R/input_DEPRECATED.R
In Don-Li/CAB: The Computational Analysis of Behaviour
# #### Simulation inputs ####
#
# #' \code{input} class
# #'
# #' When a simulation is run in the \code{CAB} package, the within-simulation information (i.e., the variables that are not pre-set before the simulation, e.g. the number of responses during an inter-reinforcement itnerval) are stored in an \code{input} object.
# #'
# #' The underlying implementation of the \code{input} class is that the \code{input} class has two slots. One slot is called \code{info}, which holds an environment. Each element in the environment is a list. For each list, one element of the list is a vector that stores the events that occurred (for example, a vector may store the response times) and the other element is a single numeric that counts the number of elements that stored in the corresponding vector. The second slot is called \code{names}, which is just for easy access of the variable names in the \code{input} object.
# #'
# #' Before using a \code{input} object to store data or count things in a simulation, set it up with the \code{setup.input_monitor} function.
# #'
# #' A \code{show} method for the \code{input} class has been defined for printing \code{input} objects (see below; \code{input.show()}). An associated function \code{remove.input.show()} has been defined for removing the \code{show} method.
# #'
# #' @slot info An \code{environment} that contains a list, which in turn contains a vector to store events that occur in the simulation, as well as a numeric to count the events. The vector that contains the data is called \code{data} and the numeric that stores the counts is \code{counts}.
# #' @slot names Stores the names of the variables held in the \code{info} slot.
# #'
# #' @section Make a new \code{input} object:{
# #' Before doing a simulation, a \code{input} object needs to be constructed to store the data that is generated (e.g. response times) and to count the instances of some particular event (e.g. number of responses).
# #'
# #' Note that when \code{input} object is first constructed, each of the variables in the \code{info} slot will be a vector of \code{NaN} of size 1.
# #'
# #' \subsection{Usage}{
# #' \code{make.input( var_names )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{var_names}}{A vector of character strings that give names for the events to be stored. See example.}
# #' }
# #' }
# #' \subsection{Value}{
# #' A \code{input} object is returned.
# #' }
# #' }
# #'
# #' @examples
# #' #### Create an "input" for storing the variables: "time_input", "resp_time", "rft_time", "rft_setup", and to count the events: "resp_counter", "rft_counter". ####
# #' var_names = c( "time_input", "vect", "resp_time", "rft_time", "rft_setup" )
# #' my_input = make.input( var_names )
# #' my_input
# #'
# #' #### Indexing on an "input" object ####
# #' # Extract the response times
# #' response_times = my_input[ v = "resp_time" ]
# #' # Remember that for a newly created "input" object, the variable contains a single \code{NaN} in the \code{data} vector and a zero in the \code{counts} vector.
# #'
# #' #### Set up an "input" object ####
# #' # Set the "input" to hold a maximum of 10 response times, 11 reinforcement times, and 20 "time_input". Note that the length for "rft_setup" is not specified, so it becomes the specified maximum (20).
# #' length_list = list( resp_time = 5, rft_time = 11, time_input = 20 )
# #' setup.input( my_input, length_list )
# #' my_input
# #'
# #' # Set up "input" to hold 50 elements for all variables
# #' setup.input( my_input, 50 )
# #' my_input
# #'
# #' # Set the first element of the "time_input" variable to 0, set the fifth element of the "time_input" variable to 1, and set the associated "counts" to 100.
