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}}
......
......@@ -7,13 +7,13 @@
using namespace Rcpp;
bool isgood( NumericVector s, NumericVector t, double tol)
{
{
int i=0;
for( i=0 ; i < t.size() ; i++){
if(t[i] != NA_REAL)
if ( ( logExpXminusExpY( s[i], t[i] ) - t[i] ) > log(tol) )
if ( ( logExpXminusExpY( s[i], t[i] ) - t[i] ) > log(tol) )
return 0;
}
}
return 1;
}
......@@ -27,13 +27,13 @@ NumericVector genhypergeo_series_pos( NumericVector U,
const bool check_conds,
const bool polynomial)
{
NumericVector fac( z.size() );
NumericVector temp( z.size() );
NumericVector series( z.size() );
LogicalVector greater( z.size() );
int i=0,j=0;
if(check_conds){
if(is_true(any(U<0)) || is_true(any(L<0)) || is_true(any(z<0))){
stop("All arguments must be positive.");
......@@ -41,7 +41,7 @@ NumericVector genhypergeo_series_pos( NumericVector U,
}
if(check_mod){
if( U.size() > (L.size()+1) ){
greater = abs(z)>0;
} else if(U.size() > L.size()) {
......@@ -55,16 +55,16 @@ NumericVector genhypergeo_series_pos( NumericVector U,
for( i = 0 ; i < z.size() ; i++){
if( greater[i] ) z[i] = NA_REAL;
}
}
}
}
if(maxiter==0){
return z*0+fac;
}
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] );
......@@ -75,14 +75,14 @@ NumericVector genhypergeo_series_pos( NumericVector U,
}
temp = clone(series);
}
if(polynomial){
return series;
}else{
Rcpp::warning("Series not converged.");
return z * NA_REAL;
return z * NA_REAL;
}
}
......@@ -7,21 +7,21 @@ double proptest_like_Rcpp(double lo, Rcpp::NumericVector y, Rcpp::NumericVector
using namespace Rcpp;
// [[Rcpp::export]]
NumericMatrix metropProportionRcpp(NumericVector y, NumericVector n, double p0, double rscale, int iterations, bool doInterval,
NumericVector interval, bool intervalCompl, bool nullModel, int progress, Function callback, double callbackInterval)
NumericMatrix metropProportionRcpp(NumericVector y, NumericVector n, double p0, double rscale, int iterations, bool doInterval,
NumericVector interval, bool intervalCompl, bool nullModel, int progress, Function callback, double callbackInterval)
{
RNGScope scope;
// setting last_cb to the beginning of the epoch
// setting last_cb to the beginning of the epoch
// ensures that the callback is called once, first
time_t last_cb = static_cast<time_t>(int(0));
time_t last_cb = static_cast<time_t>(int(0));
int i = 0;
double Ubounds[2], mu = log( p0 / ( 1 - p0 ) );
double candidate, z, trans_lo;
bool inInterval, valid_lo = true;
// For intervals
if( doInterval){
if( interval.size() == 0){
......@@ -32,28 +32,28 @@ 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 ) ) );
double lo_sd = exp ( 0.5 * ( ln_p0 + Rf_pexp( -ln_p0, 1, 1, 1 ) -
log( sum(n) + 2.0 ) - 2 * Rf_dlogis( lo0, 0, 1, 1 ) ) );
double lo = lo0;
// create progress bar
class Progress p(iterations, (bool) progress);
// Create matrix for chains
NumericMatrix chains(iterations, 1);
if(nullModel){
std::fill(chains.begin(), chains.end(), mu);
return chains;
}
if(doInterval){
Ubounds[0] = Rf_pnorm5( interval[0], lo0, lo_sd, 1, 0 );
Ubounds[1] = Rf_pnorm5( interval[1], lo0, lo_sd, 1, 0 );
}
// Start sampler
for( i = 0 ; i < iterations ; i++ )
{
......@@ -61,18 +61,18 @@ NumericMatrix metropProportionRcpp(NumericVector y, NumericVector n, double p0,
// Check interrupt
if (Progress::check_abort() )
Rcpp::stop("Operation cancelled by interrupt.");
p.increment(); // update progress
// Check callback
if( RcppCallback( &last_cb, callback, ( 1000.0 * ( i + 1 ) ) / iterations, callbackInterval) )
Rcpp::stop("Operation cancelled by callback function.");
// sample delta
// sample delta
if(doInterval){
if(intervalCompl){
candidate = Rf_runif(0, Ubounds[0] + 1 - Ubounds[1]);
if( candidate > Ubounds[0])
if( candidate > Ubounds[0])
candidate = candidate - Ubounds[0] + Ubounds[1];
}else{
candidate = Rf_runif(Ubounds[0], Ubounds[1]);
......@@ -81,23 +81,23 @@ NumericMatrix metropProportionRcpp(NumericVector y, NumericVector n, double p0,
}else{
candidate = Rf_rnorm( lo0, lo_sd );
}
// Metropolis-Hastings step
z = proptest_like_Rcpp(candidate, y, n, mu, rscale) -
z = proptest_like_Rcpp(candidate, y, n, mu, rscale) -
proptest_like_Rcpp(lo, y, n, mu, rscale) +
Rf_dnorm4(lo, lo0, lo_sd, 1) -
Rf_dnorm4(lo, lo0, lo_sd, 1) -
Rf_dnorm4(candidate, lo0, lo_sd, 1);
if(doInterval){
trans_lo = Rf_pnorm5(lo, lo0, lo_sd, 1, 0 );
inInterval = ( Ubounds[0] > trans_lo ) && ( Ubounds[1] < trans_lo );
if( (inInterval && intervalCompl) || (!inInterval && !intervalCompl) )
valid_lo = false;
}
if( ( Rf_rexp(1) > -z ) || !valid_lo ){
lo = candidate;
lo = candidate;
}
// copy to chains
......@@ -113,7 +113,7 @@ double proptest_like_Rcpp(double lo, NumericVector y, NumericVector n, double mu
int i;
double theta = 1 / ( 1 + exp(-lo) );
double logdens = Rf_dlogis( lo, mu, rscale, 1);
for( i = 0; i < y.size() ; i++ ){
logdens += Rf_dbinom( y[i], n[i], theta, 1);
}
......
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