Changes between Version 6 and Version 7 of NetworkDynamicConverterFunctions


Ignore:
Timestamp:
10/01/12 21:07:45 (7 years ago)
Author:
skyebend
Comment:

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  • NetworkDynamicConverterFunctions

    v6 v7  
    3636nD to vertex spells : '''get.vertex.activity() - sortof, returns list not matrix'' 
    3737 
    38 nD to toggles : ? 
    39  
    4038== Problem == 
    4139 
    … …  
    4745Separate functions for each type of conversion. Name functions by schemas they are converting, not by object types of arguments because toggles and spells are both represented with data frames.  (maybe only keep an "as.data.frame" function aliased to most common use case? ).  I think so far only duration.matrix() is a published method, so that may be the only one we have to keep around.  
    4846 
    49  networkDynamicFromToggles(startNet=NULL,edge.toggles=NULL,vertex.toggles=NULL):: fill in edges and/or vertex spells in starting network using toggles.  Toggles arguments can be anything convertible into a matrix. For edges will assume first columns are [tail,head,time]. What times assumed for ties in initial network? 
     47 networkDynamic(base.net=NULL,network.list=NULL,edge.toggles=NULL,vertex.toggles=NULL,edge.spells=NULL,vertex.spells=NULL):: fill in edges and/or vertex spells in starting network using toggles.  Toggles arguments can be anything convertible into a matrix.  
    5048 
    51  networkDynamicFromSpells(startNet=NULL, edge.spells=NULL,vertex.spells=NULL, ...<rest of network properties>):: create/populate a nD using edge and/or vertex spells? Spells are any object convertible into a matrix. Edges assume format as [tail,head,onset,terminus], vertices [vertex.id,onset,terminus] 
     49 For edge.toggles, assume first columns are [tail,head,time]. What times assumed for ties in initial network? 
    5250 
    53  networkDynamicFromNetworks(network.list,onsets=seq(from=0,length=length(network.list)),termini=seq(from=1,length=length(network.list),vertex.pid=NULL):: create a nD object using a list of networks (or objects like matrices convertible to networks). Timing of each panel of vertex and edges . spells taken from onsets and termini arguments (defaults to [0,1].[1,2] etc..). If vertex.pid is set to the name of a network attribute, use that attribute as the vertex. id when constructing a network (for when inputs are not the same sizes. Censoring of starting / ending networks? 
     51 edge.spells format as [tail,head,onset,terminus] 
     52 
     53 vertex.spells [vertex.id,onset,terminus]  
     54 
     55 onsets=seq(from=0,length=length(network.list)) 
     56  
     57 termini=seq(from=1,length=length(network.list) 
     58  
     59 vertex.pid=NULL 
     60  
     61 network.list:: create a nD object using a list of networks (or objects like matrices convertible to networks). Timing of each panel of vertex and edges . spells taken from onsets and termini arguments (defaults to [0,1].[1,2] etc..). If vertex.pid is set to the name of a network attribute, use that attribute as the vertex. id when constructing a network (for when inputs are not the same sizes. Censoring of starting / ending networks? 
    5462 
    5563 get.vertex.activity(nD, v=1:network.size(x),as.spellList=FALSE):: currently this returns a list of spell matrices, one for each v specified.  Add argument to return same info as a single spell matrix [onset.terminus,vertex.id].  Sort order by onset,terminus,vertex.id? Include attributes? 
    … …  
    5765 get.edge.activity(networkDynamic,as.spellList=FALSE):: currently this returns a list of spell matrices.  Add "start" and "end" arguments for specifying censoring. Add argument to return same info as a single spell matrix [onset,terminus,tail,head,left.censored, right.censored, duration, edge.id]. Sort order by onset,terminus,tail,head,eid?.  
    5866 
    59  get.vertex.toggles(networkDynamic,base.net=FALSE):: Return an array of toggles [vertex.id,onset,terminus]. Optionally return a list, the first element of which is $base.net and has a network object with the first state of the network, second element ($toggles) is the toggle array. 
    60  
    6167 get.slice.networks(networkDynamic, start=min(get.change.times(networkDynamic),end=max(get.change.times(networkDynamic),time.step=1,duration=1, rule="any"):: return a list with a series of networks produced by network.extract.  Allow specifying a series of onsets, termini  instead of / in addition to  start,step,duration,end ? 
    62  
    63 === Some alternate name ideas == 
    64  
    65 nDToSpells 
    66  
    67 as.nd.spells 
    6868 
    6969 
    … …  
    7272Should we use "fake" S3 method names to be consistent?  (i.e. networkDynamic.spell.list) 
    7373 
    74 Is it better to pass in a network object to be populated, or specify full list of network options (directed,bipartite,etc)?  
     74Is it better to pass in a network object to be populated YES, or specify full list of network options (directed,bipartite,etc)?  
    7575  
    7676For matrix input formats, better to assume column order, or allow specifying column indicies/names? 
    … …  
    7878Preferred format for returned data objects? (array, matrix, data.frame)? 
    7979 
    80 Censoring behavior (Inf should not automatically be censored, right) 
     80Censoring behavior (Inf should not automatically be censored, right)  change to start.censored, end.censored. 
    8181 
    8282Implement for multiple head/tail set, or just return error? 
    … …  
    9090Support for non-numeric,non integer input ids. '''pid=attrName''' Sort into alphabetic order, assign to ids 1:n 
    9191 
     92Remove: to-toggle methods.  
     93 
     94Add "include.censoring=T" attribute 
    9295 
    9396 
    … …  
    100103 
    101104 
     105