Merge pull request #260 from TahminaMojumder/functionCollectionClass

Function collection class

Author: florianhartig

BayesianTools/R/blockUpdate.R

@@ -1,3 +1,4 @@
+
 #' Determine the groups of correlated parameters
 #' @author Stefan Paul
 #' @param chain MCMC chain including only the parameters (not logP, ll, logP)

BayesianTools/R/classBayesianOutput.R

@@ -1,5 +1,6 @@
 # NOTE: The functions in this class are just templates that are to be implemented for all subclasses of BayesianOutput. They are not functional. 
 
+
 #' Extracts the sample from a bayesianOutput
 #' @author Florian Hartig
 #' @param sampler an object of class mcmcSampler, mcmcSamplerList, smcSampler, smcSamplerList, mcmc, mcmc.list, double, numeric

BayesianTools/R/classLikelihood.R

@@ -1,3 +1,4 @@
+
 #' Creates a standardized likelihood class#'
 #' @author Florian Hartig
 #' @param likelihood log likelihood density
@@ -106,6 +107,7 @@ createLikelihood <- function(likelihood, names = NULL, parallel = F, catchDuplic
 
 #library(mvtnorm)
 #library(sparseMVN)
+
 #' Normal / Gaussian Likelihood function
 #' @author Florian Hartig
 #' @param predicted vector of predicted values
@@ -136,9 +138,9 @@ likelihoodAR1 <- function(predicted, observed, sd, a){
   n = length(observed)
 
   res = predicted - observed
-  
+
   # this calculates the unconditional LL for this data, see e.g. http://stat.unicas.it/downloadStatUnicas/seminari/2008/Julliard0708_1.pdf
-  
+
   ll =  0.5 * (  - n * log(2*pi)
                  - n * log(sd^2) 
                  + log( 1- a^2 )

BayesianTools/R/classMcmcSamplerList.R

@@ -12,7 +12,6 @@ createMcmcSamplerList <- function(mcmcList){
   return(mcmcList)
 }
 
-
 #' @author Stefan Paul
 #' @method summary mcmcSamplerList
 #' @export

BayesianTools/R/classPrior.R

@@ -261,7 +261,6 @@ createPriorDensity <- function(sampler, method = "multivariate", eps = 1e-10, lo
 
 #' @author Maximilian Pichler
 #' @export
-
 print.prior <- function(x, ...){
   cat('Prior: \n\n')
 

BayesianTools/R/classSMCSamplerList.R

@@ -1,3 +1,4 @@
+
 #' Convenience function to create an object of class SMCSamplerList from a list of mcmc samplers
 #' @author Florian Hartig
 #' @param ... a list of MCMC samplers
@@ -35,7 +36,6 @@ plot.smcSamplerList <- function(x, ...){
   marginalPlot(x, ...)
 }
 
-
 #' @export
 getSample.smcSamplerList <- function(sampler, parametersOnly = T, coda = F, start = 1, end = NULL, thin = 1,
                                      numSamples = NULL, whichParameters = NULL, reportDiagnostics = FALSE, ...){

BayesianTools/R/codaFunctions.R

@@ -104,5 +104,4 @@ convertCoda <- function(sampler, names = NULL, info = NULL, likelihood = NULL){
   }else stop("sampler must be of class 'coda::mcmc' or 'coda::mcmc.list'")
   }
   return(out)
-}
-
+}