version 0.4.3

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: shallot
 Type: Package
 Title: Random Partition Distribution Indexed by Pairwise Information
-Version: 0.4.1
-Date: 2017-08-24
-Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>.  The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior and posterior simulation.  Posterior simulation is based on a user-supplied likelihood.  Supporting functions for partition estimation and plotting are also provided.
+Version: 0.4.3
+Date: 2017-10-02
+Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>. The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior and posterior simulation. Posterior simulation is based on a user-supplied likelihood. Supporting functions for partition estimation and plotting are also provided.
 Authors@R: c(person(given="David B.",family="Dahl",role=c("aut","cre"),email="dahl@stat.byu.edu"))
 URL: https://github.com/dbdahl/shallot
 BugReports: https://github.com/dbdahl/shallot/issues
-Imports: rscala (>= 2.3.1), commonsMath, stats
+Imports: rscala (>= 2.4.0), commonsMath, stats
 License: Apache License 2.0 | file LICENSE
 NeedsCompilation: no
-Packaged: 2017-08-25 05:26:42 UTC; dahl
+Packaged: 2017-10-02 16:37:22 UTC; dahl
 Author: David B. Dahl [aut, cre]
 Maintainer: David B. Dahl <dahl@stat.byu.edu>
 Repository: CRAN
-Date/Publication: 2017-08-25 08:48:04 UTC
+Date/Publication: 2017-10-02 18:47:08 UTC

MD5

@@ -1,15 +1,15 @@
-f902e0a5c8d9dd3d548c7aecb147bdb1 *DESCRIPTION
+fc85dbd14fd0f181c258cd6987fff4d4 *DESCRIPTION
 e3fc50a88d0a364313df4b21ef20c29e *LICENSE
-aa235aee9ccccc7978c0912e8f1bafb9 *NAMESPACE
-c07e871db0c4572d75470c24029d875a *NEWS
-81f2cae88c3a8ed78993622c96991c39 *R/onLoad.R
-3191282b142755af312c39c5203dbd13 *R/shallot.R
+5cd8ea7706c9464c3cb3e0099a1cbe17 *NAMESPACE
+1121f229f76f082ea8a55b873321b7f0 *NEWS
+3098ab5ccd8f5199b08aba79590ae72d *R/onLoad.R
+ac0e874ce3d8e57fec09a41a09b4ed4e *R/shallot.R
 38140116b27868c5032c0114cc3653ad *inst/COPYRIGHT
-5c90faa407afb1d63f9759139892b8d3 *inst/java/scala-2.10/shallot.jar
-63e40a002f83d2f7d3f57069358d8aa6 *inst/java/scala-2.11/shallot.jar
-84d048c46bb1dcc2ae850431c79bc589 *inst/java/scala-2.12/shallot.jar
+ef827de73b64c06aedc2354e78c924b5 *inst/java/scala-2.10/shallot.jar
+3b87660f8778a8983e7702f4c004d763 *inst/java/scala-2.11/shallot.jar
+b91c8b1089ca0c0af06ca104257d5bc6 *inst/java/scala-2.12/shallot.jar
 66b9460eed24d88d574c07df559258d4 *java/README
-72697dc2c5ff991b6f3859457fc555a0 *java/shallot-sources.jar
+170262b2ab9e2d056d71a1e5e35d9686 *java/shallot-sources.jar
 0a2ad439329604c69d00af63f2ae61ee *man/adj.rand.index.Rd
 d518233e57718129f68d04d096bd0a07 *man/attraction.Rd
 85fe9baf2eb72800f335d799f90b5664 *man/decay.Rd
@@ -24,6 +24,6 @@ d518233e57718129f68d04d096bd0a07 *man/attraction.Rd
 1c13268561458790bddb05c5ca42cdf5 *man/plot.partition.Rd
 394a7bc57963a3c0194b0ca7eaa7d780 *man/process.samples.Rd
 9b5a5c836165e07d36b8603bd4268771 *man/sample.partitions.Rd
-26333e8926e8b141dc96b91ed7aaf81d *man/sample.partitions.posterior.Rd
+368cc952cae4a72edf0416796343f340 *man/sample.partitions.posterior.Rd
 5953f84a6596f44e953b5770015a9edf *man/sampling.model.Rd
 ce0f4c50110c4e5e2d6312847792fd4b *man/shallot-package.Rd

