version 0.2.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pivmet
 Type: Package
 Title: Pivotal Methods for Bayesian Relabelling and k-Means Clustering
-Version: 0.1.1
-Date: 2019-02-26
+Version: 0.2.0
+Date: 2019-06-23
 Author: Leonardo Egidi[aut, cre], 
         Roberta Pappadà[aut], 
         Francesco Pauli[aut], 
@@ -21,13 +21,13 @@ Encoding: UTF-8
 LazyData: true
 LazyLoad: yes
 SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
-Depends: bayesmix, rjags, runjags, mvtnorm, RcmdrMisc
-Imports: cluster, mclust, MASS
+Depends: bayesmix, rjags, mvtnorm, RcmdrMisc
+Imports: cluster, mclust, MASS, corpcor, runjags, rstan
 Suggests: knitr, rmarkdown
 VignetteBuilder: knitr
 RoxygenNote: 6.1.0
 BuildManual: yes
 NeedsCompilation: no
-Packaged: 2019-02-26 21:03:11 UTC; leoeg
+Packaged: 2019-06-24 16:34:12 UTC; leoeg
 Repository: CRAN
-Date/Publication: 2019-02-26 21:20:17 UTC
+Date/Publication: 2019-06-24 16:50:03 UTC

MD5

@@ -1,36 +1,36 @@
-e3460cc3f00cca35b2f91e55b5a92265 *DESCRIPTION
-2ba3e5413467ea7dda94c752dab896cb *NAMESPACE
-05f9200123d96779efe4be97be8f0d2a *NEWS.md
-e2cfa8aaca079247d19a52c0059b74a9 *R/bayes_mcmc.R
-a5b574520f3f1ff12d8cac35b353109b *R/mus.R
-1a4644cd0d648ad63199f43c28dcafbb *R/musk.R
-0b62e6ed58f60ed5a90572b329db8b0b *R/pivotal.R
-4916fa5f41c07ec54d839124f09ea613 *R/plot.R
-08a9933013c9d227fead6c812e9a7627 *R/relab.R
-db18079ce149fc084091bcd7339daf5a *R/sim.R
-406852041931cb6ebfd8d7522a846f2b *README.md
+b1bb55055b5109870d8a8dbc9831f3a3 *DESCRIPTION
+5d9f03ce2737ba18b95fdc5bb9af8cf4 *NAMESPACE
+1408e32bed72983ffb72525b7886e30e *NEWS.md
+289515c40ba1d4f146c914dca542a818 *R/bayes_mcmc.R
+4d44c58648506db591eb555dd52f0d0e *R/mus.R
+68c6d00c9e15c8f79d91246288890b3f *R/musk.R
+d4ed00a925ec98b801a718df387e3895 *R/pivotal.R
+9fe17395d40d8b65d166ba0dde949cb8 *R/plot.R
+32d5653664bf73e0bf89351d0810c513 *R/relab.R
+94e689ce4cad315e568e8500bc70d9cb *R/sim.R
+87606bf157b96b52f5b702f34951f885 *README.md
 510662c227cf4dd72a8bcf3ae43469f2 *build/vignette.rds
-fbf92eacd515f45b1ccab06ba282871e *inst/doc/K-means_clustering_using_the_MUS_algorithm.R
-8cb889dcf75ebac54b2579eb36324c03 *inst/doc/K-means_clustering_using_the_MUS_algorithm.Rmd
-9346371c5a57fe66d30369f12aa5316d *inst/doc/K-means_clustering_using_the_MUS_algorithm.html
-70af9646e377b07ed3eefeb492cb2e85 *inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.R
-2a78ea777ce43c0ca31a918e82ac7799 *inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.Rmd
-6596a8db75a6d8f69a90bcdf71a054b4 *inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.html
-cfdf608ee093ff41f61b6ba919ad2598 *man/MUS.Rd
+83e37e5245796587040cd7fbd6a66a90 *inst/doc/K-means_clustering_using_the_MUS_algorithm.R
+3ff415f107be9ed39ef989e2680befdf *inst/doc/K-means_clustering_using_the_MUS_algorithm.Rmd
+41dd29112371ace304d7a3745aac47e9 *inst/doc/K-means_clustering_using_the_MUS_algorithm.html
+e5aaf256b4eb70e3a1995ec90c8cb9be *inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.R
+2287794ea6095c7226a72baa3a0ff00d *inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.Rmd
+1474980080f02950b82b8b0cdae7a62d *inst/doc/Relabelling_in_Bayesian_mixtures_by_pivotal_units.html
+14b018d2b8d5b3ff6060ce2dc9be103a *man/MUS.Rd
 83b55b9e457e02bcfb781b0781f06bf2 *man/figures/README-kmeans_plots-1.png
 387d2506d151432d2ab11212700884fa *man/figures/README-musk-1.png
-a56838fd984b431c97b6b6705da9e62a *man/figures/README-plot-1.png
-740c6da7197b90caf69ca79cf89be87e *man/figures/README-plot-2.png
-ffabdc20678eb778c1a4689d1655a373 *man/piv_KMeans.Rd
-e239df65885ed2aa99fbf4ee3233c832 *man/piv_MCMC.Rd
-3ceca1e0f6c9e41a50ec32e600ab480a *man/piv_plot.Rd
-0e03c4296229bcb8c399c82a0557a684 *man/piv_rel.Rd
-3fac2abf6389c4692d6f8ab060c63280 *man/piv_sel.Rd
-92048d5feb4ee68f4c640e91a21b8d56 *man/piv_sim.Rd
+9bb0dfd1d8cdbfa77d0772d3c20c3de9 *man/figures/README-plot-1.png
+3d48ce33fa5475a43821cfcc735faba4 *man/figures/README-plot-2.png
+0d02a9db83f0edc9cf8d03726fe5697e *man/piv_KMeans.Rd
+3fd1b7bef45588816d749483b83dcd8d *man/piv_MCMC.Rd
+280286df4cd9476e674cc91530a7bfdf *man/piv_plot.Rd
+a3c65e21d5b6ceb0ad32842638343f47 *man/piv_rel.Rd
+63c33936022c37de6581db9f5a410ec3 *man/piv_sel.Rd
+60cc646bc8387133c832cca8488694ca *man/piv_sim.Rd
 d565fe1d140bd6770f832d28a6606458 *tests/testthat/test-bayesMCMC.R
 1cd9a2b29c1aa0cc8934f47a77800059 *tests/testthat/test-bayesMCMCbiv.R
 c410e73d8c2d40bdb9c3fe39c6c184fe *tests/testthat/test-mus.R
 e2d84ff6c6e19838a8101d236bcd74bb *tests/testthat/testthat.R
-8cb889dcf75ebac54b2579eb36324c03 *vignettes/K-means_clustering_using_the_MUS_algorithm.Rmd
-2a78ea777ce43c0ca31a918e82ac7799 *vignettes/Relabelling_in_Bayesian_mixtures_by_pivotal_units.Rmd
-c40ea5486f5ac2d0c57b4159691465cc *vignettes/ref.bib
+3ff415f107be9ed39ef989e2680befdf *vignettes/K-means_clustering_using_the_MUS_algorithm.Rmd
+2287794ea6095c7226a72baa3a0ff00d *vignettes/Relabelling_in_Bayesian_mixtures_by_pivotal_units.Rmd
+4ba2fe1c5cb39e918396e888bd206053 *vignettes/ref.bib

