Changes between Version 19 and Version 20 of StatnetComponents


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Timestamp:
02/10/14 23:12:54 (6 years ago)
Author:
morrism
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  • StatnetComponents

    v19 v20  
    22 
    33= statnet Components = 
    4 A list of the core packages and extensions of statnet. 
     4A list of the core packages and extensions that are part of the statnet software. 
    55 
    6 * '''statnet 2014.2.0''' is integrated set of tools for the representation, visualization, analysis, and simulation of network data. It is a 'meta' package that depends on the set of core packages to provide its basic functionality for static and dynamic network modeling.  This is implemented using the R mechanism of "Depends" which can be seen [http://cran.r-project.org/web/packages/statnet/ here].  A number of packages have been written that extend the basic functionality of statnet to network-related applications from epidemic models and valued ergms to relational event models, network movie making, and writing custom terms.   
     6* [[#Description|Description]] 
     7* [[#CorePackages|Core Packages]] 
     8* [[#ExtensionPackages|Extension Packages]] 
     9* [[Installation|Instructions for downloading and installing R and statnet]] 
     10 
     11 
     12== Description == 
     13 
     14* '''statnet''' is integrated set of tools for the representation, visualization, analysis, and simulation of network data. It is a 'meta' package that depends on the set of core packages to provide its basic functionality for static and dynamic network modeling.  This is implemented using the R mechanism of "Depends" which can be seen [http://cran.r-project.org/web/packages/statnet/ here].  A number of packages have been written that extend the basic functionality of statnet to network-related applications from epidemic models and valued ergms to relational event models, network movie making, and writing custom terms.   
    715 
    816Users can either install '''statnet''', which will automatically install the core packages and their dependencies, or individual packages from either the core or extended list (which will automatically install the necessary dependencies for that package).  
     
    1018The current versions of core packages and extensions are listed below.  The statnet development team releases updates and bug fixes a couple of times each year.  So if it has been a few months since you installed the software, you should check for updates.  
    1119 
    12 == Core packages == 
    13 * '''ergm 3.1.2''' is a collection of functions to fit, simulate from, plot and evaluate exponential family random graph models. The main functions within the ergm package are ''ergm'', a function to fit exponential-family random graph models in which the probability of a network is dependent upon a vector of network statistics specified by the user; ''simulate'', a function to simulate random networks using an ERGM; and ''gof'', a function to evaluate the goodness of fit of an ERGM to the data. ergm contains many other functions as well; for a guide to the basic types of functionality these functions provide, see Hunter et al. (2008), Morris, Handcock, and Hunter (2008), and Goodreau et al. (2008). The ergm package also contains some of the classic network datasets (including Sampson's monastery data and the Padgett Florentine networks). The list of available datasets can be found by typing the R command: data(). The datasets are listed at the end of the output. [http://cran.r-project.org/web/packages/ergm/news.html news and changes] [http://cran.r-project.org/web/packages/ergm CRAN link] 
    14  
    15 * '''network 1.9.0''' is a package to create, store, modify and plot the data in network objects. The network object class, defined in the network package (Butts, Handcock, and Hunter 2007; Butts 2008), can represent a range of relational data types and it supports arbitrary vertex / edge / network attributes. Data stored as network objects can then be analyzed using all of the component packages in the statnet suite. [http://cran.r-project.org/web/packages/network/ChangeLog news and changes] [http://cran.r-project.org/web/packages/network CRAN link] 
    16  
    17 * '''networkDynamic 0.6.2''': A package with routines to facilitate the handling of network objects with complex temporal data. (Leslie-Cook, Almquist, Krivitsky, Bender-deMoll, Hunter, Morris, Butts 2012). [http://cran.r-project.org/web/packages/networkDynamic/ChangeLog new and changes] [http://cran.r-project.org/web/packages/networkDynamic CRAN link] 
    18  
    19 * '''statnet.common 3.1.1''': Common R scripts and utilities used by the statnet project software. [http://cran.r-project.org/web/packages/statnet.common/ CRAN link] 
    20  
    21 * '''tergm 3.1.4''': Separable Temporal ERGMs for modeling discrete relational dynamics with statnet  (Krivitsky and Handcock 2013) [http://cran.r-project.org/web/packages/tergm/news.html news and changes] [http://cran.r-project.org/web/packages/tergm/ CRAN link] 
