version 0.4-4

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: coalescentMCMC
-Version: 0.4-1
-Date: 2015-03-03
+Version: 0.4-4
+Date: 2022-04-22
 Title: MCMC Algorithms for the Coalescent
 Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr"))
 Depends: ape, coda, lattice
-Imports: Matrix, phangorn, stats
+Imports: Matrix, phangorn, splines, stats, utils
 ZipData: no
-Description: Flexible framework for coalescent analyses in R. It includes a main function running the  MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters.
+Description: Flexible framework for coalescent analyses in R. It includes a main function running the  MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.
 License: GPL (>= 2)
-Packaged: 2015-03-03 21:24:35 UTC; paradis
+NeedsCompilation: yes
+Packaged: 2022-04-22 08:56:29 UTC; paradis
 Author: Emmanuel Paradis [aut, cre, cph]
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
-NeedsCompilation: yes
 Repository: CRAN
-Date/Publication: 2015-03-03 22:37:48
+Date/Publication: 2022-04-22 09:30:05 UTC

MD5

@@ -1,26 +1,30 @@
 0632cc7589c46bbf4981f0a778f1ef2a *COPYING
-f51b06a8c6b3a34c0376f4f9fd109c8f *DESCRIPTION
-29206b62bdac65785dc20125ee11fde0 *NAMESPACE
-97c98369b47541d6ca43b5032ef7f899 *NEWS
-dc1c97bf85142d88fdb0f0639d70e0fb *R/coalescentMCMC.R
-5f2eb5752f0e5d2e8109756e9489eb85 *R/dcoal.R
-99f16e5f12e18e822d8bd7e8a591e53b *R/sim.coalescent.R
-bdfa63a5f7f7d1413274673bbcee1d82 *R/treeOperators.R
-d85e17220990885e7d898858088064ea *R/zzz.R
-a48d066c8a0eb34450760b24e22ee9f4 *build/vignette.rds
-dfa3ae7f0e0bc0918691ff5894094c03 *inst/doc/CoalescentModels.R
-3c1e57130cbd9694fa95ddcefd4846be *inst/doc/CoalescentModels.Rnw
-ac0aeaf5e66c22308381b874e194bed0 *inst/doc/CoalescentModels.pdf
-83b0eb578a55e346730ddbf10b188d76 *inst/doc/Running_coalescentMCMC.R
-79c0aea8246510ddf02bacfb7603edf4 *inst/doc/Running_coalescentMCMC.Rnw
-5aff5a815e22e71643954e033f8d7f9f *inst/doc/Running_coalescentMCMC.pdf
-a1da10023e73129ff1531cb9e6ef546f *man/coalesceMCMC.Rd
-9aa980aea36886b18ac6a09b823765da *man/coalescentMCMC-internal.Rd
-f768c542f46f407ec6cce19410f749cc *man/dcoal.Rd
-9fa17366f9188c12d89064f7372af119 *man/sim.coalescent.Rd
-90b1945d199985a0b7162999b6f140d0 *man/treeOperators.Rd
-2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
-c3e22b2a119684f9a878926188ddd39e *src/coalescentMCMC.c
-3c1e57130cbd9694fa95ddcefd4846be *vignettes/CoalescentModels.Rnw
-79c0aea8246510ddf02bacfb7603edf4 *vignettes/Running_coalescentMCMC.Rnw
-926f24b46ead272ee5d5f742d386b807 *vignettes/coalescentMCMC.bib
+e95071068f5faa753bfd8c162eef5d47 *DESCRIPTION
+bf2615cfe3c15629cd26bf35f851930c *NAMESPACE
+c22c5e49b8a8463b8ed8ef272e0b17e9 *NEWS
+cbce23f7277606fbb1055d3832cfc46e *R/coalescentMCMC.R
+e53a99e1c1aa6cd92d10c0ec492bfd9e *R/dcoal.R
+5ddd94fae2cecbb404994f823628bf36 *R/plotTHETA.R
+edd9205b9728def46aea36a94d141457 *R/sim.coalescent.R
+efec2bf345b536dd6b847bba0a7f90b5 *R/treeOperators.R
+b5fc59f9495eab37448da7273115c33c *R/zzz.R
+ebe75dd213a04844b80d0c7ed447cbf5 *build/vignette.rds
+98a85e3f6bf0b854ebb530c08c9b8f9a *inst/CITATION
+cf8ba3043d2f9ce1a3676d3f70f2908f *inst/doc/CoalescentModels.R
+76e719b8fc27af1740a5d1b7f9497d2b *inst/doc/CoalescentModels.Rnw
+7c506f58826d80a34599df34ea1c48ac *inst/doc/CoalescentModels.pdf
+546262c89a4ac13bb5f3ada87497db8e *inst/doc/Running_coalescentMCMC.R
+6cc0100dbd1adc13443c8e7aaae9656c *inst/doc/Running_coalescentMCMC.Rnw
+50daaffcfe3d99401cc4a9c175c164c8 *inst/doc/Running_coalescentMCMC.pdf
+fa8a8c6fe34880490cb99d280df1cbbd *man/coalesceMCMC.Rd
+b7c79ff61d42d1f56ee4b3935a39921f *man/dcoal.Rd
+a300f82b4c8956adc82616e612877132 *man/getMCMCtrees.Rd
+c3d261dd707fe65345f8f2ab78fd7e01 *man/plotTHETA.Rd
+4718050893c9844f1845a5d5eacdfc21 *man/proba.coalescent.Rd
+e9ddc99a52cd2bb3eaa7209784adff0b *man/sim.coalescent.Rd
+325ec7d81af158537e4b2c59e55f2fac *man/subset.coalescentMCMC.Rd
+595078471db03b2deffc9ad54ffa8e70 *man/treeOperators.Rd
+ba3506a7a5e0e05ceb315c954cbb12dc *src/coalescentMCMC.c
+76e719b8fc27af1740a5d1b7f9497d2b *vignettes/CoalescentModels.Rnw
+6cc0100dbd1adc13443c8e7aaae9656c *vignettes/Running_coalescentMCMC.Rnw
+b4ff74e28ec9d668a434c7740a5956cf *vignettes/coalescentMCMC.bib