# #' assign.input( my_input, v = "time_input", indices = c(1, 5), values = c(0, 1 ), counts = 100 )
# #'
# #' # Store a sequence of "1" in the "resp_time" vector. Also, note the value of the associated "counts"
# #' next.input( my_input, "resp_time", 1 )
# #' my_input
# #' next.input( my_input, "resp_time", 1 )
# #' my_input
# #' next.input( my_input, "resp_time", 1 )
# #' my_input
# #'
# #' #Set the "resp_time" values to be twice larger than the previously specified "resp_time_value"
# #' fx = function( x, y ) x * y
# #' transform.input( my_input, "resp_time", fx, y = 2 )
# #' my_input
# #' transform.input( my_input, "resp_time", fx, y = 2 )
# #' my_input
# #' # Set the "resp_time" values to be thrice larger
# #' transform.input( my_input, "resp_time", fx, y = 3 )
# #' my_input
# #'
# #' #Get the last element in an "input" variable data vector
# #' tail.input( my_input, "resp_time" )
# #'
# #' #Reset
# #' reset.input( my_input, "resp_time" )
# #' my_input
# #'
# #' @rdname class.input
# #' @export class.input
#
# class.input = setClass( "input", slots = list( info = "environment", names = "character" ) )
#
# #' @rdname class.input
# #' @export make.input
#
# make.input = function( var_names ){
# dummy_list = lapply( var_names, function(x) list( data = NaN, counts = 0 ) )
# names( dummy_list ) = var_names
# new( "input", info = list2env( dummy_list, parent = emptyenv() ), names = var_names )
# }
#
# #' @rdname class.input
# #' @section Indexing on an \code{input} object:{
# #' \subsection{Usage}{
# #' \code{"["( x, v )}
# #' or
# #' \code{input[v]}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{x}}{An \code{input} object.}
# #' \item{\code{v}}{A string specifting a variable in the \code{input} object.}
# #' \item{\code{input}}{An \code{input} object.}
# #' }
# #' }
# #' \subsection{Value}{
# #' Returns the vector in the \code{input} object that is specified by \code{v}. See example.
# #' }
# #' }
# #' @export index.input
#
# index.input = setMethod( "[", signature( x = "input" ),
# function( x, v ){
# x@info[[v]]
# }
# )
#
# #' @rdname class.input
# #' @format The \code{show} method for the \code{input} class prints the names of the variables in the \code{input} object as well as the events/counts that they store. Remove this \code{show} method by calling \code{remove.input.show().}
# #' @export input.show
#
# input.show = setMethod( "show", signature( object = "input" ),
# function( object ){
# variables = object@names
# cat( "Input object: \n" )
# lapply( variables, input.show_helper, object = object )
# }
# )
#
# input.show_helper = function( x, object ){
# cat( x, "\n" )
# print( object@info[[x]] )
# cat( "\n" )
# }
#
# # #' @rdname class.input
# # #' @export remove.input.show
# #
# # remove.input.show = function() removeMethod( "show", signature( object = "input" ) )
#
# #' @rdname class.input
# #' @aliases setup.input
# #' @section Set up a \code{input} object for a simulation:{
# #' \subsection{Usage}{
# #' \code{setup.input( input, lengths )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}}.
# #' \item{\code{lengths}}{Either a \code{list} or a single numeric, giving the length of the data storage vectors. See details.}
# #' }
# #' }
# #' \subsection{Details}{
# #' If the argument for \code{lengths} is a list, the names of each element in the list should be a \code{"vect"} variable. The element associated with the name gives the length of the \code{"vect"} vector and fills it with \code{NaN}. If some \code{"vect"} variables are not given in the list, then they are set to be the length of the longest \code{"vect"} specified by the user.
# #'
# #' If the argument is a single numeric, then all of the variables of \code{"vect"} are set to be \code{NaN} vectors of the specified length.
# #' }
# #' \subsection{Value}{
# #' Returns a \code{input} object with each \code{"vect"} variable being a vector filled with \code{NaN} of the specified length.