NAMESPACE

@@ -6,19 +6,62 @@ export(piv_plot)
 export(piv_sim)
 export(MUS)
 export(piv_KMeans)
-import(runjags)
 import(rjags)
 import(bayesmix)
 import(mvtnorm)
+#import(rstan)
+importFrom(rstan,
+           #rstan-package,
+           #as.array,
+           As.mcmc.list,
+           check_hmc_diagnostics ,
+           #Diagnostic plots ,
+           expose_stan_functions ,
+           extract ,
+           extract_sparse_parts ,
+           #log_prob-methods ,
+           #loo.stanfit ,
+           lookup ,
+           makeconf_path ,
+           monitor ,
+           optimizing ,
+           #pairs.stanfit,
+           #print ,
+           read_rdump,
+           read_stan_csv,
+           #rstan-plotting-functions,
+           rstan.package.skeleton ,
+           rstan_gg_options ,
+           rstan_options ,
+           sampling ,
+           set_cppo ,
+           sflist2stanfit ,
+           stan,
+           stanc ,
+           #stanfit-class ,
+           #stanmodel-class ,
+           #stan_demo ,
+           stan_model,
+           stan_rdump ,
+           stan_version ,
+           #summary-methods ,
+           traceplot ,
+           vb
+           )
+importFrom(runjags, extract.runjags)
+importFrom(runjags, run.jags)
+importFrom(runjags, dump.format)
+importFrom(runjags, add.summary)
+importFrom(corpcor, is.positive.definite)
 importFrom(MASS, mvrnorm)
 importFrom(mclust, adjustedRandIndex)
 importFrom(RcmdrMisc, KMeans)
 importFrom(cluster, pam, diana)
 importFrom("grDevices", "trans3d")
 importFrom("graphics", "axis", "barplot", "hist", "matplot", "par",
-             "persp", "plot", "points")
+             "persp", "plot", "points", "lines")
 importFrom("stats", "as.dist", "cutree", "dist", "hclust", "kmeans",
-             "median", "rnorm")
+             "median", "rnorm", "density")
 importFrom("utils", "combn")
 
 

NEWS.md

@@ -1,3 +1,12 @@
+# pivmet 0.2.0
+
+* rstan now incorporated to fit mixtures
+* piv_plot improved
+* Fix the case k=2 with piv_KMeans
+* piv_KMeans faster
+* Fix some bugs of the MUS algorithm
+* Efficient mixtures with rstan
+
 # pivmet 0.1.1
 
 * Fix duplicate entries of the vignette source