NAMESPACE

@@ -2,14 +2,24 @@ useDynLib(coalescentMCMC, .registration = TRUE)
 
 export(.coalescentMCMCenv, cleanMCMCtrees, coalescentMCMC, dcoal,
        dcoal.linear, dcoal.step, dcoal.time, dcoal.time2,
-       EdgeLengthJittering, getLastTree, getMCMCstats, getMCMCtrees,
-       NeighborhoodRearrangement, saveMCMCtrees, sim.coalescent,
-       TipInterchange)
+       getLastTree, getMCMCstats, getMCMCtrees,
+       NeighborhoodRearrangement, plotTHETA,
+       proba.coalescent, saveMCMCtrees, sim.coalescent)
 
 importFrom(ape, as.phylo, branching.times, dist.dna, Ntip,
            reorder.phylo, write.nexus, write.tree)
 importFrom(coda, mcmc)
-importFrom(phangorn, phyDat, pml)
+importFrom(graphics, axis, lines, mtext, plot, points, segments)
+importFrom(grDevices, col2rgb, rgb)
+importFrom(phangorn, phyDat, pml, upgma)
 importFrom(Matrix, Matrix)
-importFrom(stats, hclust, rbinom, reorder, runif)
+importFrom(splines, bs)
+importFrom(stats, BIC, hclust, nlminb, pchisq, rbinom, reorder, runif)
 importFrom(lattice, histogram)
+importFrom(utils, packageVersion)
+
+S3method(AIC, coalescentMCMC)
+S3method(anova, coalescentMCMC)
+S3method(BIC, coalescentMCMC)
+S3method(logLik, coalescentMCMC)
+S3method(subset, coalescentMCMC)

NEWS

@@ -1,9 +1,49 @@
+		CHANGES IN coalescentMCMC VERSION 0.5
+
+
+NEW FEATURES
+
+    o coalescentMCMC() now returns an object of class
+      c("coalescentMCMC", "coda").
+
+    o Five more "tree moves" are now available during the MCMCs. These
+      moves are from Drummond et al. 2002 (Genetics, 161:1307).
+
+    o There are methods logLik, anova, AIC, and BIC for the class
+      "coalescentMCMC".
+
+    o The new function plotTHETA plots the variation in THETA
+      predicted from an output of coalescentMCMC() and a set of trees.
+
+    o The new function proba.coalescent calculates probabilities of
+      coalescence using exact or approximate formula.
+
+    o The new function subset.coalescentMCMC makes possible to extract
+      flexibly a subset from an output of coalescentMCMC().
+
+    o coalescentMCMC() has a new model "bsplines".
+
+
+BUG FIXES
+
+    o A bug was fixed in the calculations of coalescent pdfs.
+
+    o Some bugs were fixed in coalescentMCMC(). The code is also
+      faster.
+
+
+OTHER CHANGES
+
+    o Updated NAMESPACE file for r-devel.
+
+
+
 		CHANGES IN coalescentMCMC VERSION 0.4-1
 
 
 NEW FEATURES
 
-    o The new function sim.coalescent() simulates and visualises
+    o The new function sim.coalescent simulates and visualises
       coalescent for pedagogic purposes.