# #' }
# #' }
# #'
# #' @exportMethod setup.input
#
# setGeneric( "setup.input", function( input, lengths ) standardGeneric( "setup.input" ) )
#
# setMethod( "setup.input", signature( input = "input", lengths = "list" ),
# function( input, lengths ){
# vect_dims = input@names
# specified_lengths = vect_dims[ vect_dims %in% names( lengths ) ]
# maximum = max( unlist(lengths, use.names = F ) )
# for ( i in vect_dims ){
# if ( i %in% specified_lengths ){
# input@info[[i]]$data <- rep( NaN, lengths[[i]] )
# input@info[[i]]$counts <- 0
# }
# else{
# input@info[[i]]$data <- rep( NaN, maximum )
# input@info[[i]]$counts <- 0
# }
# }
# }
# )
#
# #' @rdname class.input
# #' @exportMethod setup.input
#
# setMethod( "setup.input", signature( input = "input", lengths = "numeric" ),
# function( input, lengths ){
# if ( length(lengths) > 1 ) stop( "'lengths' must be a single numeric" )
# vect_dims = input@names
# for ( i in vect_dims ){
# input@info[[i]]$data <- rep( NaN, lengths )
# input@info[[i]]$counts <- 0
# }
# }
# )
#
# #' @rdname class.input
# #' @aliases assign.input
# #' @section Assign values to variables in a \code{input} object:{
# #' This function is for assiging the \code{i}th to \code{j}th element of a variable in an \code{input} object. See examples.
# #' \subsection{Usage}{
# #' \code{assign.input( input, v, indices, values, counts = NULL)}
# #' }
# #' \subsection{Arugments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' \item{\code{indices}}{An optional argument. A numeric vector specifying which indices of the variable vector to be changed.}
# #' \item{\code{values}}{An optional argument. A vector of values to be assigned.}
# #' \item{\code{counts}}{An optional argument to change the \code{counts} associated with \code{v}}.
# #' }
# #' }
# #' \subsection{Details}{
# #' As a side effect of the way that the assignment is done, if a value is assigned to a variable that does not exist, it will be created and put into the \code{input} environment, with the just the \code{data} vector without \code{counts}.
# #' Also as a side effect of the way that the assignment is done, if the \code{data} vector for a variable is of length 5 and a value is assigned to index 10, the intervening elements (6 to 9) will be \code{NA}.
# #' }
# #' }
# #' @exportMethod assign.input
#
# setGeneric( "assign.input", function( input, v ,indices, values, counts = NULL ) standardGeneric("assign.input") )
#
# setMethod( "assign.input", signature( input = "input", v = "character", indices = "numeric"),
# function( input, v, indices = NULL, values = NULL, counts = NULL ){
# if ( !is.null( indices ) & !is.null( values ) ){
# input@info[[ v ]]$data[ indices ] <- values
# }
# if ( !is.null( counts ) ){
# input@info[[v]]$counts <- counts
# }
# }
# )
#
# #' @rdname class.input
# #' @aliases next.input
# #' @section Assign the next empty (i.e. first non-\code{NaN}) element in a variable in an \code{input} object:{
# #' When conducting a simulation, it is often convenient to set the next element that is stored in an \code{input} variable without having to explicitly track where the next available element is. Because the \code{input} variables are a vector filled with \code{NaN} by default (see the above methods), this amounts to using \code{assign.input} to assign the first \code{NaN} element in an \code{input} variable to some value. Because this function is intended to be used to enter data during a simulation, the \code{counter} that is associated with the variable is automatically incremented with each call to the \code{next.input} method.
# #' \subsection{Usage}{
# #' \code{next.input( input, v, value )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' \item{\code{value}}{A value to place in the next available element in the data vector for \code{v}.}
# #' }
# #' }
# #' \subsection{Details}{
# #' Note that the new value for the associated \code{counts} will be incremented by 1. Hence, if additional changes are made to the \code{data} vector associated with \code{v}, say with the \code{assign.input}, then the \code{counts} will not be correct.
# #' Also, note that the \code{next.input} function finds the next available element in the vector by taking the index that is 1 larger than the associated \code{counts}. Hence, this will overwrite any stored information in the index regardless if it is \code{NaN}.
