Commit a7274da7 authored by Andreas Tille's avatar Andreas Tille

Update upstream source from tag 'upstream/0.9.12-4.2'

Update to upstream version '0.9.12-4.2'
with Debian dir 06e2d9e9b5d371e4773c7165340dd93a976e2f4f
parents b5ca5d9e 8621eeca
Package: BayesFactor
Type: Package
Title: Computation of Bayes Factors for Common Designs
Version: 0.9.12-4.1
Date: 2018-05-08
Version: 0.9.12-4.2
Date: 2018-05-09
Authors@R: c(person("Richard D.", "Morey", role = c("aut", "cre", "cph"), email = "richarddmorey@gmail.com"),
person("Jeffrey N.", "Rouder", role = "aut", email = "jrouder@uci.edu"),
person("Tahira", "Jamil", role = c("ctb","cph"), email = "tahjamil@gmail.com"),
......@@ -26,7 +26,7 @@ LazyLoad: yes
LinkingTo: Rcpp (>= 0.11.2), RcppEigen (>= 0.3.2.2.0)
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-05-08 10:22:00 UTC; richard
Packaged: 2018-05-19 07:25:56 UTC; richard
Author: Richard D. Morey [aut, cre, cph],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb, cph],
......@@ -35,4 +35,4 @@ Author: Richard D. Morey [aut, cre, cph],
Alexander Ly [ctb, cph]
Maintainer: Richard D. Morey <richarddmorey@gmail.com>
Repository: CRAN
Date/Publication: 2018-05-08 11:28:10 UTC
Date/Publication: 2018-05-19 14:58:52 UTC
697c86cec4893d0419f2b45c5cbbd12b *DESCRIPTION
cfe8d6d0f23df800cea270cea7b926dc *DESCRIPTION
95366d8415ab5bc2015b009e0fd2a932 *NAMESPACE
aafeccda09cb8629e09836c420d4ece3 *NEWS
cae93a6084aaac4587fa7196a4897913 *R/BayesFactorPCL-package.R
81148e022101a781a9f29d5755c475a9 *NEWS
491d8e8953ebaa3af17133c1cbe77d94 *R/BayesFactorPCL-package.R
c07f5aa20300bf63952c1c2fc4e5fac2 *R/RcppExports.R
440b11c82aa5d6e6a426221b7435ff7c *R/aaClasses.R
8699eea296aefd7c890042d7e385e876 *R/aaGenerics.R
......@@ -56,19 +56,19 @@ cce3e64b98c058acf95f32ff45c104a8 *R/version.R
94e24dbb4ed809a1ac870cdb432ed510 *data/raceDolls.rda
1ccf4cdfbb6ee831b5c60dc2ca0d04ca *inst/doc/compare_lme4.R
664d69ff793b89ef5cb940b5c31a9d94 *inst/doc/compare_lme4.Rmd
e7557d7d9e079b62c28ebecc3a44eb46 *inst/doc/compare_lme4.html
e90b86302e89d96e0cd97a0513819584 *inst/doc/compare_lme4.html
3444667beceae04bc51450d8537a4954 *inst/doc/index.R
ab8952192cc7b37a4343c4fedf54a791 *inst/doc/index.Rmd
7fbf239f48829fef418ac580858b3b34 *inst/doc/index.html
2d29f2810c40e744c87d3c326553efc7 *inst/doc/manual.R
a7b4cbadefef5294e9e4d273fbb280f4 *inst/doc/manual.Rmd
a7f5b98c4de93712f1a54ea8ab343924 *inst/doc/manual.html
4f97b016e04857b94623b04f7ca1cf86 *inst/doc/manual.html
4152a2af90c99e372f47508e1ec3f6f4 *inst/doc/odds_probs.R
12a83925c5eb48221cea2851782311aa *inst/doc/odds_probs.Rmd
b94bfba6d70d2efbb2b6fbabbdc54857 *inst/doc/odds_probs.html
f9bf5c511d1310a38a3ea461bed0d584 *inst/doc/odds_probs.html
