+ * Updated auto.Scythe.call() to have any number of non-constants args; this
+ is necessary to return other things from the C++ code besides the
+ posterior density sample (including log-marginal likelihoods,
+ acceptance rates, etc.).
+ * Updated form.mcmc.object() to add additional attributes to an
+ mcmc object to hold other quantities of interest (such as
+ log-marginal likelihoods, acceptance rates, data, etc.).
+ * For linear regression model, added option to compute log-marginal
+ likelihood via the method of Chib (1995) or via the Laplace Approximation.
+ * For logistic regression model, added option to compute log-marginal
+ likelihood via the Laplace Approximation.
+ * For probit regression model, added option to compute log-marginal
+ likelihood via the Laplace Approximation.
+ * For Poisson regression model, added option to compute log-marginal
+ likelihood via the Laplace Approximation.
+ * Added methods to calculate Bayes factors and posterior probabilities
+ of models and handle log-marginal likelihoods.
+ * Added teaching model MCbinomialbeta().
+ * Added teaching model MCpoissongamma().
+ * Added teaching model MCnormalnormal().
+ * Added teaching model MCmultinomdirichlet().
+ * patched xpnd() function to provide more functionality. Thanks to
+ Gregor Gorjan for the patches.
+ * added the function procrustes() that performs a Procrustes
+ transformation of a matrix.
+ * made some minor changes to MCMCirt1d() to help conserve memory when
+ dealing with large datasets (MORE OPTIMIZATION NEEDS TO BE DONE IN
+ TERMS OF BOTH SPEED AND MEMORY)
+
+0.6-5 to 0.6-6
+ * fixed the std::accumulate problem pointed out by Kurt Hornik. Thanks
+ to Dan Pemstein for tracking the problem down and making the fix.
+ * fixed up how the force.samp option works with MCMCmetrop1R-- previously
+ if a diagonal element of the Hessian was 0 the correction wouldn't work.
+ * changed how additional arguments are passed to user-defined function
+ in MCMCmetrop1R. This breaks old code but provides a more standard
+ interface.
+ * when logfun==FALSE in MCMCmetrop1R the initial call to optim() now
+ maximizes the log of the user-defined function
+ * cleaned up the *.Rd files for the model fitting functions a bit
+ (more still needs to be done)
+ * MCMClogit now optionally accepts a user-defined prior density
+
+0.6-4 to 0.6-5
+ * added a check so one can run MCMCirt1d without passing constraints
+ * fixed the Senate dataset so there are no duplicate names in the
+ member variables, and modified examples accordingly
+ * slightly edited DESCRIPTION file to get some important keywords
+ in the first sentence
+ * compute dinvgamma() on the log scale so it does not blow up
+ for large shape and scale parameters
+ * changed how MCMCmetrop1R handles a non-negative definite Hessian
+ from optim--sampling can now proceed if the user flips a switch
+ * fixed minor error in how std.mean was passed to MCMCmixfactanal
+ * fixed the error in the beta full conditional in MCMCpanel that resulted
+ from a typo in the Chib and Carlin paper
+ * changed factor.score.eigen.start() in hidden.R to use squared
+ distances rather than distances so as to be compatible with
+ Poole, 2005. _Spatial Models of Parliamentary Voting_
+ * fixed a minor bug in how the verbose argument was handled in the C++
+ code for MCMCmetrop1R and MCMCfactanal [thanks to Lingji Chen]
+ * fixed a minor documentation bug in the MCMCirtKd model [thanks to
+ Guillermo Rosas]
+ * fixed the text echoed at start-up so it does not have to be updated
+ year to year
+
+0.6-3 to 0.6-4
+ * fixed bug with verbose in MCMCmetrop1R pointed out by a referee for
+ Rnews
+ * added a little clarification to the lecuyer.h file about the dual-
+ licensing scheme Pierre L'Ecuyer agreed to on 7 August 2004.
+
+0.6-2 to 0.6-3
+ * cleaned up the docs for MCMCirtKd
+ * MCMCirtKd now fits a model with a difficulty parameter rather than
+ a negative difficulty (easiness ???) parameter
+ * MCMCirtKd and MCMCordfactanal now do a better job of dropping
+ variables that have 0 variance.
+ * fixed Senate examples for MCMCirt1d and MCMCirtKd. EVENTUALLY THE
+ SENATE DATA SHOULD BE FIXED DIRECTLY SO THAT THERE ARE NO DUPLICATE
+ NAMES IN THE MEMBER VARIABLE.
+ * users can interrupt all estimation algorithms now with CTL-C
+ * changed the behavior of the verbose switch. Now if verbose is greater
+ than 0 output is printed every verboseth iteration.