# #' }
# #' }
# #' @export next.input
#
# setGeneric( "next.input", function( input, v, value ) standardGeneric( "next.input" ) )
#
# setMethod( "next.input", signature( input = "input", v = "character", value = "numeric" ),
# function( input, v, value ){
# input@info[[ v ]]$counts = input@info[[ v ]]$counts + 1
# input@info[[ v ]]$data[ input@info[[ v ]]$counts ] <- value
# }
# )
#
# #' @rdname class.input
# #' @aliases transform.input
# #' @section Assign the next empty element in a variable in an \code{input} object by transformation:{
# #' When conducing a simulation, the \code{next.input} method can be used to set the next available index in a \code{input} variable to some value. In some cases, it may be necessary for the new value to be dependent on the most recent value. An example of this is if a simulation specifies that the \code{i}th response time must be the same as the \code{i-1}th response time. See example.
# #' \subsection{Usage}{
# #' transform.input( input, v , FUN, ... )
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' \item{\code{FUN}}{A function.}
# #' \item{\code{...}}{Additional arguments for \code{FUN}.}
# #' }
# #' }
# #' \subsection{Details}{
# #' The \code{transform.input} method takes the first unspecified argument for \code{FUN} as the most recent non-empty element in the variable \code{v}. By this, it is meant that the value before the one that is to be specified by the \code{transform.input} function.
# #' Further, the underlying implementation is that the \code{transform.input} function matches the arguments in \code{...} with the formal arguments of the function \code{FUN}. The first unmatched argument is assigned to be the most recent non-empty element in the \code{v} vector. Then, the \code{next.input} function is called. Hence, all of the cautions that must be applied with \code{next.input} should also be applied to \code{transform.input}.
# #' }
# #' }
#
# setGeneric( "transform.input", function( input, v, FUN, ... ) standardGeneric( "transform.input" ) )
#
# setMethod( "transform.input", signature( input = "input", v = "character", FUN = "function" ),
# function( input, v, FUN, ... ){
# transform.input_helper( input, v, FUN, ... )
# }
# )
#
# transform.input_helper = function( input, v, FUN, ... ){
# dot_list = list( ... )
# formals = names( formals( args( FUN ) ) )
# unmatched_args = formals[ !formals %in% names( dot_list ) ]
# previous_value = input@info[[ v ]]$data[ input@info[[ v ]]$counts ]
# new_arg_list = c( previous_value, dot_list )
# names( new_arg_list )[1] = unmatched_args
# next.input( input, v, do.call( FUN, new_arg_list ) )
# }
#
# #' @rdname class.input
# #' @aliases tail.input
# #' @section Get the last element in a variable in an \code{input} object:{
# #' To extract the last element, by which we mean the index that corresponds to the value of the associated \code{counts}, use the \code{tail.input()} function.
# #' \subsection{Usage}{
# #' \code{tail.input( input, v )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' }
# #' }
# #' }
#
# setGeneric( "tail.input", function( input, v ) standardGeneric( "tail.input" ) )
#
# setMethod( "tail.input", signature( input = "input", v = "character" ),
# function( input, v ){
# input@info[[ v ]]$data[ input@info[[ v ]]$counts ]
# }
# )
#
# #' @rdname class.input
# #' @aliases reset.input
# #' @section To reset the values stored in a variable \code{data} and \code{counts}:{
# #' The \code{reset.input()} function is for resetting the values in the \code{data} to \code{NaN} and counts to zero for a variable in an \code{input} object.
# #' \subsection{Usage}{
# #' \code{reset.input( input, v )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' }
# #' }
# #' }
# #'
# #' @exportMethod reset.input
#
# setGeneric( "reset.input", function( input, v ) standardGeneric( "reset.input" ) )
#
# setMethod( "reset.input", signature( input = "input", v = "character" ),
# function( input, v ){
# count = input@info[[v]]$counts
# input@info[[v]]$data[1:count] = NaN
# input@info[[v]]$counts = 0
# }
# )
#
#
#
#
#
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# #### Simulation inputs ####
#
# #' \code{input} class
# #'
# #' When a simulation is run in the \code{CAB} package, the within-simulation information (i.e., the variables that are not pre-set before the simulation, e.g. the number of responses during an inter-reinforcement itnerval) are stored in an \code{input} object.