58f497699627aeed95274ddbc16df40c *inst/doc/priors.R
00453f4aedb7029cdcb99427110a9d34 *inst/doc/priors.Rmd
6d38988ef7e9644b0d0b155c267eb469 *inst/doc/priors.html
070cbb131001c03a28d9922b4c15ebd6 *inst/doc/priors.html
e9400e851188414778e46499702c6108 *inst/include/BayesFactor.h
bc49293e445773685371f62db735b84e *inst/include/BayesFactor_RcppExports.h
b668c9d076209546253781c4d10668de *inst/tests/test-anovaBF.R
......@@ -85,7 +85,7 @@ b8385f6b77a6cc5586bf20d291d8cc80 *man/BFBayesFactor-class.Rd
f0b76247ecba5ad3dff41cb8110c5fde *man/BFManual.Rd
4b64080b5990a403e688aec94ed7d596 *man/BFodds-class.Rd
9304ffca3dde3d69feaa44a40e1888d0 *man/BFprobability-class.Rd
7e4fdfa7bb1a03a31e72a1f97ee49e3b *man/BayesFactor-package.Rd
17ad812613d2590083d93d592a968270 *man/BayesFactor-package.Rd
44d8b51b16971e22a6b4fbc4ed9d1372 *man/anovaBF.Rd
96031aed3232a0c95b3f7e03c82cb447 *man/as.BFBayesFactor.Rd
b9af1dff97bc70504d84797e7d0e8bfd *man/as.BFprobability.Rd
......@@ -127,7 +127,7 @@ c88b84670252fa37824f50594416f2d8 *man/recompute-methods.Rd
cd40a4d89842450277508d0ae22d3933 *src/bfcommon.h
d14368c4a1e2cd464c68087174d0d2a3 *src/corr.cpp
6da84348ccc705c261aa769904cff53f *src/dinvgamma.cpp
b2f02e6281807c79291769241c346954 *src/genhypergeo_series_pos.cpp
f90adad6b8d2b196e492d0692a747282 *src/genhypergeo_series_pos.cpp
d9e574331b181fd8193e4006ca4506eb *src/interruptable_progress_monitor.h
f1e03bbe1a2447bb1a81f85bac0ae7c5 *src/interrupts.cpp
bc59a64d2e4892e0035300804ee5b1a3 *src/interrupts.h
......@@ -144,7 +144,7 @@ d40c49c6774ce3b89212b4dec70ac2c7 *src/linearRegGibbsRcpp.cpp
f798d4a788dcde608cfcb6c320ec0f7a *src/metattest.cpp
6a212c285b0775a7fa73418ffc2e0c1f *src/progress.cpp
5dc79805599ea7f30493fb68e4bec666 *src/progress.h
5c8a2425c2016f5b8f65b4288964ccdd *src/proportion.cpp
609c48b8936bfd93aa8d6caa71d6669a *src/proportion.cpp
7a3aec551441e2b3a0c7c5707da6b6d7 *src/rmvnorm.cpp
529528f24f00037c1c8ea5b3f81994b0 *src/ttestIndepRcpp.cpp
90216ff6ac99895044e9dd0e3e9a5f8f *src/ttestRcpp.cpp
......
CHANGES IN BayesFactor VERSION 0.9.12-4.2
CHANGES
* Fixed issue preventing Solaris compilation (affected 0.9.12-4 and 0.9.12-4.1)
CHANGES IN BayesFactor VERSION 0.9.12-4
CHANGES
......
......@@ -8,7 +8,7 @@
#'regression, correlations, proportions, and contingency tables.
#'
#'\tabular{ll}{ Package: \tab BayesFactor\cr Type: \tab Package\cr Version: \tab
#'0.9.12-4.1\cr Date: \tab 2018-5-08\cr License: \tab GPL 2.0\cr LazyLoad: \tab
#'0.9.12-4.2\cr Date: \tab 2018-5-09\cr License: \tab GPL 2.0\cr LazyLoad: \tab
#'yes\cr } The following methods are currently implemented, with more to follow:
#'
#'general linear models (including linear mixed effects models): \code{\link{generalTestBF}}, \code{\link{lmBF}}
......
