The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

Application to flight data

1 The dataset

library(graphicalExtremes)
library(ggplot2)
library(igraph)

C:4cd061984267.R

The flights dataset contains daily total delays of major U.S. airlines. For details, see the corresponding documentation page. Below, we plot all airports in the dataset.

plotFlights(plotConnections = FALSE, map = "world", xyRatio = 2)

C:4cd061984267.R

To perform an example application, we follow Section 6 of Hentschel et al. (2022). The subset of airports analyzed there is obtained through a previous clustering step, whose results are available through the function getFlightDelayData(). For more detailed explanations of the individual methods see Vignette “applicationDanube” and the help pages of applied functions. Note: Due to size restrictions, the CRAN version of this package contains only a part of the full dataset. A version of this package with the complete dataset is available on GitHub.

# Get IATAs from Texas cluster
IATAs <- getFlightDelayData('IATAs', 'tcCluster')

# Plot airports + connections (indicating number of flights by thickness)
plotFlights(
    IATAs,
    useAirportNFlights = TRUE,
    useConnectionNFlights = TRUE
)

C:4cd061984267.R

For hyperparameter tuning and model comparison purposes, we will use a train-test-split, utilizing some data to estimate the graph structure and parameter matrix, and the remaining data to compute a likelihood value.

# Check whether all dates from the train-test-split are available
# (due to size restrictions, the CRAN version of this package does not contain all dates)
allDatesAvailable <- tryCatch({
    getFlightDelayData('dates', dateFilter = c('tcAll'))
    TRUE
}, error = function(...) FALSE)
cat('All dates avilable:', allDatesAvailable, '\n')
#> All dates avilable: FALSE

# Create train and test data sets
if(allDatesAvailable){
    # Use train-test-split and threshold p from article
    matEst <- drop(getFlightDelayData('delays', 'tcCluster', 'tcTrain'))
    matVal <- drop(getFlightDelayData('delays', 'tcCluster', 'tcTest'))
    p <- 0.95
} else {
    # Take all available dates that do not contain NAs
    mat <- drop(getFlightDelayData('delays', 'tcCluster', 'all'))
    rowHasNA <- apply(is.na(mat), 1, any)
    mat <- mat[!rowHasNA, ]
    
    # Split dates in half
    splitInd <- floor(nrow(mat)/2)
    matEst <- mat[1:splitInd,]
    matVal <- mat[(splitInd+1):nrow(mat),]
    
    # Use a lower threshold to compensate for the smaller dataset
    p <- 0.8
}

C:4cd061984267.R

This function will be used later to compare fitted parameters to empirical ones.

# Compute the empirical extremal correlation matrix
emp_chi_mat <- emp_chi(matEst, p = p)

# Utility function to plot fitted parameters against true/empirical ones
plot_fitted_params <- function(G0, G1, xlab = 'Empirical', ylab = 'Fitted'){
    return(
        ggplot()
        + geom_point(aes(
            x = G0[upper.tri(G0)],
            y = G1[upper.tri(G1)]
        ))
        + geom_abline(slope = 1, intercept = 0)
        + xlab(xlab)
        + ylab(ylab)
    )
}

C:4cd061984267.R

2 Fitting a model to the flight graph

As a baseline for graphical modelling, we consider the graph with edges representing at least monthly connections between airports.

# Compute undirected flights per connection between selected airports
nYears <- dim(flights$flightCounts)[3]
flightsPerConnection <- apply(flights$flightCounts[IATAs,IATAs,], c(1, 2), sum)
flightsPerConnectionUD <- flightsPerConnection + t(flightsPerConnection)

# Make flight graph from adjacency matrix
A <- 1 * (flightsPerConnectionUD > nYears * 12)
flight_graph <- graph_from_adjacency_matrix(A, diag = FALSE, mode = "undirected")

# Plot flight graph
plotFlights(IATAs, graph = flight_graph, clipMap = 1.3, xyRatio = 1)

C:4cd061984267.R

Given the flight_graph object, we fit a Hüsler–Reiss model with that graphical structure.

