version 3.1.0

DESCRIPTION

@@ -1,16 +1,18 @@
 Package: Bclim
 Type: Package
-Title: Bayesian Palaeoclimate Reconstruction from Pollen
-Version: 2.3.1
-Date: 2014-04-15
-Author: Andrew Parnell, Thinh Doan and James Sweeney
+Title: Bayesian Palaeoclimate Reconstruction from Pollen Data
+Version: 3.1.0
+Date: 2016-06-11
+Author: Andrew Parnell
 Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>
-Depends: MASS, mclust
-Imports: hdrcde, statmod
-Suggests: Bchron, doMC, foreach
-Description: This package takes pollen/time data from lake cores and produces a Bayesian posterior distribution of palaeoclimate from that location after fitting a non-linear non-Gaussian state-space model.
+Description: Takes pollen and chronology data from lake cores and produces a Bayesian posterior distribution of palaeoclimate from that location after fitting a non-linear non-Gaussian state-space model. For more details see the paper Parnell, A. C., et al. (2015), Bayesian inference for palaeoclimate with time uncertainty and stochastic volatility. Journal of the Royal Statistical Society: Series C (Applied Statistics), 64: 115–138. 
+Imports: MASS, mclust, graphics, statmod, ggplot2
+Suggests: Bchron, knitr
+Encoding: UTF-8
 License: GPL (>= 2)
-Packaged: 2014-04-17 14:26:45 UTC; aparnell
-NeedsCompilation: yes
+LazyData: TRUE
+VignetteBuilder: knitr
+NeedsCompilation: no
+Packaged: 2016-06-11 20:26:49 UTC; andrewparnell
 Repository: CRAN
-Date/Publication: 2014-04-18 08:39:17
+Date/Publication: 2016-06-12 09:40:19