......@@ -341,14 +341,14 @@ t.la = system.time(bfs.la &lt;- anovaBF(y ~ A*B*C + ID, data = effects,
</code></pre>
<pre><code>## user system elapsed
## 9.090 0.157 9.865
## 8.700 0.106 9.084
</code></pre>
<pre><code class="r">t.la
</code></pre>
<pre><code>## user system elapsed
## 4.601 0.053 4.796
## 4.440 0.044 4.550
</code></pre>
<pre><code class="r">plot(log(extractBF(sort(bfs.is))$bf),log(extractBF(sort(bfs.la))$bf),
......@@ -516,7 +516,7 @@ bfEff &lt;- colMeans(B5out[,1:10])
<!-- html table generated in R 3.5.0 by xtable 1.8-2 package -->
<!-- Tue May 8 11:21:26 2018 -->
<!-- Sat May 19 08:25:28 2018 -->
<table border=1>
<tr> <th> </th> <th> lmer fixed effects </th> </tr>
......@@ -563,7 +563,7 @@ sideBySide &lt;- data.frame(BayesFactor=bfEff,lmer=reparLmer)
<!-- html table generated in R 3.5.0 by xtable 1.8-2 package -->
<!-- Tue May 8 11:21:26 2018 -->
<!-- Sat May 19 08:25:28 2018 -->
<table border=1>
<tr> <th> </th> <th> BayesFactor </th> <th> lmer </th> </tr>
......@@ -593,7 +593,7 @@ abline(0,1, lty=2)
<hr/>
<p><em>This document was compiled with version 0.9.12-4.1 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
<p><em>This document was compiled with version 0.9.12-4.2 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
</body>
......@@ -2249,7 +2249,7 @@ Ly, A., Verhagen, A. J. &amp; Wagenmakers, E.-J. (2015). Harold Jeffreys&#39;s D
<p>Social media icons by <a href="http://www.awicons.com/">Lokas Software</a>.</p>
<p><em>This document was compiled with version 0.9.12-4.1 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
<p><em>This document was compiled with version 0.9.12-4.2 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
</body>
......@@ -407,7 +407,7 @@ post.prob
<p>Social media icons by <a href="http://www.awicons.com/">Lokas Software</a>.</p>
<p><em>This document was compiled with version 0.9.12-4.1 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
<p><em>This document was compiled with version 0.9.12-4.2 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
</body>
......
......@@ -428,7 +428,7 @@ t.test(x~grp,data=dat,paired=TRUE)
<hr/>
<p><em>This document was compiled with version 0.9.12-4.1 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
<p><em>This document was compiled with version 0.9.12-4.2 of BayesFactor (R version 3.5.0 (2018-04-23) on x86_64-apple-darwin15.6.0).</em></p>
</body>
......
......@@ -13,7 +13,7 @@ regression, correlations, proportions, and contingency tables.
}
\details{
\tabular{ll}{ Package: \tab BayesFactor\cr Type: \tab Package\cr Version: \tab
0.9.12-4.1\cr Date: \tab 2018-5-08\cr License: \tab GPL 2.0\cr LazyLoad: \tab
0.9.12-4.2\cr Date: \tab 2018-5-09\cr License: \tab GPL 2.0\cr LazyLoad: \tab
yes\cr } The following methods are currently implemented, with more to follow:
general linear models (including linear mixed effects models): \code{\link{generalTestBF}}, \code{\link{lmBF}}
......
......@@ -64,7 +64,7 @@ NumericVector genhypergeo_series_pos( NumericVector U,
for ( i = 0; i < maxiter; i++ ) {
fac = fac + sum(log( U + i) ) - sum( log( L + i ) ) + log(z) - log( i + 1 );
fac = fac + sum(log( U + i) ) - sum( log( L + i ) ) + log(z) - log( i + 1.0 );
for( j = 0 ; j < z.size() ; j++ ){
series[j] = logExpXplusExpY( temp[j], fac[j] );
......
......@@ -32,10 +32,10 @@ NumericMatrix metropProportionRcpp(NumericVector y, NumericVector n, double p0,
}
// starting values
double ln_p0 = log( sum(y) + 1 ) - log( sum(n) + 2 );
double ln_p0 = log( sum(y) + 1.0 ) - log( sum(n) + 2.0 );
double lo0 = Rf_qlogis( ln_p0, 0, 1, 1, 1 );
double lo_sd = exp ( 0.5 * ( ln_p0 + Rf_pexp( -ln_p0, 1, 1, 1 ) -
log( sum(n) + 2 ) - 2 * Rf_dlogis( lo0, 0, 1, 1 ) ) );
log( sum(n) + 2.0 ) - 2 * Rf_dlogis( lo0, 0, 1, 1 ) ) );
double lo = lo0;
// create progress bar
......
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