version 2.2

DESCRIPTION

@@ -1,17 +1,18 @@
 Package: Bclim
 Type: Package
 Title: Bayesian Palaeoclimate Reconstruction from Pollen
-Version: 2.1
-Date: 2012-06-18
+Version: 2.2
+Date: 2013-01-23
 Author: Andrew Parnell, Thinh Doan and James Sweeney
 Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>
 Depends: mclust, hdrcde, statmod, MASS
 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.
-License: GPL (> 2)
-Packaged: 2012-06-21 11:28:30 UTC; andrewparnell
+        state-space model. This latest version fixes a bug where
+        volatilities were estimated incorrectly
+License: GPL (>= 2)
+Packaged: 2013-01-23 13:15:04 UTC; aparnell
 Repository: CRAN
-Date/Publication: 2012-06-22 05:42:18
+Date/Publication: 2013-01-23 16:20:13

MD5

@@ -1,31 +1,31 @@
-80b2f4ee1626d401c712ddd63d3ccea0 *DESCRIPTION
-af121cad74c504d64bd80caf0a2640f8 *NAMESPACE
+3055d527f9894b4cb6ee8d6b238ac748 *DESCRIPTION
+8e419122bd6a5b07a3a495d573138afc *NAMESPACE
+5f2912b0a548a38cd6d4eb0cf7b7e477 *R/Bclim-internal.R
+c6f874826f8e6697c8eec0b90413f529 *R/Bclim.R
 f776eb835eb11d4c792b0cf2cca720e5 *R/BclimCompile.R
-a620ff083452b9c4b375ecc23fcbc3c4 *R/BclimInterp.R
+4cff32608adc1207131105a1982713e9 *R/BclimInterp.R
 af57a23af5cd03c0f897ade4349cb3d2 *R/BclimLayer.R
-761805ea8ab41e32ec315b2065eb6a55 *R/BclimMCMC.R
-645e6ad9edbe2262d5a66f6c631b8e42 *R/BclimMixPar.R
+041a88b7f1a4e3db237178fe3c5422f8 *R/BclimMCMC.R
+c382207be84fe453dc5d4b7c35c4da95 *R/BclimMixPar.R
 89588b14f7687294d938dd3f7ca1b1cc *R/BclimMixSer.R
 856245e1980b34b2eea6bb3f130c9c08 *R/BclimRun.R
-5a49d5a089a94c542e156c58340dd6c7 *R/IGb.R
-49e12baf19dd1ca736d363d561343e18 *R/IGp.R
-159639435b3bc30535e839516d5b7cf6 *R/IGrv.R
-ae7de8c8b413e9cd687dcacab7ec7a3a *R/NIGB.R
-c4c4b74e9f3177cf7ef6130e01636081 *R/NIGp3.R
+f48b41d0a322f1bfa36fac12444f3bd4 *R/NIGB.R
+3c8d4d5c7857fb8cf3a1eb8a841642f2 *R/NIGp3.R
 9b83e343f86b627f055a360f78511deb *R/plotBclim.R
 d385f12dbe1227314f75a2b58b53e2ea *R/plotBclimVol.R
-54dbbd2174637d2b96a74f65066706ea *R/zzz.R
-79d3bbeec2f031b8b540de2d8291df8f *man/Bclim-package.Rd
-1baa9cbbb86f16e4b508a30b5a6f2e85 *man/BclimCompile.Rd
-3604dcb5b47d278420a3357235e6797f *man/BclimInterp.Rd
+eba7fbd97a896a794b26ebcee5e784fc *man/Bclim-package.Rd
+3b3ae1db0dd7153c87186a432aeff7c6 *man/BclimCompile.Rd
+844027ba79272149b55c70e30dde004a *man/BclimInterp.Rd
 cb66a992d9bdf6fdd8f0c9449f573f4f *man/BclimLayer.Rd
-d8a8f65896e65e2fb267f8e42265de98 *man/BclimMCMC.Rd
-8e663516c0b187ae1ae3eeb99b45a8a6 *man/BclimMixPar.Rd
-e84429c8ecbf2f98bcdefe298eab802e *man/BclimMixSer.Rd
-3b2c60bb1b8212f936d4d8f9829ebfeb *man/BclimRun.Rd
-b0a7474ed56d099f97d9633de18b009b *man/plotBclim.Rd
-11f1d95937b7b6d8c1cf8d48f909fd28 *man/plotBclimVol.Rd
-27c1cba70042855c1032932a5c7f3626 *src/BclimMCMC3D.c
+fd2b950219625b2cc6fed00790569963 *man/BclimMCMC.Rd
+bc6b60f2b815ecf01afe6d3379879482 *man/BclimMixPar.Rd
+d3e0c28f0ba477c4b69f042d18564b1f *man/BclimMixSer.Rd
+d098a650d48d745dfcd4ef089baa1cb4 *man/BclimRun.Rd
+2a5fdad1ccd8655ef2a5a9457b876578 *man/NIGB.Rd
+78acf6ecd9f34501621bb24312632701 *man/NIGp3.Rd
+f46732a1c4585ce1457b92572090dde7 *man/plotBclim.Rd
+d869628c17b2764282187b609858549e *man/plotBclimVol.Rd
+5b72d41aaa4cd831235669faa9f3e617 *src/BclimMCMC3D.c
 efa94aa42c370a9851dca166219f9c0f *src/PalaeoRecon3D.c
-9594b50dc5caaf135522c553475a55a9 *src/use.c
+effde32cdc7ea252698c65b8e9b48b58 *src/use.c
 1c8929a0e47b44cb06b0586a95adbbac *src/use.h