     20------- 
    2221 
    2322 
    24 == Extension packages == 
     23== Core Packages == 
    2524 
    26 * '''degreenet 1.2''': This package was developed for the degree distributions of networks. It implements likelihood-based inference, bootstrapping, and model selection, and it includes power-law models such as the Yule and Waring as well as a range of alternative models that have been proposed in the literature. (Handcock 2003b). The theory behind these methods is described in Jones and Handcock (2003a,b); Handcock and Jones (2004, 2006). [http://cran.r-project.org/web/packages/degreenet/ CRAN link] 
     25* [http://cran.r-project.org/web/packages/ergm  ergm] is a collection of functions to fit, simulate from, plot and evaluate exponential family random graph models. The main functions within the ergm package are ''ergm'', a function to fit exponential-family random graph models in which the probability of a network is dependent upon a vector of network statistics specified by the user; ''simulate'', a function to simulate random networks using an ERGM; and ''gof'', a function to evaluate the goodness of fit of an ERGM to the data. ergm contains many other functions as well; for a guide to the basic types of functionality these functions provide, see Hunter et al. (2008), Morris, Handcock, and Hunter (2008), and Goodreau et al. (2008). The ergm package also contains some of the classic network datasets (including Sampson's monastery data and the Padgett Florentine networks). The list of available datasets can be found by typing the R command: data(). The datasets are listed at the end of the output. [http://cran.r-project.org/web/packages/ergm/news.html news and changes]  
    2726 
    28 * '''EpiModel 0.95''': A package of Tools for building, solving, and plotting mathematical models of infectious disease, including simulations of epidemics on on networks and coupled network dynamics (tergm).  [http://cran.r-project.org/web/packages/EpiModel/news.html news and changes] [http://cran.r-project.org/web/packages/EpiModel/ CRAN link] 
     27* [http://cran.r-project.org/web/packages/network network] is a package to create, store, modify and plot the data in network objects. The network object class, defined in the network package (Butts, Handcock, and Hunter 2007; Butts 2008), can represent a range of relational data types and it supports arbitrary vertex / edge / network attributes. Data stored as network objects can then be analyzed using all of the component packages in the statnet suite. [http://cran.r-project.org/web/packages/network/ChangeLog news and changes]  
    2928 
    30 * '''ergm.count 3.1.1''':  A set of extensions for the ergm package to fit weighted networks whose edge weights are counts.  (Krivitsky, 2012). [http://cran.r-project.org/web/packages/ergm.count/ CRAN link] 
     29* [http://cran.r-project.org/web/packages/networkDynamic networkDynamic]: A package with routines to facilitate the handling of network objects with complex temporal data. (Leslie-Cook, Almquist, Krivitsky, Bender-deMoll, Hunter, Morris, Butts 2012). [http://cran.r-project.org/web/packages/networkDynamic/ChangeLog new and changes]  
    3130 
    32 * '''ergm.userterms 3.1.1''': A template package to demonstrate the use of user-specified statistics for use in ergm models.  (Handcock, Hunter, Butts, Goodreau, Krivitsky, Morris 2012). [http://cran.r-project.org/web/packages/ergm.userterms/ CRAN link] 
     31* [http://cran.r-project.org/web/packages/statnet.common/ statnet.common]: Common R scripts and utilities used by the statnet project software.  
    3332 
    34 * '''latentnet 2.5.0''': A package to fit and evaluate latent position and cluster models for statistical networks based on Hoff, Raftery, and Handcock (2002) and Handcock, Raftery, and Tantrum (2007). The probability of a tie is expressed as a function of distances between these nodes in a latent space as well as functions of observed dyadic level covariates. For details about this package, see Krivitsky and Handcock (2008). [http://cran.r-project.org/web/packages/latentnet/ChangeLog news and changes] [http://cran.r-project.org/web/packages/latentnet/ CRAN link] 
     33* [http://cran.r-project.org/web/packages/tergm/ tergm]: Separable Temporal ERGMs for modeling discrete relational dynamics with statnet  (Krivitsky and Handcock 2013) [http://cran.r-project.org/web/packages/tergm/news.html news and changes]  
    3534 
    36 * '''ndtv 0.5.1''' (Network Dynamic Temporal Visualization): Exports dynamic network data in the form of networkDynamic objects as animated movies or other representations of relational structure and node attributes that change over time (Bender-deMoll 2012). [http://cran.r-project.org/web/packages/ndtv/ChangeLog news and changes] [http://cran.r-project.org/web/packages/ndtv/ CRAN link] 
     35------- 
    3736 
    38 * '''netperm 0.2''': This package provides simulation and inference tools for exponential families of permutation models on relational structures (Butts 2006). 
