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 Cao et al. (2000)
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 set of star-topology
                        networks with links between a subset of routers
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 & Airoldi (2011)
cmu                     CMU data from Blocker & Airoldi (2011)
decomposeA              Compute pivoted decomposition of routing matrix
                        A into full-rank and remainder, as in Cao et
                        al. 2000, via the QR decomposition.
diag_ind                Make vector of 1-dimensional diagonal indices
                        for square matrix
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
                        point-to-point flow
grad_iid                Compute analytic gradient of Q-function for
                        locally IID EM algorithm of Cao et al. (2000)
grad_smoothed           Compute analytic gradient of Q-function for
                        smoothed EM algorithm of Cao et al. (2000)
gravity                 Run tomogravity estimation on complete time
                        series of aggregate flows
gravity.fit             Gravity estimation for a single time point
ipfp                    Function to run basic IPFP (iterative
                        proportional fitting procedure)
llCalibration           Evaluate marginal log-likelihood for
                        calibration SSM
locally_iid_EM          Run EM algorithm to obtain MLE for locally IID
                        model of Cao et al. (2000)
m_estep                 Compute conditional expectations for EM
                        algorithms of Cao et al. (2000)
mle_filter              Filtering & smoothing at MLE for calibration
                        SSM
move_step               Move step of sample-resample-move algorithm for
                        multilevel state-space model
obj.tomogravity         Objective function of Zhang et al. 2003
phi_init                Simple initialization for phi in model of Cao
                        et al. (2000)
smoothed_EM             Run EM algorithm to obtain MLE (single time)
                        for smoothed model of Cao et al. (2000)
strphour                Convert time string to decimal hour
thin                    Thinning vector of indices for MCMC
tomogravity             Run tomogravity estimation on complete time
                        series of aggregate flows
tomogravity.fit         Tomogravity estimation for a single time point
                        using L-BFGS-B
twMCMC                  Function to run MCMC sampling for model of
                        Tebaldi & West (1998)
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)