# #'
# #' The underlying implementation of the \code{input} class is that the \code{input} class has two slots. One slot is called \code{info}, which holds an environment. Each element in the environment is a list. For each list, one element of the list is a vector that stores the events that occurred (for example, a vector may store the response times) and the other element is a single numeric that counts the number of elements that stored in the corresponding vector. The second slot is called \code{names}, which is just for easy access of the variable names in the \code{input} object.
# #'
# #' Before using a \code{input} object to store data or count things in a simulation, set it up with the \code{setup.input_monitor} function.
# #'
# #' A \code{show} method for the \code{input} class has been defined for printing \code{input} objects (see below; \code{input.show()}). An associated function \code{remove.input.show()} has been defined for removing the \code{show} method.
# #'
# #' @slot info An \code{environment} that contains a list, which in turn contains a vector to store events that occur in the simulation, as well as a numeric to count the events. The vector that contains the data is called \code{data} and the numeric that stores the counts is \code{counts}.
# #' @slot names Stores the names of the variables held in the \code{info} slot.
# #'
# #' @section Make a new \code{input} object:{
# #' Before doing a simulation, a \code{input} object needs to be constructed to store the data that is generated (e.g. response times) and to count the instances of some particular event (e.g. number of responses).
# #'
# #' Note that when \code{input} object is first constructed, each of the variables in the \code{info} slot will be a vector of \code{NaN} of size 1.
# #'
# #' \subsection{Usage}{
# #' \code{make.input( var_names )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{var_names}}{A vector of character strings that give names for the events to be stored. See example.}
# #' }
# #' }
# #' \subsection{Value}{
# #' A \code{input} object is returned.
# #' }
# #' }
# #'
# #' @examples
# #' #### Create an "input" for storing the variables: "time_input", "resp_time", "rft_time", "rft_setup", and to count the events: "resp_counter", "rft_counter". ####
# #' var_names = c( "time_input", "vect", "resp_time", "rft_time", "rft_setup" )
# #' my_input = make.input( var_names )
# #' my_input
# #'
# #' #### Indexing on an "input" object ####
# #' # Extract the response times
# #' response_times = my_input[ v = "resp_time" ]
# #' # Remember that for a newly created "input" object, the variable contains a single \code{NaN} in the \code{data} vector and a zero in the \code{counts} vector.
# #'
# #' #### Set up an "input" object ####
# #' # Set the "input" to hold a maximum of 10 response times, 11 reinforcement times, and 20 "time_input". Note that the length for "rft_setup" is not specified, so it becomes the specified maximum (20).
# #' length_list = list( resp_time = 5, rft_time = 11, time_input = 20 )
# #' setup.input( my_input, length_list )
# #' my_input
# #'
# #' # Set up "input" to hold 50 elements for all variables
# #' setup.input( my_input, 50 )
# #' my_input
# #'
# #' # Set the first element of the "time_input" variable to 0, set the fifth element of the "time_input" variable to 1, and set the associated "counts" to 100.