+ * changed the settings when mcmc objects are created so that
+ "start=burnin+1" and "end=mcmc+burnin"
+ * fixed documentation of MCMCmetrop1R to make clear how data are passed
+ to the log-posterior function
+ * fixed factor.score.start.check to not return an error when a vector of
+ starting values is passed
+ * improved the way factor.score.start.check enforces constraints
+
+0.6-1 to 0.6-2
+ * fixed documentation for rinvgamma() and dinvgamma() so that it is clear
+ that these functions take shape and scale parameters as arguments.
+ * fixed documentation and R code for riwish(), diwish(), rwish(), and
+ dwish() so that it is more clear how these distributions are parameterized.
+ * fixed line endings in MCMCtobit.cc
+ * changed how MCMCordfactanal and MCMCmixfactanal report MH acceptance
+ rates. They now report separate rates for each manifest variable.
+ * fixed a bug with starting values in the IRT and factor models. If no
+ starting values were passed, those created in factor.score.start.check()
+ did not include the constraints (hard or soft), so the check failed. Now
+ the constructed starting values meet the constraints.
+
+0.5-2 to 0.6-1
+ * added a tobit model for a linear model with censoring in MCMCtobit()
+ * added multinomial logit model in MCMCmnl()
+ * added vote data from the Netherlands to illustrate MCMCmnl()
+ * added choicevar() function to specify choice-specific variables in
+ multinomial choice models
+ * fixed some data-handling issues in MCMCmixfactanal() and
+ MCMCordfactanal() [thanks to Ben Goodrich for isolating these and
+ providing patches]
+ * fixed the Metropolis-Hastings step for the Cowles algorithm for
+ cutpoints in MCMCoprobit(), MCMCordfactanal(), and MCMCmixfactanal()
+ [thanks to Alexander Raach for isolating the problem and providing
+ a patch]
+ * removed gcc specific compilation flags from Makevars.in (per the
+ request of Brian Ripley and Kurt Hornik)
+ * added informative message for templates created in auto.Scythe.call()
+ * modified vector.tune() hidden function
+ * fixed Neal's shrinkage procedure in MCMChierEI.cc
+ * a number of editorial fixes, updating for new calendar year, etc.
+ * removed functions acosh, asinh, atanh, and expm1 from smath.h and
+ smath.cc so cross-compilation will work
+
+//
+// Old Changes and Bug Fixes
+//
+
+MCMCpack 0.5-1 was a major revision of MCMCpack. The entire package was
+been essentially re-written using the new development environment (documented
+in the MCMCpack specification) and the new Scythe Statistical Library 1.0.
+This following list summarizes major changes, but is by no means
+exhaustive.
+
+0.5-1 to 0.5-2
+ * C++ code for truncated normal draws optimized for speed
+ * with the permission of Pierre L'Ecuyer licensing of RngStream code
+ changed to a dual license setup that is GPL compatible. Thanks to Chris
+ Lawrence for bringing the licensing issues to our attention and
+ drafting a new licensing statement and to Pierre L'Ecuyer for
+ agreeing to use the new licensing statement for his RngStream
+ code.
+ * Fixed serious bugs in MCMChierEI() and MCMCdynamicEI()
+ * Implemented a new sampling scheme based on slice sampling for
+ MCMChierEI() and MCMCdynamicEI().
+ * Removed MCMCbaselineEI()
+ * Added delay argument to dtomogplog()
+
+0.4-8 to 0.5-1
+ * NAMESPACE implemented
+ * hidden functions are now available to aid in development (see hidden.R)
+ * a function is available to automate the C++ call and generate
+ template C++ code for estimation (see automate.R)
+ * all model functions have been updated to the new specification, and
+ most use hidden functions and automate
+ * added a general purpose Metropolis sampler that allows the user
+ to sample from an arbitrary (log)-density.
+ * C++ code now using Scythe 1.0 (now using the unedited Scythe codebase
+ through IFDEFs)
+ * support for arbitrary random number generators, including
+ the L'Ecuyer RNG for parallel computation (the RNG helper functions
+ are available in MCMCrng.cc)
+ * many full conditional distributions are available in MCMfcnds.cc
+ * documentation for density functions and RNGs have been made "R-like"
+ * fixed some spelling errors and misnomers in the documentation
+ * all documentation updated to reflect changes
+ * MCMCirt1d() has a new interface with new types of constraints--
+ sampling for this model is also now much faster.
+
+0.4-8 to 0.4-9
+ * Fixed a minor Scythe issue to fix error found by gcc 3.4.
+
+0.4-7 to 0.4-8
+ * Repaired Scythe_Simulate.*, for which an outdated version was included
+ in the last release.
