networkTomography: Tools for network tomography

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networkTomography implements the methods developed and evaluated in Blocker and Airoldi (2011) and Airoldi and Blocker (2012). These include the authors' own dynamic multilevel model with calibration based upon a Gaussian state-space model in addition to implementations of the methods of Tebaldi & West (1998; Poisson-Gamma model with MCMC sampling), Zhang et al. (2002; tomogravity), Cao et al. (2000; Gaussian model with mean-variance relation), and Vardi (1996; method of moments). Data from the 1router network of Cao et al. (2000), the Abilene network of Fang et al. (2007), and the CMU network of Blocker and Airoldi (2011) are included for testing and reproducibility.

Author
Alexander W Blocker, Paul Koullick, Edoardo Airoldi
Date of publication
2014-01-10 07:28:23
Maintainer
Alexander W Blocker <ablocker@gmail.com>
License
LGPL-2
Version
0.3
URLs

View on CRAN

Man pages

abilene
Abilene data from Fang et al. (2007)
agg
Function to aggregate results from matrix to matrix
bayesianDynamicFilter
Function for inference with multilevel state-space model
bell.labs
Bell Labs 1router data from Cao et al. (2000)
buildPrior
Construct prior from calibration model estimates
buildRoutingMat
Build routing matrices for linked star topologies; that is, a...
buildRoutingMatrix
Build routing matrix from table of link relationships
buildStarMat
Build routing matrix for star network topology
calcN
Compute total traffic from a particular time.
calibration_ssm
Estimation for the linear SSM calibration model of Blocker &...
cmu
CMU data from Blocker & Airoldi (2011)
decomposeA
Compute pivoted decomposition of routing matrix A into...
diag_ind
Make vector of 1-dimensional diagonal indices for square...
diag_mat
Make diagonal matrix from vector
dobj.dxt.tomogravity
Analytic gradient of objective function of Zhang et al. 2003
getActive
Check for deterministically-known OD flows at single time
getSrcDstIndices
Find indices of source and destination for each...
grad_iid
Compute analytic gradient of Q-function for locally IID EM...
grad_smoothed
Compute analytic gradient of Q-function for smoothed EM...
gravity
Run tomogravity estimation on complete time series of...
gravity.fit
Gravity estimation for a single time point
ipfp
Function to run basic IPFP (iterative proportional fitting...
llCalibration
Evaluate marginal log-likelihood for calibration SSM
locally_iid_EM
Run EM algorithm to obtain MLE for locally IID model of Cao...
m_estep
Compute conditional expectations for EM algorithms of Cao et...
mle_filter
Filtering & smoothing at MLE for calibration SSM
move_step
Move step of sample-resample-move algorithm for multilevel...
obj.tomogravity
Objective function of Zhang et al. 2003
phi_init
Simple initialization for phi in model of Cao et al. (2000)
Q_iid
Q function for locally IID EM algorithm of Cao et al. (2000)
Q_smoothed
Q function for smoothed EM algorithm of Cao et al. (2000)
R_estep
Compute conditional covariance matrix for EM algorithms of...
smoothed_EM
Run EM algorithm to obtain MLE (single time) for smoothed...
strphour
Convert time string to decimal hour
thin
Thinning vector of indices for MCMC
tomogravity
Run tomogravity estimation on complete time series of...
tomogravity.fit
Tomogravity estimation for a single time point using L-BFGS-B
twMCMC
Function to run MCMC sampling for model of Tebaldi & West...
vardi.algorithm
Run algorithm of Vardi (1996) given B and S matrices
vardi.compute.BS
Compute B and S matrices in algorithm of Vardi (1996)
vardi.iteration
Execute single iteration for algorithm of Vardi (1996)

Files in this package

networkTomography
networkTomography/src
networkTomography/src/Makevars
networkTomography/src/Makevars.win
networkTomography/src/ipfp.c
networkTomography/NAMESPACE
networkTomography/data
networkTomography/data/cmu.rda
networkTomography/data/abilene.rda
networkTomography/data/bell.labs.rda
networkTomography/R
networkTomography/R/parseTopology.R
networkTomography/R/caoEtAl.R
networkTomography/R/twMCMC.R
networkTomography/R/ssmMle.R
networkTomography/R/data.R
networkTomography/R/ipfp.R
networkTomography/R/tomogravity.R
networkTomography/R/ssmMCMC.R
networkTomography/R/lib.R
networkTomography/R/vardi.algorithm.R
networkTomography/R/gravity.R
networkTomography/R/imports.R
networkTomography/README.md
networkTomography/MD5
networkTomography/DESCRIPTION
networkTomography/man
networkTomography/man/gravity.fit.Rd
networkTomography/man/buildRoutingMat.Rd
networkTomography/man/strphour.Rd
networkTomography/man/Q_iid.Rd
networkTomography/man/diag_mat.Rd
networkTomography/man/gravity.Rd
networkTomography/man/tomogravity.fit.Rd
networkTomography/man/buildRoutingMatrix.Rd
networkTomography/man/llCalibration.Rd
networkTomography/man/dobj.dxt.tomogravity.Rd
networkTomography/man/m_estep.Rd
networkTomography/man/calibration_ssm.Rd
networkTomography/man/Q_smoothed.Rd
networkTomography/man/tomogravity.Rd
networkTomography/man/grad_iid.Rd
networkTomography/man/vardi.iteration.Rd
networkTomography/man/R_estep.Rd
networkTomography/man/move_step.Rd
networkTomography/man/smoothed_EM.Rd
networkTomography/man/getSrcDstIndices.Rd
networkTomography/man/twMCMC.Rd
networkTomography/man/ipfp.Rd
networkTomography/man/bell.labs.Rd
networkTomography/man/bayesianDynamicFilter.Rd
networkTomography/man/getActive.Rd
networkTomography/man/diag_ind.Rd
networkTomography/man/calcN.Rd
networkTomography/man/locally_iid_EM.Rd
networkTomography/man/agg.Rd
networkTomography/man/thin.Rd
networkTomography/man/obj.tomogravity.Rd
networkTomography/man/cmu.Rd
networkTomography/man/phi_init.Rd
networkTomography/man/mle_filter.Rd
networkTomography/man/decomposeA.Rd
networkTomography/man/grad_smoothed.Rd
networkTomography/man/vardi.algorithm.Rd
networkTomography/man/buildStarMat.Rd
networkTomography/man/abilene.Rd
networkTomography/man/buildPrior.Rd
networkTomography/man/vardi.compute.BS.Rd