MD5

@@ -1,27 +1,30 @@
-a8f48f85af68c7fb7e284f820a54aa36 *DESCRIPTION
-2f113365dfbb6c37cf8748a3a09bac07 *NAMESPACE
-c6f874826f8e6697c8eec0b90413f529 *R/Bclim.R
-276e9d9aea394b90e58fbfcf9f45253c *R/BclimCompile.R
-fa6543be87cf722c53fe6a046e918762 *R/BclimInterp.R
-0595934946efef63e52463392895e476 *R/BclimLayer.R
-5d5c2210cce82ea17fcc11839bbc97fa *R/BclimMCMC.R
-b5af690c5e7e0c3d19da9a480d23a767 *R/BclimMixPar.R
-58f1410cb5c2c35da61f24e2b5266f83 *R/BclimMixSer.R
-856245e1980b34b2eea6bb3f130c9c08 *R/BclimRun.R
-254beb9b64f7819c7ff3846767f8a44e *R/plotBclim.R
-9a1092b29526425879e14855de9144e6 *R/plotBclimVol.R
-90f8e07927a8651a6deeb9eb5a87fdea *R/zzz.R
-a68bbc80ffe7b1c1e5d50110ac6d6c06 *man/Bclim-package.Rd
-63baf8f9f1b0106d60434f345faaf428 *man/BclimCompile.Rd
-844027ba79272149b55c70e30dde004a *man/BclimInterp.Rd
-4132c98098e3d0e0749d6f09b99ba77e *man/BclimLayer.Rd
-80aea2ad9cdc6706ea63c9b56fae4463 *man/BclimMCMC.Rd
-bfdbdd437f2f9bf65b3021933d9bb81d *man/BclimMixPar.Rd
-afb588a381b69654837f58ecb4128afd *man/BclimMixSer.Rd
-2ab97fc9ac914c86d95970d3fd267141 *man/BclimRun.Rd
-9efb7750817a00efb8d54f706abb1ae7 *man/plotBclim.Rd
-466695715b643ea20742560c271a83d1 *man/plotBclimVol.Rd
-46000bef71469cd91818dbbd68818493 *src/BclimMCMC3D.c
-efa94aa42c370a9851dca166219f9c0f *src/PalaeoRecon3D.c
-384ae2930ede0489a28287fb2fa5eb59 *src/use.c
+2213e922dcfe670cc413fe5a7777433d *DESCRIPTION
+de5016cca295753521a1ad5c68a04f0b *NAMESPACE
+07b3f7ed8f0e03de857884ce0da8b137 *R/climate_histories.R
+903585fca998ece915c90892e98bdb35 *R/layer_clouds.R
+7e44dc0f4eaad314a60993662bfc66d0 *R/plot.climate_histories.R
+ce5a912bbc7aac7e7dbc94572e07169d *R/plot.layer_clouds.R
+a6613a21613d33dd0c9dbaa660f2ccf9 *R/summary.climate_histories.R
+2d41f0c1f4204f7eb4d73b03ca7ecf8b *build/vignette.rds
+4100dc26432058488906c65ee1ac5856 *inst/doc/Bclim.R
+afabf7aec18a6fd9f8e74c7aa216419a *inst/doc/Bclim.Rmd
+e045174248f10dfa2174e65eab4c6156 *inst/doc/Bclim.html
+4fca4f08d85d5bbbc6cf27eaa9847a93 *inst/extdata/Monticchio_chron.txt
+0376e9e2dd8743c18806720c07a0cc39 *inst/extdata/Monticchio_pollen.txt
+be693dcf6c89e9baeeb96ac84da66ef3 *inst/extdata/Roya.dat
+724408f688df578967f04f245a013a1c *inst/extdata/Roya_pollen.txt
+8db85f262f45280f8230f3cb31db050d *inst/extdata/Roya_pollen_depths.txt
+5c694eea84b758c680981e8d8fcaaa75 *man/Bclim-package.Rd
+3cb2153bee54384aee3cbf8401164255 *man/climate_histories.Rd
+d09dbd215938bdb91788514e06d0ad1c *man/layer_clouds.Rd
+d3c161a392168017fb3ac2626c204f71 *man/plot.climate_histories.Rd
+503eeb9dd862adc0a949fcdeeae43992 *man/plot.layer_clouds.Rd
+8d1351ceb59165e318cabcd16271374f *man/summary.climate_histories.Rd
+5a63c51d9dc943bbf737d5770b63b757 *src/BclimMCMC3D.c
+8e5637fe69d18d62e299de1b010c83ef *src/PalaeoRecon3D.c
+9424adb3f1dc7eaebc7dbc83266ba7a5 *src/use.c
 6dab0cf9547153c2ecf4bc9825dd9fca *src/use.h
+afabf7aec18a6fd9f8e74c7aa216419a *vignettes/Bclim.Rmd
+be693dcf6c89e9baeeb96ac84da66ef3 *vignettes/Roya.dat
+724408f688df578967f04f245a013a1c *vignettes/Roya_pollen.txt
+8db85f262f45280f8230f3cb31db050d *vignettes/Roya_pollen_depths.txt

NAMESPACE

@@ -2,7 +2,16 @@ exportPattern("^[[:alpha:]]+")
 
 useDynLib(Bclim)
 
-import(MASS)
-import(mclust)
-importFrom(statmod,rinvgauss)
-importFrom(hdrcde,hdr)
+importFrom("MASS","kde2d")
+importFrom("mclust","Mclust","mclustBIC")
+importFrom("statmod","rinvgauss")
+importFrom("graphics","filled.contour")
+importFrom("grDevices", "contourLines", "rgb")
+importFrom("graphics", "axis", "grid", "lines", "plot", "polygon")
+importFrom("stats", "median", "quantile", "rnorm", "runif", "var")
+importFrom("utils", "write.table")
+
+S3method(plot,climate_histories)
+S3method(plot,layer_clouds)
+S3method(summary,climate_histories)
+