    3937 
    40 * '''networkDynamicData 0.1.0''' A collection of puplic dynamic network datasets from various sources and multiple authors represented in networkDynamic format [http://cran.r-project.org/web/packages/networkDynamicData/ CRAN link] 
     38== Extension Packages == 
    4139 
    42 * '''networksis 2.1-2''': A package to simulate bipartite networks with fixed marginals through sequential importance sampling (Admiraal and Handcock 2007). [http://cran.r-project.org/web/packages/networksis/ CRAN link] 
     40* [http://cran.r-project.org/web/packages/degreenet/ degreenet]: This package was developed for the degree distributions of networks. It implements likelihood-based inference, bootstrapping, and model selection, and it includes power-law models such as the Yule and Waring as well as a range of alternative models that have been proposed in the literature. (Handcock 2003b). The theory behind these methods is described in Jones and Handcock (2003a,b); Handcock and Jones (2004, 2006).  
    4341 
    44 * '''relevent 1.0-3''': A package with tools to fit relational event models (Butts 2012). [http://cran.r-project.org/web/packages/relevent/ChangeLog news and changes] [http://cran.r-project.org/web/packages/relevent/ CRAN link] 
     42* [http://cran.r-project.org/web/packages/EpiModel/ EpiModel]: A package of Tools for building, solving, and plotting mathematical models of infectious disease, including simulations of epidemics on on networks and coupled network dynamics (tergm).  [http://cran.r-project.org/web/packages/EpiModel/news.html news and changes]  
    4543 
    46 * '''sna 2.3-2''': A set of tools for traditional social network analysis (Butts 2008). [http://cran.r-project.org/web/packages/sna/ChangeLog news and changes] [http://cran.r-project.org/web/packages/sna/ CRAN link] 
     44* [http://cran.r-project.org/web/packages/ergm.count/ ergm.count]:  A set of extensions for the ergm package to fit weighted networks whose edge weights are counts.  (Krivitsky, 2012).  
     45 
     46* [http://cran.r-project.org/web/packages/ergm.userterms/ ergm.userterms]: A template package that demonstrates to users how to write user-specified statistics for use in ergm models.  (Handcock, Hunter, Butts, Goodreau, Krivitsky, Morris 2012).  
     47 
     48* [http://cran.r-project.org/web/packages/latentnet/ latentnet]: A package to fit and evaluate latent position and cluster models for statistical networks based on Hoff, Raftery, and Handcock (2002) and Handcock, Raftery, and Tantrum (2007). The probability of a tie is expressed as a function of distances between these nodes in a latent space as well as functions of observed dyadic level covariates. For details about this package, see Krivitsky and Handcock (2008). [http://cran.r-project.org/web/packages/latentnet/ChangeLog news and changes]  
     49 
     50* [http://cran.r-project.org/web/packages/ndtv/ ndtv] (Network Dynamic Temporal Visualization): Exports dynamic network data in the form of networkDynamic objects as animated movies or other representations of relational structure and node attributes that change over time (Bender-deMoll 2012). [http://cran.r-project.org/web/packages/ndtv/ChangeLog news and changes]  
     51 
     52* [http://cran.r-project.org/web/packages/networkDynamicData/ networkDynamicData]: A collection of puplic dynamic network datasets from various sources and multiple authors represented in networkDynamic format  
     53 
     54* [http://cran.r-project.org/web/packages/networksis/ networksis]: A package to simulate bipartite networks with fixed marginals through sequential importance sampling (Admiraal and Handcock 2007).  
     55 
     56* [http://cran.r-project.org/web/packages/relevent/ relevent]: A package with tools to fit relational event models (Butts 2012). [http://cran.r-project.org/web/packages/relevent/ChangeLog news and changes]  
     57 
     58* [http://cran.r-project.org/web/packages/sna/ sna]: A set of tools for traditional social network analysis (Butts 2008). [http://cran.r-project.org/web/packages/sna/ChangeLog news and changes]  
    4759 
    4860Information on these packages is available in the online users guide and in their runtime help files. These packages are installed during the standard statnet installation process, or during any update. These packages also require other R packages for their use that are automatically installed during the installation process. 
     
    5163 
    5264* '''rSonia''': Provides a set of methods to facilitate exporting data and parameter settings and launching SoNIA, which stands for Social Network Image Animator (Bender-deMoll and !McFarland 2003). SoNIA http://sonia.stanford.edu facilitates interactive browsing of dynamic network data and exporting animations as a !QuickTime Apple (1999) movies. Much of this functionality is now provided by the '''ndtv''' package.  
     65 
     66* '''netperm 0.2''': This package provides simulation and inference tools for exponential families of permutation models on relational structures (Butts 2006)  contact Carter Butts for more information.