NAMESPACE

@@ -1,3 +1,5 @@
 exportPattern("^[[:alpha:]]+")
 
 useDynLib(Bclim)
+
+export(Bclim, BclimLayer, BclimMixPar, BclimMixSer, BclimMCMC, BclimCompile, BclimInterp, plotBclim, plotBclimVol)

R/Bclim-internal.R

@@ -0,0 +1,134 @@
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+1243023464L, -1478943674L, 812944852L)
+.onAttach <-
+function(libname, pkgname) {
+    Bclimver <- read.dcf(file=system.file("DESCRIPTION", package=pkgname), 
+                      fields="Version")
+    packageStartupMessage(paste(pkgname, Bclimver))
+    packageStartupMessage("Welcome to Bclim. Type help(Bclim) to get started.")
+    packageStartupMessage("See http://mathsci.ucd.ie/~parnell_a/Bclim.html for updates, bugs and a tutorial.")
+}

R/Bclim.R

@@ -0,0 +1,65 @@
+Bclim <-
+function(pollen.loc,chron.loc,core.name="Core",time.grid=seq(0,14,length=100),rsfile,nchrons=10000,parallel=FALSE,save.as.you.go=TRUE) {
+
+  if(!file.exists(pollen.loc)) stop(cat("Pollen data not found. Check",pollen.loc))
+  if(!file.exists(chron.loc)) stop(cat("Chronology data not found. Check",chron.loc))
+
+  pollen.data <- as.matrix(read.table(pollen.loc,header=TRUE))
+  temp.chron <- read.table(chron.loc,nrows=5)
+
+  # Some error handling
+  if(ncol(pollen.data)!=28) stop("Number of pollen taxa should be 28")
+  if(nrow(pollen.data)!=ncol(temp.chron)) stop("Number of columns in chronology should be the same 
+                                               as the number of rows in the pollen data")
+
+  ### Run Stage 1 - calculate layer posteriors
+  cat("Stage 1 of 4: calculating layer posteriors...\n")
+  step1filename <- paste(gsub(" ","_",core.name),"_step1.RData",sep="")
+  if(!file.exists(step1filename)) {
+    step1 <- BclimLayer(pollen.loc,rsfile)
+    if(save.as.you.go) save(step1,file=paste(gsub(" ","_",core.name),"_step1.RData",sep=""))
+  } else {
+    load(step1filename) 
+  }
+
+  ### Run Stage 2
+  cat("Stage 2 of 4: approximating as mixtures of Gaussians...\n")
+  step2filename <- paste(gsub(" ","_",core.name),"_step2.RData",sep="")
+  if(!file.exists(step2filename)) {
+    if(parallel) {
+      step2 <- BclimMixPar(step1)
+    } else {
+      step2 <- BclimMixSer(step1)
+    }
+    if(save.as.you.go) save(step2,file=paste(gsub(" ","_",core.name),"_step2.RData",sep=""))
+  } else {
+    load(step2filename)
+  }
+
+  ### Run Stage 3
+  cat("Stage 3 of 4: estimating parameters...\n")
+  step2$Chronsfile <- chron.loc
+  step3filename <- paste(gsub(" ","_",core.name),"_step3.RData",sep="")
+  if(!file.exists(step3filename)) {
+    step3 <- BclimMCMC(step2,chron.loc,nchron=nchrons)
+    if(save.as.you.go) save(step3,file=paste(gsub(" ","_",core.name),"_step3.RData",sep=""))
+  } else {
+    load(step3filename)
+  }
+
+  ### Run Stage 4
+  cat("Stage 4 of 4: interpolating onto grid...\n")
+  step4filename <- paste(gsub(" ","_",core.name),"_step4.RData",sep="")
+  if(!file.exists(step4filename)) {
+    step4 <- BclimInterp(step2,step3,time.grid)
+    if(save.as.you.go) save(step4,file=paste(gsub(" ","_",core.name),"_step4.RData",sep=""))
+  } else {
+    load(step4filename) 
+  }
+
+  # Output results
+  cat("Compiling results...\n")
+  results <- BclimCompile(step1,step2,step3,step4,core.name=core.name)
+  cat("Done!\n")
+  return(results)
+}