# #' assign.input( my_input, v = "time_input", indices = c(1, 5), values = c(0, 1 ), counts = 100 )
# #'
# #' # Store a sequence of "1" in the "resp_time" vector. Also, note the value of the associated "counts"
# #' next.input( my_input, "resp_time", 1 )
# #' my_input
# #' next.input( my_input, "resp_time", 1 )
# #' my_input
# #' next.input( my_input, "resp_time", 1 )
# #' my_input
# #'
# #' #Set the "resp_time" values to be twice larger than the previously specified "resp_time_value"
# #' fx = function( x, y ) x * y
# #' transform.input( my_input, "resp_time", fx, y = 2 )
# #' my_input
# #' transform.input( my_input, "resp_time", fx, y = 2 )
# #' my_input
# #' # Set the "resp_time" values to be thrice larger
# #' transform.input( my_input, "resp_time", fx, y = 3 )
# #' my_input
# #'
# #' #Get the last element in an "input" variable data vector
# #' tail.input( my_input, "resp_time" )
# #'
# #' #Reset
# #' reset.input( my_input, "resp_time" )
# #' my_input
# #'
# #' @rdname class.input
# #' @export class.input
#
# class.input = setClass( "input", slots = list( info = "environment", names = "character" ) )
#
# #' @rdname class.input
# #' @export make.input
#
# make.input = function( var_names ){
# dummy_list = lapply( var_names, function(x) list( data = NaN, counts = 0 ) )
# names( dummy_list ) = var_names
# new( "input", info = list2env( dummy_list, parent = emptyenv() ), names = var_names )
# }
#
# #' @rdname class.input
# #' @section Indexing on an \code{input} object:{
# #' \subsection{Usage}{
# #' \code{"["( x, v )}
# #' or
# #' \code{input[v]}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{x}}{An \code{input} object.}
# #' \item{\code{v}}{A string specifting a variable in the \code{input} object.}
# #' \item{\code{input}}{An \code{input} object.}
# #' }
# #' }
# #' \subsection{Value}{
# #' Returns the vector in the \code{input} object that is specified by \code{v}. See example.
# #' }
# #' }
# #' @export index.input
#
# index.input = setMethod( "[", signature( x = "input" ),
# function( x, v ){
# x@info[[v]]
# }
# )
#
# #' @rdname class.input
# #' @format The \code{show} method for the \code{input} class prints the names of the variables in the \code{input} object as well as the events/counts that they store. Remove this \code{show} method by calling \code{remove.input.show().}
# #' @export input.show
#
# input.show = setMethod( "show", signature( object = "input" ),
# function( object ){
# variables = object@names
# cat( "Input object: \n" )
# lapply( variables, input.show_helper, object = object )
# }
# )
#
# input.show_helper = function( x, object ){
# cat( x, "\n" )
# print( object@info[[x]] )
# cat( "\n" )
# }
#
# # #' @rdname class.input
# # #' @export remove.input.show
# #
# # remove.input.show = function() removeMethod( "show", signature( object = "input" ) )
#
# #' @rdname class.input
# #' @aliases setup.input
# #' @section Set up a \code{input} object for a simulation:{
# #' \subsection{Usage}{
# #' \code{setup.input( input, lengths )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}}.
# #' \item{\code{lengths}}{Either a \code{list} or a single numeric, giving the length of the data storage vectors. See details.}
# #' }
# #' }
# #' \subsection{Details}{
# #' If the argument for \code{lengths} is a list, the names of each element in the list should be a \code{"vect"} variable. The element associated with the name gives the length of the \code{"vect"} vector and fills it with \code{NaN}. If some \code{"vect"} variables are not given in the list, then they are set to be the length of the longest \code{"vect"} specified by the user.
# #'
# #' If the argument is a single numeric, then all of the variables of \code{"vect"} are set to be \code{NaN} vectors of the specified length.
# #' }
# #' \subsection{Value}{
# #' Returns a \code{input} object with each \code{"vect"} variable being a vector filled with \code{NaN} of the specified length.