# Fit the model
model_fit <- fmpareto_graph_HR(
    data = matEst,
    graph = flight_graph,
    p = p,
    method = "vario"
)

# Compute likelihood/ICs
flights_loglik_graph <- loglik_HR(
    data = matVal,
    p = p,
    graph = flight_graph,
    Gamma = model_fit
)
cat("Flight graph test-loglikelihood =", round(flights_loglik_graph['loglik'], 2), "\n")
#> Flight graph test-loglikelihood = -7831.91

# Plot fitted parameters
plot_fitted_params(emp_chi_mat, Gamma2chi(model_fit))

C:4cd061984267.R

3 Fitting a tree model

Next, we fit an extremal tree model to the flight delays using emst().

# Fit the model
flights_emst_fit <- emst(data = matEst, p = p, method = "vario")

# Compute likelihood/ICs
flights_loglik_tree <- loglik_HR(
    data = matVal,
    p = p,
    Gamma = flights_emst_fit$Gamma,
    graph = flights_emst_fit$graph
)
cat("Tree test-loglikelihood =", round(flights_loglik_tree['likelihood'], 2), "\n")
#> Tree test-loglikelihood = NA

# Plot fitted graph, parameters
plotFlights(
    IATAs,
    graph = flights_emst_fit$graph,
    xyRatio = 1,
    clipMap = 1.3
)
plot_fitted_params(emp_chi_mat, Gamma2chi(flights_emst_fit$Gamma))

C:4cd061984267.R

4 Fitting a general model

Lastly, we fit a general graphical model with eglearn(), using a suitable list of penalization parameters.

# Fit the model
rholist <- seq(0, 0.50, length.out = 11)
flights_eglearn_fit <- eglearn(matEst, p = p, rholist = rholist, complete_Gamma = TRUE)

# Compute likelihood/ICs
flights_loglik <- sapply(seq_along(rholist), FUN = function(j) {
    loglik_HR(
        data = matVal,
        p = p,
        Gamma = flights_eglearn_fit$Gamma[[j]],
        graph = flights_eglearn_fit$graph[[j]]
    )
})

C:4cd061984267.R

The “best” penalization parameter can be chosen e.g. such that the test-likelihood is maximized

ggplot(
    mapping = aes(x = rholist, y = flights_loglik['loglik', ])) +
    geom_line() +
    geom_point(shape = 21, size = 3, stroke = 1, fill = "white") +
    geom_hline(aes(yintercept = flights_loglik_graph['loglik']), lty = "dashed") +
    geom_hline(aes(yintercept = flights_loglik_tree['loglik']), lty = "dotted") +
    xlab("rho") +
    ylab("Log-likelihood") +
    scale_x_continuous(
        breaks = rholist,
        labels = round(rholist, 3),
        sec.axis = sec_axis(
            trans = ~., breaks = rholist,
            labels = sapply(
                flights_eglearn_fit$graph,
                igraph::gsize
            ),
            name = "Number of edges"
        )
)


best_index <- which.max(flights_loglik['loglik',])
cat('Best rho =', rholist[best_index], '\n')
#> Best rho = 0.1
cat('Corresponding test-loglikelihood =', flights_loglik['loglik', best_index])
#> Corresponding test-loglikelihood = -7263.573

C:4cd061984267.R

We plot the estimated graph and parameters of the best fitted model.

best_graph <- flights_eglearn_fit$graph[[best_index]]
best_Gamma <- flights_eglearn_fit$Gamma[[best_index]]
plotFlights(IATAs, graph = best_graph, clipMap = 1.3, xyRatio = 1)
plot_fitted_params(emp_chi_mat, Gamma2chi(best_Gamma))

C:4cd061984267.R

References

Hentschel, M., Engelke, S., and Segers, J. (2022). Statistical inference for Hüsler-Reiss graphical models through matrix completions. arXiv. https://doi.org/10.48550/ARXIV.2210.14292

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.