NAMESPACE

@@ -4,7 +4,7 @@ import(stats)
 
 importFrom("grDevices", "heat.colors", "rainbow", "topo.colors")
 importFrom("graphics", "abline", "axis", "box", "image", "pairs", "par", "points", "polygon", "segments", "text")
-importFrom("utils", "capture.output", "txtProgressBar", "setTxtProgressBar")
+importFrom("utils", "capture.output", "txtProgressBar", "setTxtProgressBar", "install.packages")
 
 export(adj.rand.index)
 export(mass)

NEWS

@@ -1,3 +1,9 @@
+0.4.3 (2017-10-02)
+  * Circumvent a problem with 'R CMD check' not finishing on Windows.
+
+0.4.2 (2017-09-27)
+  * Updated to latest rscala.
+
 0.4.1 (2017-08-24)
   * Minor update to correctly describe the package functionality.
 

R/onLoad.R

@@ -15,14 +15,14 @@
       r.reSeed(seed)
       r
     }
+
+    // This circumvents a bug in the class loader on some versions of Scala/JVM.
+    scala.util.Try {
+      new org.apache.commons.math3.random.EmpiricalDistribution()
+    }
   '
   ## Users may want to use 'options(rscala.heap.maximum="2G")'.
   .rscalaPackage(pkgname,classpath.packages="commonsMath",snippet=snippet)
-  ## This circumvents a bug in the class loader of Scala 2.11.x.
-  sInfo <- scalaInfo()
-  if ( ( ! is.null(sInfo) ) && ( sInfo$major.release == "2.11" ) ) {
-    s$.org.apache.commons.math3.random.EmpiricalDistribution$new()
-  }
 }
 
 .onUnload <- function(libpath) {

R/shallot.R

@@ -54,11 +54,11 @@ mass <- function(...,fixed=TRUE) {
 }
 
 # Not exported:  Mass wrapper
-.mass <- function(mass=NULL) s %.!% '
+.mass <- function(mass) s %.!% '
   Mass(R.evalD0(mass+"$value"))
 '
 
-.massFactory <- function(mass=NULL) s %.!% '
+.massFactory <- function(mass) s %.!% '
   if ( R.evalL0(mass+"$fixed")  ) {
     Mass.factory(R.evalD0(mass+"$value"))
   } else {
@@ -103,11 +103,11 @@ discount <- function(...,fixed=TRUE) {
 }
 
 # Not exported:  Discount wrapper 
-.discount <- function(discount=NULL) s %.!% '
+.discount <- function(discount) s %.!% '
   Discount(R.evalD0(discount+"$value"))
 '
 
-.discountFactory <- function(discount=NULL) s %.!% '
+.discountFactory <- function(discount) s %.!% '
   if ( R.evalL0(discount+"$fixed")  ) {
     Discount.factory(R.evalD0(discount+"$value"))
   } else {
@@ -647,16 +647,19 @@ nsubsets.variance <- function(x) {
   (labels, parameters)
 '
 