# #' }
# #' }
# #'
# #' @exportMethod setup.input
#
# setGeneric( "setup.input", function( input, lengths ) standardGeneric( "setup.input" ) )
#
# setMethod( "setup.input", signature( input = "input", lengths = "list" ),
# function( input, lengths ){
# vect_dims = input@names
# specified_lengths = vect_dims[ vect_dims %in% names( lengths ) ]
# maximum = max( unlist(lengths, use.names = F ) )
# for ( i in vect_dims ){
# if ( i %in% specified_lengths ){
# input@info[[i]]$data <- rep( NaN, lengths[[i]] )
# input@info[[i]]$counts <- 0
# }
# else{
# input@info[[i]]$data <- rep( NaN, maximum )
# input@info[[i]]$counts <- 0
# }
# }
# }
# )
#
# #' @rdname class.input
# #' @exportMethod setup.input
#
# setMethod( "setup.input", signature( input = "input", lengths = "numeric" ),
# function( input, lengths ){
# if ( length(lengths) > 1 ) stop( "'lengths' must be a single numeric" )
# vect_dims = input@names
# for ( i in vect_dims ){
# input@info[[i]]$data <- rep( NaN, lengths )
# input@info[[i]]$counts <- 0
# }
# }
# )
#
# #' @rdname class.input
# #' @aliases assign.input
# #' @section Assign values to variables in a \code{input} object:{
# #' This function is for assiging the \code{i}th to \code{j}th element of a variable in an \code{input} object. See examples.
# #' \subsection{Usage}{
# #' \code{assign.input( input, v, indices, values, counts = NULL)}
# #' }
# #' \subsection{Arugments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' \item{\code{indices}}{An optional argument. A numeric vector specifying which indices of the variable vector to be changed.}
# #' \item{\code{values}}{An optional argument. A vector of values to be assigned.}
# #' \item{\code{counts}}{An optional argument to change the \code{counts} associated with \code{v}}.
# #' }
# #' }
# #' \subsection{Details}{
# #' As a side effect of the way that the assignment is done, if a value is assigned to a variable that does not exist, it will be created and put into the \code{input} environment, with the just the \code{data} vector without \code{counts}.
# #' Also as a side effect of the way that the assignment is done, if the \code{data} vector for a variable is of length 5 and a value is assigned to index 10, the intervening elements (6 to 9) will be \code{NA}.
# #' }
# #' }
# #' @exportMethod assign.input
#
# setGeneric( "assign.input", function( input, v ,indices, values, counts = NULL ) standardGeneric("assign.input") )
#
# setMethod( "assign.input", signature( input = "input", v = "character", indices = "numeric"),
# function( input, v, indices = NULL, values = NULL, counts = NULL ){
# if ( !is.null( indices ) & !is.null( values ) ){
# input@info[[ v ]]$data[ indices ] <- values
# }
# if ( !is.null( counts ) ){
# input@info[[v]]$counts <- counts
# }
# }
# )
#
# #' @rdname class.input
# #' @aliases next.input
# #' @section Assign the next empty (i.e. first non-\code{NaN}) element in a variable in an \code{input} object:{
# #' When conducting a simulation, it is often convenient to set the next element that is stored in an \code{input} variable without having to explicitly track where the next available element is. Because the \code{input} variables are a vector filled with \code{NaN} by default (see the above methods), this amounts to using \code{assign.input} to assign the first \code{NaN} element in an \code{input} variable to some value. Because this function is intended to be used to enter data during a simulation, the \code{counter} that is associated with the variable is automatically incremented with each call to the \code{next.input} method.
# #' \subsection{Usage}{
# #' \code{next.input( input, v, value )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' \item{\code{value}}{A value to place in the next available element in the data vector for \code{v}.}
# #' }
# #' }
# #' \subsection{Details}{
# #' Note that the new value for the associated \code{counts} will be incremented by 1. Hence, if additional changes are made to the \code{data} vector associated with \code{v}, say with the \code{assign.input}, then the \code{counts} will not be correct.
# #' Also, note that the \code{next.input} function finds the next available element in the vector by taking the index that is 1 larger than the associated \code{counts}. Hence, this will overwrite any stored information in the index regardless if it is \code{NaN}.
