Remove old code

3 files changed, 0 insertions, 232 deletions

diff --git a/R/datacheck.R b/R/datacheck.R
deleted file mode 100644
index 7c40473..0000000
--- a/R/datacheck.R
+++ /dev/null
@@ -1,36 +0,0 @@
-
-data.check <- function(x,name,verbose=TRUE){
-  
-  test = FALSE
-  
-  if(is.data.frame(x)){
-    if(!is.null(dim(x))){
-      if(verbose){cat('\nConverting data frame \'',name,'\' to matrix.\n',sep="")}
-      x = as.matrix(x)
-    } else {
-      if(verbose){cat('\nConverting data frame',name,'to vector.\n')}
-      x = as.vector(x)}
-  }
-  
-  
-  if (is.numeric(x)&&is.matrix(x)){
-    #if(1%in%dim(x)){
-    #  if(verbose){cat('\nConverting 1-column matrix \'',name,'\' to vector\n',sep="")}
-    #  x = as.vector(x)
-    #}
-    test = TRUE
-  }
-  
-  if(is.numeric(x)&&is.array(x)&&!test){
-    test = TRUE
-  }
-  
-  if (is.numeric(x)&&is.vector(x)&&!test){
-    test = TRUE
-  }
-  
-  if(test){
-    return(x)
-  } else{return('error')}
-  
-}
diff --git a/R/geninits.R b/R/geninits.R
deleted file mode 100644
index e62ba0f..0000000
--- a/R/geninits.R
+++ /dev/null
@@ -1,86 +0,0 @@
-
-gen.inits <- function(inits,n.chains,seed,parallel){
-  
-  if(!is.null(seed)){
-    warning("The 'seed' argument will be deprecated in the next version. You can set it yourself with set.seed() instead.") 
-    #Save old seed if it exists
-    if(exists('.Random.seed')){
-      old.seed <- .Random.seed
-    }   
-    #Generate seed for each chain
-    set.seed(seed)
-
-  }
-
-  #Error check and run init function if necessary
-  if(is.list(inits)){
-    if(length(inits)!=n.chains){stop('Length of initial values list != number of chains')}
-    init.values <- inits
-  } else if(is.function(inits)){
-    init.values <- list()
-    for (i in 1:n.chains){
-      init.values[[i]] <- inits()
-    }
-  } else if(is.null(inits)){
-    init.values <- NULL
-    
-  } else {stop('Invalid initial values. Must be a function or a list with length=n.chains')}
-  
-  #Add random seed info if specified
-  if(!is.null(seed)){
-    
-    init.rand <- floor(runif(n.chains,1,100000))
-    
-    #Restore old seed if it exists
-    if(exists('old.seed')){
-      assign(".Random.seed", old.seed, pos=1)
-    }
-    
-    #Add random seeds to inits
-    if(is.null(inits)){
-      init.values <- vector("list",length=n.chains)
-      for(i in 1:n.chains){
-        init.values[[i]]$.RNG.name="base::Mersenne-Twister"
-        init.values[[i]]$.RNG.seed=init.rand[i]
-      }
-      
-    } else if(is.list(init.values)){
-        for(i in 1:n.chains){
-          init.values[[i]]$.RNG.name="base::Mersenne-Twister"
-          init.values[[i]]$.RNG.seed=init.rand[i]
-        }
-      
-    } else if (is.function(inits)){
-        for (i in 1:n.chains){
-          init.values[[i]]$.RNG.name="base::Mersenne-Twister"
-          init.values[[i]]$.RNG.seed=init.rand[i]
-        }
-      
-    } 
- 
-    
-  #If seed is not set
-  } else {
-    
-    other.RNG <- all(c(".RNG.name",".RNG.seed")%in%names(init.values[[1]]))
-    
-    needs.RNG <- is.null(init.values)|!other.RNG
-    
-    #If parallel and no custom RNG has been set, add one. Otherwise all chains will start with same seed.
