eventHistory: Event History Creation
In zeehio/msProcess: Protein Mass Spectra Processing

Description Usage Arguments Value S3 METHODS See Also Examples

The S+Proteome module provides a wealth of preprocessing functionality, some or all of which may be used as a preface for subsequent classification investigations. This function allows the user to document the processing pipeline by adding text to a particular attribute of an object that describes the current processing state. Each process in the pipeline is referred to as an event. This function will typically not be called directly by the user and will alternatively be called from within various preprocessing functions.

1	eventHistory(x, ..., sub.label=" ", time.stamp=date(), action="append")

`x`	an object of any class.
`...`	one or more named lists, each containing named character vectors describing an event to register. Each list must be in the form EventName = list(proc2="Description 1", proc2="Description 2") and so on. Here, EventName is a character string defining the name of the event, and the named list variables proc1 and proc2 are character strings that define the specific proceedings for that event. Each of these proceedings is descibed more thoroughly by the assigned character string. If for a given event, the user wishes only to register the name of the event sans extra proceedings information, it is allowable to make the call ala `eventHistory(x, "Event A", "Event B")` and so on. In this case, each character string is taken to mean the name of the corresponding event.
`action`	a character string defining the action to take with the new history information. Supported values are as follows: prepend Prepend new history to the existing event history. append Append new history to the existing event history. replace Replace the event history with the new history. merge Update old events which have a common event name with new events. The uncommon events are appended. Default: `"append"`.
`sub.label`	a character string used to preface the proceedings lines for each event when a history summary is printed on the command line. Default: `" " (3 blanks)`.
`time.stamp`	a character string defining a time stamp for the process(es) being documented. This time stamp will be automatically added to each process in the event. Default: `date()`.

a replication of the original object, with an attached attribute of class eventHistory containing a vector of formatted character strings defining the processing history of the input object.

@lsb

event data access. Input either a character string or an integer defining the registered event in the history.

print

pretty-prints the event history. Optional arguments for this method are

pre: Character string to preface each event header. Default: paste("[", attr(x, "index"), "]", sep = "").

assignEvent, isProcessRecorded, existHistory, getHistory, eventHistory.

## create a list of simple objects 
z <- list(dog="chihuahua", vals=1:5, colors=c("red","green","blue"))

## remove mean from vals and document as a history 
## event 
z$vals <- z$vals - mean(z$vals)
z <- eventHistory(z, "Process A"=list(values="mean removed"))

## now sort the colors and change the dog name, 
## and document both actions in the same call 
## to msHistory as separate processes 
z$colors <- sort(z$colors)
z$dog    <- "pomeranian"
z <- eventHistory(z, "Process B"=list(colors="sorted alphabetically"),
    "Process C"=list(dog="name change", result="more hair"))

## add an event without proceedings 
z <- eventHistory(z, "Event A", "Event B")

## print the history 
print(getHistory(z))

## replace some of the events with new information 
z <- eventHistory(z, "Event A"=list(show="pony"), "Process A",
action="merge")
print(getHistory(z))

## prepend some new events 
z <- eventHistory(z, new=list(alpha="first greek letter"),
    action="prepend")
print(getHistory(z))

## replace event history altogether 
z <- eventHistory(z, newest=list(omega="final greek letter"),
    action="replace")
print(getHistory(z))

## return an object of class eventHistory, i.e., 
## not attached to any other object 
eventHistory(NULL,
    symphony=list(string="violins and cellos", percussion="drums",
       reed="flutes and oboes"))