tseries class

R/analysis_online.R

@@ -120,7 +120,7 @@ analysis_online <- function(L, Time, t1, t2, beta, kappa, mul,
   }
 
   # store analysis results in practical R format, replacing entries as new data is added
-  resultsfile <- "omeas.summary.RData"
+  resultsfile <- "omeas.summary.Rdata"
 
   resultsum <- list()
   if(file.exists(resultsfile)){
@@ -227,8 +227,8 @@ analysis_online <- function(L, Time, t1, t2, beta, kappa, mul,
       if(trajlabel){
         filelabel <- sprintf("%s_traj%06d-%06d",filelabel,min(omeas.cnums),max(omeas.cnums))
       }
-      message("Writing online measurements RData to ", sprintf("onlineout.%s.RData",filelabel), "\n")
-      save(onlineout,file=sprintf("onlineout.%s.RData",filelabel))
+      message("Writing online measurements Rdata to ", sprintf("onlineout.%s.Rdata",filelabel), "\n")
+      save(onlineout,file=sprintf("onlineout.%s.Rdata",filelabel))
 
       plotcounter <- plotcounter+1
       dpaopp_filename <- sprintf("%02d_dpaopp_%s",plotcounter,filelabel)

R/bootstrap.nlsfit.R

@@ -1278,20 +1278,6 @@ plot.bootstrapfit <- function(x, ..., col.line="black", col.band="gray", opacity
   lines(x=X, y=Y, col=col.line, lty=lty, lwd=lwd)
 }
 
-#' residual_plot
-#'
-#' generic residual_plot method
-#'
-#' @param x the object to plot
-#' @param ... additional parameters to be passed on to specialised functions
-#' 
-#' @return
-#' No return value.
-#' 
-#' @export
-residual_plot <- function (x, ...) {
-  UseMethod("residual_plot", x)
-}
 
 #' @export
 residual_plot.bootstrapfit <- function (x, ..., error_fn = x$error.function, operation = `/`) {

R/cf.R

@@ -419,7 +419,7 @@ is_empty.cf <- function (.cf) {
 #'         with elements `boot`, `boot.R`, `boot.l`, `sim`, `endcorr`,
 #'         `resampling_method`, `boot_dim`, `icf` and, optionally
 #'         `iboot_dim` (if both `cf1` and `cf2` contain imaginary parts).
-resampling_is_compatible <- function(cf1, cf2){
+resampling_is_compatible.cf <- function(cf1, cf2){
 
   res <- list()
   res$boot <- ( inherits(cf1, 'cf_boot') & inherits(cf2, 'cf_boot') )
@@ -453,7 +453,7 @@ resampling_is_compatible <- function(cf1, cf2){
 #'         with elements `boot`, `boot.R`, `boot.l`, `sim`, `endcorr`,
 #'         `resampling_method`, `boot_nrow`, `icf` and, optionally
 #'         `iboot_nrow` (if both `cf1` and `cf2` contain imaginary parts).
-resampling_is_concatenable <- function(cf1, cf2){
+resampling_is_concatenable.cf <- function(cf1, cf2){
   res <- list()
   res$boot <- ( inherits(cf1, 'cf_boot') & inherits(cf2, 'cf_boot') )
   res$seed <- (cf1$seed == cf2$seed)

R/generics.R

@@ -0,0 +1,114 @@
+#' residual_plot
+#'
+#' generic residual_plot method
+#'
+#' @param x the object to plot
+#' @param ... additional parameters to be passed on to specialised functions
+#' 
+#' @return
+#' No return value.
+#' 
+#' @export
+residual_plot <- function (x, ...) {
+  UseMethod("residual_plot", x)
+}
+
+#' generic function to extract a fitted mass
+#'
+#' @description
+#' One of the main analysis tasks in \link{hadron} is the estimation
+#'   of energy levels or masses from correlation functions. The
+#'   corresponding analysis functions return objects, typically lists,
+#'   containing the masses or energy levels. `extract_mass` is a
+#'   generic function to extrac such fitted mass values.
+#' 
+#' @param object Object to extract the mass from.
+#'
+#' @return Numeric. The mass value.
+#'
+#' @export
+extract_mass <- function (object) {
+  UseMethod('extract_mass')
+}
+
+#' generic function to check if resampling samples are compatible
+#'
+#' @description
+#' When binary operations are performed on resampled data, it is
+#' necessary to check if the samples are compatible, at the very
+#' least they must have the same dimensions.
+#' 
+#' @details
+#' Note that since R's double dispatch doesn't really work with S3
+#' classes, the class of \code{x} decides which method is called.
+#' 
+#' @param x lhs object
+#' @param y rhs object
+#'
+#' @return 
+#' list of booleans which correspond to the results of checks
+#' for equality of different properties of the resampling samples
+#'
+#' @export
+resampling_is_compatible <- function(x,y){
+  UseMethod('resampling_is_compatible', x)
+}
+
+#' generic function to check if resampling samples are concatenable
+#'
+#' @description
+#' When we want to combine resampled data along an axis orthogonal
+#' to the axis of samples (for example, if we want to turn two
+#' vectors with 'boot.R' samples into a matrix with 2 columns),
+#' then we need to check if the number of samples for both
+#' data are the same.
+#' 
+#' @details
+#' Note that since R's double dispatch doesn't really work with S3
+#' classes, the class of \code{x} decides which method is called.
+#' 
+#' @param x lhs object
+#' @param y rhs object
+#'
+#' @return
+#' list of booleans which correspond to the results of checks
+#' for equality of different properties of the resampling samples
+#'
+#' @export
+resampling_is_concatenable <- function(x,y){
+  UseMethod('resampling_is_concatenable', x)
+}
+
+#' generic function to multiply two objects with each other
+#'
+#' @details
+#' Note that since R's double dispatch doesn't really work with S3
+#' classes, the class of \code{x} decides which method is called.
+#'
+#' @description
+#' 
+#' 
+#' @export
+mul <- function(x, y, ...){
+  UseMethod('mul', x)
+}
+
+#' generic function to add two objects to each other
+#'
+#' This function provides 
+#'
+#' @export
+add <- function(x, y, ...){
+  UseMethod('add', x)
+}
+
+#' @export
+subtract <- function(x, y, ...){
+  UseMethod('subtract', x)
+}
+
+#' generic function to divide objects by each other
+#' @export
+div <- function(x, y, ...){
+  UseMethod('div', x)
+}

R/removeTemporal.cf.R

@@ -291,24 +291,6 @@ dispersion_relation <- function (energy, momentum_d, extent_space, plus = TRUE,
   return (energy_out)
 }
 
-#' generic function to extract a fitted mass
-#'
-#' @description
-#' One of the main analysis tasks in \link{hadron} is the estimation
-#'   of energy levels or masses from correlation functions. The
-#'   corresponding analysis functions return objects, typically lists,
-#'   containing the masses or energy levels. `extract_mass` is a
-#'   generic function to extrac such fitted mass values.
-#' 
-#' @param object Object to extract the mass from.
-#'
-#' @return Numeric. The mass value.
-#'
-#' @export
-extract_mass <- function (object) {
-  UseMethod('extract_mass')
-}
-
 #' specialisation of \link{extract_mass} to objects of type
 #' `effectivemassfit`
 #'