# #' }
# #' }
# #' @export next.input
#
# setGeneric( "next.input", function( input, v, value ) standardGeneric( "next.input" ) )
#
# setMethod( "next.input", signature( input = "input", v = "character", value = "numeric" ),
# function( input, v, value ){
# input@info[[ v ]]$counts = input@info[[ v ]]$counts + 1
# input@info[[ v ]]$data[ input@info[[ v ]]$counts ] <- value
# }
# )
#
# #' @rdname class.input
# #' @aliases transform.input
# #' @section Assign the next empty element in a variable in an \code{input} object by transformation:{
# #' When conducing a simulation, the \code{next.input} method can be used to set the next available index in a \code{input} variable to some value. In some cases, it may be necessary for the new value to be dependent on the most recent value. An example of this is if a simulation specifies that the \code{i}th response time must be the same as the \code{i-1}th response time. See example.
# #' \subsection{Usage}{
# #' transform.input( input, v , FUN, ... )
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' \item{\code{FUN}}{A function.}
# #' \item{\code{...}}{Additional arguments for \code{FUN}.}
# #' }
# #' }
# #' \subsection{Details}{
# #' The \code{transform.input} method takes the first unspecified argument for \code{FUN} as the most recent non-empty element in the variable \code{v}. By this, it is meant that the value before the one that is to be specified by the \code{transform.input} function.
# #' Further, the underlying implementation is that the \code{transform.input} function matches the arguments in \code{...} with the formal arguments of the function \code{FUN}. The first unmatched argument is assigned to be the most recent non-empty element in the \code{v} vector. Then, the \code{next.input} function is called. Hence, all of the cautions that must be applied with \code{next.input} should also be applied to \code{transform.input}.
# #' }
# #' }
#
# setGeneric( "transform.input", function( input, v, FUN, ... ) standardGeneric( "transform.input" ) )
#
# setMethod( "transform.input", signature( input = "input", v = "character", FUN = "function" ),
# function( input, v, FUN, ... ){
# transform.input_helper( input, v, FUN, ... )
# }
# )
#
# transform.input_helper = function( input, v, FUN, ... ){
# dot_list = list( ... )
# formals = names( formals( args( FUN ) ) )
# unmatched_args = formals[ !formals %in% names( dot_list ) ]
# previous_value = input@info[[ v ]]$data[ input@info[[ v ]]$counts ]
# new_arg_list = c( previous_value, dot_list )
# names( new_arg_list )[1] = unmatched_args
# next.input( input, v, do.call( FUN, new_arg_list ) )
# }
#
# #' @rdname class.input
# #' @aliases tail.input
# #' @section Get the last element in a variable in an \code{input} object:{
# #' To extract the last element, by which we mean the index that corresponds to the value of the associated \code{counts}, use the \code{tail.input()} function.
# #' \subsection{Usage}{
# #' \code{tail.input( input, v )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' }
# #' }
# #' }
#
# setGeneric( "tail.input", function( input, v ) standardGeneric( "tail.input" ) )
#
# setMethod( "tail.input", signature( input = "input", v = "character" ),
# function( input, v ){
# input@info[[ v ]]$data[ input@info[[ v ]]$counts ]
# }
# )
#
# #' @rdname class.input
# #' @aliases reset.input
# #' @section To reset the values stored in a variable \code{data} and \code{counts}:{
# #' The \code{reset.input()} function is for resetting the values in the \code{data} to \code{NaN} and counts to zero for a variable in an \code{input} object.
# #' \subsection{Usage}{
# #' \code{reset.input( input, v )}
# #' }
# #' \subsection{Arguments}{
# #' \describe{
# #' \item{\code{input}}{An object of class \code{input}.}
# #' \item{\code{v}}{A character string specifying a variable in the \code{input} object.}
# #' }
# #' }
# #' }
# #'
# #' @exportMethod reset.input
#
# setGeneric( "reset.input", function( input, v ) standardGeneric( "reset.input" ) )
#
# setMethod( "reset.input", signature( input = "input", v = "character" ),
# function( input, v ){
# count = input@info[[v]]$counts
# input@info[[v]]$data[1:count] = NaN
# input@info[[v]]$counts = 0
# }
# )
#
#
#
#
#
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