Changes between Version 21 and Version 22 of statnetChanges


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Timestamp:
11/10/14 14:08:58 (5 years ago)
Author:
skyebend
Comment:

updated content from package changelogs, added info for network and networkDynamic

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  • statnetChanges

    v21 v22  
    1 Overview of changes, see individual packages NEWS or changelog files for more specific details 
     1 
    22== Changes to statnet packages in 2014.11 release == 
    33 
    4 These are changes that may affect users' code or experimental results. 
     4These are changes that may affect users' code or experimental results. Below is a summary of each of the packages NEWS or changelog files. 
    55 
    6 === statnet === 
     6=== statnet 2014.11=== 
    77 
    88* statnet will automatically check for package updates when it loads. #671 
     
    2727=== tergm 3.2 === 
    2828 
    29 * Allows simpler specification of offset values in formation model, when using stergm.EGMME with target statistics. Usage examples: [[wiki:tergmUsage]] 
     29NEW FEATURES 
    3030 
    31 * Offset terms in the target formula are automatically removed. This includes the case where the target is set equal to formation ({{{targets = "formation"}}}) #1006 
     31* Speed improvements. Internal data handling has been modified to avoid allocating (and passing around) a large matrix of tie ages unless the formula/model explicitly requires tie duration information. This increases speed of model initialization, which is especially helpful when simulating a network where the model must be re-initialized at each timestep (i.e. models with vital dynamics). 
    3232 
    3333* Use Carnegie approximation for initializing formation models with offset term;  
     
    4343  will no longer result in an error. 
    4444 
     45* Offset terms in the target formula are automatically removed. This includes the case where the target is set equal to formation (targets = "formation"). Use Carnegie approximation for initializing formation models with offset term. 
     46 
     47* The simulate.networkDynamic and related function now make use of networkDynamics persistant id (PID) functionality. If the network does not have any persistent.ids defined for vertices, a vertex.pid will be attached in a vertex attribute named 'tergm_pid' to facilitate 'bookkeeping' between the networkDynamic argument and the simulated network time step. 
     48 
     49* Parallel functionality: tergm can take user-created clusters as the control.stergm(parallel) control parameter. This is the recommended method for using tergm on a high-performance computing cluster. See ergm-parallel. Functionality is now implemented via the parallel package, direct dependence on snow package is removed 
     50 
     51* Addition of bipartite formation and dissolution Metropolis-Hastings proposals 
     52 
     53* Addition of a TNT dissolution proposal constraint 
     54 
     55* Inclusion of a Stergm vignette 
    4556 
    4657 
     58BUG FIXES 
     59 
     60* Namespace prefixing has been added to some functions called from external packages to deal with CRAN check warnings 
     61 
     62OTHER USER-VISIBLE CHANGES 
     63 
     64* Changes to control.stergm parameters: 
     65 
     66  - init.method If NULL (the default), the initial values are computed using the edges dissolution approximation (Carnegie et al.) when appropriate. If set to "zeros", the initial values are set to zeros. 
     67 
     68  -  SA.oh.memory = 100000 Absolute maximum number of data points per thread to store in the full optimization history. 
     69 
     70* Changes to simulate.stergm parameters: addition of duration.dependent parameter: Logical: Whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status. If TRUE, the matrix of tie ages will be allocated. 
     71* Allows simpler specification of offset values in formation model, when using stergm.EGMME with target statistics. Usage examples: [[wiki:tergmUsage]] 
     72 
     73 
     74=== network 1.11 === 
     75* minor changes to print.network to give more informative info about some network attributes 
     76* get.edge.attribute now has C-level backend 
     77* get.edge.attribute and get.edge.value now have arguments to avoid returning attribute values from 'missing' edges (na.omit) and unset/deleted edges (deleted.edges.omit) and edges with no value assigned for the attribute (null.na).  
     78* network now includes an explicit list of exported functions in NAMESPACE 
     79* the following 'internal' functions have been removed from NAMESPACE: networkOperatorSetup, switchArcDirection, readAndVectorizeLine, read.paj.simplify 
     80* network now follows R conventions for exporting some of its C-level API functions for use by other packages 
     81* get.inducedSubgraph() now has an optional 'eid' argument for inducing a network including specified edges and their incident vertices 
     82* fixed bug in as.network.matrix that caused it to ignore the na.rm argument. 
     83* added patch to which.matrix. type to handle NAs submitted by Philip Leifeld 
     84* fixed na.rm argument to as.network.matrix 
     85* changed plot function to force lazy evaluation of displaylabels=!missing(label) argument before value of label is changed 
     86 
     87=== networkDynamic 0.7 === 
     88 
     89* networkDynamic now uses (and requires) C-api exported by the network package 
     90* additional spell operations moved to C level 
     91* the networkDynamic() data conversion function as additional arguments "edge.TEA.names"" and "vertex.TEA.names" and can now load dynamic edge or vertex attributes included as extra columns to edge.spells and vertex.spells. 
     92* pids will now be removed by as.network.networkDynamic() 
     93* added read.son function for parsing SoNIA-formatted files with dynamic network data 
     94* added nd_test_nets dataset, a list networkDynamic objects with unusual configurations and parameters to be used for testing 
     95* fixed bug in spells.overlap and adding missing tests 
     96* added when.vertex.attrs.match and when.edge.attrs.match functions for getting times at which TEA attributes of network elements match specified values according to specified operators. 
     97* added nd_test_nets dataset, a list networkDynamic objects with unusual configurations and parameters to be used for testing  
     98 
     99