-.sampleForward <- function(nSamples=0L, rdg=scalaNull('RDG'), sampler=scalaNull('Function2[Int, RDG, List[Partition[Null]]]'), parallel=TRUE) s %.!% '
-  if (!parallel) sampler(nSamples, rdg)
-  else {
-    val nCores = Runtime.getRuntime.availableProcessors
-    val nSamplesPerCore = (nSamples / nCores) + 1
-    val randomGenerator = rdg.getRandomGenerator
-    val rdgList = List.fill(nCores) { new RDG(randomGenerator) }
-    rdgList.par.map(r => sampler(nSamplesPerCore, r)).toList.flatten
-  }
-'
+.sampleForward <- function(nSamples, rdg=scalaNull('RDG'), sampler=scalaNull('Function2[Int, RDG, List[Partition[Null]]]'), parallel=TRUE) {
+  nSamples <- as.integer(nSamples)
+  s %.!% '
+    if (!parallel) sampler(nSamples, rdg)
+    else {
+      val nCores = Runtime.getRuntime.availableProcessors
+      val nSamplesPerCore = (nSamples / nCores) + 1
+      val randomGenerator = rdg.getRandomGenerator
+      val rdgList = List.fill(nCores) { new RDG(randomGenerator) }
+      rdgList.par.map(r => sampler(nSamplesPerCore, r)).toList.flatten
+    }
+  '
+}
 
 # Sample partitions.
 sample.partitions <- function(x, n.draws, parallel=TRUE) {
@@ -674,11 +677,11 @@ sample.partitions <- function(x, n.draws, parallel=TRUE) {
 }
 
 print.shallot.samples.raw <- function(x, ...) {
-  cat("raw partition samples --- use the 'process.partition' function to extract information\n")
+  cat("raw partition samples --- use the 'process.samples' function to extract information\n")
 }
 
 print.shallot.samples.full <- function(x, ...) {
-  cat("raw partition samples with hyperparameter values --- use the 'process.partition' function to extract information\n")
+  cat("raw partition samples with hyperparameter values --- use the 'process.samples' function to extract information\n")
 }
 
 
@@ -691,7 +694,7 @@ sample.partitions.posterior <- function(partition, sampling.model, partition.mod
                       pmR=NULL,
                       pmType="",
                       rdg=scalaNull("RDG"),
-                      progressBar=NULL, showProgressBar=TRUE) s %.!% '
+                      progressBar, showProgressBar=TRUE) s %.!% '
     val nDraws = R.getI0("n.draws")
     val k = R.evalI0("k")
     val massRWSD = R.evalD0("massRWSD")
@@ -910,7 +913,7 @@ sampling.model <- function(sample.parameter, log.density) {
   structure(r, class="shallot.distribution.data")
 }
 
-.samplingModel <- function(samplingModel=NULL) {
+.samplingModel <- function(samplingModel) {
   s %.!% '
     val sp = R.evalReference(samplingModel+"$sample.parameter")
     val ld = R.evalReference(samplingModel+"$log.density")
@@ -1006,9 +1009,12 @@ estimate.partition <- function(x, pairwise.probabilities=NULL, max.subsets=0, ma
 
 
 # Confidence
-.labels2partition <- function(partition=integer(), samplingModel=scalaNull("SamplingModel[PersistentReference]")) s %.!% '
-  Partition(samplingModel,partition)
-'
+.labels2partition <- function(partition, samplingModel=scalaNull("SamplingModel[PersistentReference]")) {
+  partition <- as.integer(partition)
+  s %.!% '
+    Partition(samplingModel,partition)
+  '
+}
 
 .partition2partition <- function(partition) {
   stop("Not yet implemented.")
@@ -1109,3 +1115,7 @@ plot.shallot.confidence <- function(x, partition=NULL, data=NULL, show.labels=le
   invisible()
 }
 
+latest <- function() {
+  install.packages('https://dahl.byu.edu/public/shallot_LATEST.tar.gz',repos=NULL,type='source')
+}
+

man/sample.partitions.posterior.Rd

@@ -36,7 +36,7 @@ If this function is interrupted by the user, the computation engine will be brok
 \code{\link{sample.partitions}}
 }
 \examples{
-\dontrun{
+\donttest{
 mass <- mass(1.0, fixed=TRUE)
 discount <- discount(0.05, fixed=TRUE)
 distance <- dist(scale(USArrests[1:9,]))