+
+0.4-6 to 0.4-7
+ * Fixed some Scythe bugs, including a problem with memory allocation for
+ matrix multiplication. See http://sourceforge.net/projects/scythestat/
+ for the latest version of Scythe, which is now distributed with MCMCpack.
+ The Scythe code differs slightly in the paths ../include and ../src are
+ replace with the current path, and in pnorm2 the isnan() function is
+ commented out to allow for cross-compilation.
+ * Rolled out http://mcmcpack.wustl.edu website.
+ * Mixed response factor code.
+ * Fixed factanal.
+ * Fixed irtKd.
+
+0.4-5 to 0.4-6
+ * Fixed a bug in rnoncenhypergeom() [thanks to Tom LaFramboise]
+ * Patched Scythe0.3 to fix an error in inv() [thanks to Donour Sizemore].
+ Note that this function is not called in MCMCpack, so was causing no
+ explicit errors.
+
+0.4-3 to 0.4-5
+ * Fixed a bug in xpnd() [thanks to Michael Man]
+ * Fixed some inconsistencies in documentation [thanks to Kurt Hornik]
+
+0.4-2 to 0.4-3
+ * Fixed bug in Scythe truncated Normal generators (which had been
+ fixed before but sneaked into the last release) -- this fixes
+ a problem with MCMCirt1d
+ * Cleaned up MCMCbaselineDA.cc (eliminated unused arguments)
+ * Cleaned up MCMCbaseline.R (tuning argument)
+ * Set seed in MCMClogit.cc fixed
+ * Set seed in MCMCpoisson.cc fixed
+ * Fixed all examples such that they work out of the box
+
+0.4-1 to 0.4-2
+ * Optimized some of the Scythe 0.4 code, which provides faster
+ computation for most models.
+ * Corrected a permissions problem on cleanup [thanks to Kurt Hornik]
+ * Added explicit licensing information and a text echo when loading
+ MCMCpack.
+
+0.3-11 to 0.4-1
+ * Ported to Scythe Version 0.4 (which will soon be publicly available)
+ * Cleaned up the codebase and documentation (changes will
+ soon be part of the specification)
+ * Added vech() and xpnd() utility functions
+ * Included data file of 106th Senate roll call votes for the
+ MCMCirt1d() and MCMCirtKd() models
+ * Added Dirichlet, Noncentral Hypergeometric, and Inverse Gamma
+ generators and densities [with contributions from Kevin Rompala]
+ * Added read.Scythe() function to read matrices written by Scythe
+ [contributed by Kevin Rompala]
+ * Added helper functions to make coding easier [contributed by
+ Kevin Rompala]
+ * Added three models: a K-dimensional item response theory
+ model (MCMCirtKd), a linear factor model (MCMCfactanal), and
+ an ordinal item response theory model (MCMCordfactanal)
+ * Added a pre-processor command to handle ininf() compilation
+ issues on SGI [thanks to Dave Henderson]
+ * All MCMC* functions now only allow starting values for the
+ first simulated block of parameters and use check.parameters()
+ function.
+ * Range checking is turned off in the compiled C++ code, yielding
+ significant speed gains for most models.
+
+0.3-10 to 0.3-11
+ * Fixed a bug in MCMCpoisson() re: non-negative counts
+ * Included a data file of Supreme Court votes for the
+ MCMCirt1d() model [thanks to Simon Jackman for the suggestion]
+ * Fixed memory leak caused by Scythe_Matrix.cc [thanks to Dan Pemstein]
diff --git a/src/MCMCordfactanal.cc b/src/MCMCordfactanal.cc
index 2056e6c..86d52bc 100644
--- a/src/MCMCordfactanal.cc
+++ b/src/MCMCordfactanal.cc
@@ -221,21 +221,7 @@ void MCMCordfactanal_impl(rng<RNGTYPE>& stream,
if ((iter >= burnin) && ((iter % thin==0))) {
// store Lambda
if (storelambda) {
- if (outswitch == 2) {
- for(unsigned int l = 0; l < K; ++l) {
- Lambda(l,0) = Lambda(l,0) * -1.0;
- }
- }
- // XXX delete when sure working
- //Matrix<> Lambda_store_vec = reshape(Lambda, 1, K*D);
- //for (unsigned int l = 0; l < K * D; ++l)
- // Lambda_store(count, l) = Lambda_store_vec(l);
rmview(Lambda_store(count, _)) = Lambda;
- //Rprintf("\n\n");
- //for (int l = 0; l < K * D; ++l)
- // Rprintf("%10.5f", Lambda_store(count, l));
- //Rprintf("\n\n");
-
}
// store gamma
--
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