-    # if(needs.RNG&parallel){
-    if(needs.RNG){
-      
-      init.rand <- floor(runif(n.chains,1,100000))
-      
-      if(is.null(init.values)){init.values <- vector("list",length=n.chains)}
-
-      for(i in 1:n.chains){
-        init.values[[i]]$.RNG.name="base::Mersenne-Twister"
-        init.values[[i]]$.RNG.seed=init.rand[i]
-      }
-      
-    }
-  }
-
-  return(init.values) 
-}
diff --git a/R/processinput.R b/R/processinput.R
deleted file mode 100644
index c208b07..0000000
--- a/R/processinput.R
+++ /dev/null
@@ -1,110 +0,0 @@
-
-process.input = function(x,y,inits,n.chains,n.iter,n.burnin,n.thin,n.cores,DIC=FALSE,autojags=FALSE,max.iter=NULL,
-                         verbose=TRUE,parallel=FALSE,seed=NULL){
-  if(verbose){cat('\nProcessing function input.......','\n')}
-
-  #Quality control
-  if(n.iter<=n.burnin){
-    stop('Number of iterations must be larger than burn-in.\n')
-  }
-
-  if(parallel){
-    #Set number of clusters
-    p <- detectCores()
-    if(is.null(n.cores)){
-      if(is.na(p)){
-        p <- n.chains
-        if(verbose){
-          options(warn=1)
-          warning('Could not detect number of cores on the machine. Defaulting to cores used = number of chains.')
-          options(warn=0,error=NULL)
-          }
-      }
-      n.cores <- min(p,n.chains)
-    } else {
-      if(n.cores>p){
-        if(verbose){
-          options(warn=1)
-          warning(paste('You have specified more cores (',n.cores,') than the available number of cores on this machine (',p,').\nReducing n.cores to max of ',p,'.',sep=""))
-          options(warn=0,error=NULL)
-          }
-        n.cores <- p
-      }
-    }
-  }
-
-  if(autojags){
-    if(n.chains<2){stop('Number of chains must be >1 to calculate Rhat.')}
-    if(max.iter<n.burnin&verbose){
-      options(warn=1)
-      warning('Maximum iterations includes burn-in and should be larger than burn-in.')
-      options(warn=0,error=NULL)
-    }
-  }
-
-  if(n.thin>1&&(n.iter-n.burnin)<10&&verbose){
-    options(warn=1)
-    warning('The number of iterations is very low; jagsUI may crash. Recommend reducing n.thin to 1 and/or increasing n.iter.')
-    options(warn=0,error=NULL)
-  }
-
-  final.chain.length <- (n.iter - n.burnin) / n.thin
-  even.length <- floor(final.chain.length) == final.chain.length
-  if(!even.length&verbose){
-    options(warn=1)
-    warning('Number of iterations saved after thinning is not an integer; JAGS will round it up.')
-    options(warn=0,error=NULL)
-  }
-
-  #Check if supplied parameter vector is the right format
-  if((is.character(y)&is.vector(y))){
-      } else{stop('The parameters to save must be a vector containing only character strings.\n')}
-
-  #If DIC requested, add deviance to parameters (if not already there)
-  if(DIC&&(!'deviance'%in%y)){
-      params <- c(y,"deviance")
-  } else {params <- y}
-
-  #Check if supplied data object is the proper format
-  if(is.list(x)||(is.character(x)&is.vector(x))){
-  } else{stop('Input data must be a list of data objects OR a vector of data object names (as strings)\n')}
-
-  if(is.list(x)&&all(sapply(x,is.character))){
-    warning("Suppling a list of character strings to the data argument will be deprecated in the future")
-    x = unlist(x)
-  }
-
-  if((is.list(x)&&is.null(names(x)))||(is.list(x)&&any(names(x)==""))){
-    stop('At least one of the elements in your data list does not have a name\n')
-  }
-
-  #Convert a supplied vector of characters to a list of data objects
-  if((is.character(x)&is.vector(x))){
-    warning("Suppling a character vector to the data argument will be deprecated in the future")
-    temp = lapply(x,get,envir = parent.frame(2))
-    names(temp) = x
-    x = temp
-  }
-
-  #Check each component of data object for issues and fix if possible
-  for (i in 1:length(x)){
-
-    if(is.factor(x[[i]])){
-
-      stop('\nElement \'',names(x[i]) ,'\' in the data list is a factor.','\n','Convert it to a series of dummy/indicator variables or a numeric vector as appropriate.\n')
-
-    }
-
-    process <- data.check(x[[i]],name = names(x[i]),verbose=verbose)
-    if(!is.na(process[1])&&process[1]=="error"){stop('\nElement \'',names(x[i]) ,'\' in the data list cannot be coerced to one of the','\n','allowed formats (numeric scalar, vector, matrix, or array)\n')
-    } else{x[[i]] <- process}
-
-  }
-
-  #Get initial values
-  init.vals <- gen.inits(inits,n.chains,seed,parallel)
-
-  if(verbose){cat('\nDone.','\n','\n')}
-  return(list(data=x,params=params,inits=init.vals,n.cores=n.cores))
-
-}