An overview of lax

The CRAN Task View on Extreme Value Analysis provides information about R packages that perform various extreme value analyses. The lax package supplements the functionality of nine of these packages, namely eva (Bader and Yan 2020), evd (Stephenson 2002), evir (Pfaff and McNeil 2018), extRemes (Gilleland and Katz 2016), fExtremes (Wuertz, Setz, and Yohan Chalabi 2017), ismev (Heffernan and Stephenson 2018), mev (Belzile et al. 2019), POT (Ribatet and Dutang 2016) and texmex (Southworth, Heffernan, and Metcalfe 2017). Univariate extreme value models, including regression models, are supported.

The chandwich package is used to provide robust sandwich estimation of parameter covariance matrix and loglikelihood adjustment for models fitted by maximum likelihood estimation. This may be useful for cluster correlated data when interest lies in the parameters of the marginal distributions, or for performing inferences that are robust to certain types of model misspecification.

lax works in an object-oriented way, operating on R objects returned from functions in other packages that summarise the fit of an extreme value model. Loglikelihood adjustment and sandwich estimation is performed by an alogLik S3 method. We demonstrate this using the following running example, which involves fitting a Generalised Extreme Value (GEV) regression model. Firstly, we use the ismev package to produce the fitted GEV regression model object on which alogLik will operate, and illustrate what can be done with the objects returned from alogLik. We use the ismev package because it provides an example of a case where we need to refit the model in order to obtain the information that we need to perform adjusted inferences. Then we repeat the adjustment using seven of the other eight packages. The POT package specialises in Generalised Pareto (GP) modelling, for which we use a different example.

GEV regression of annual maximum temperatures

This example is based on the analysis presented in Section 5.2 of Chandler and Bate (2007). The data, which are available in the data frame ow, are a bivariate time series of annual maximum temperatures, recorded in degrees Fahrenheit, at Oxford and Worthing in England, for the period 1901 to 1980. If interest is only in the marginal distributions of high temperatures in Oxford and Worthing, then we might fit a GEV regression model in which some or all of the parameters may vary between Oxford and Worthing. However, we should adjust for the cluster dependence between temperatures recorded during the same year.

ismev

The gev.fit() function in ismev fits GEV regression models. It allows covariate effects in any of the (location, scale and shape) parameters of the GEV distribution. However, an object returned from gev.fit() does not provide all the information about a fitted regression model that alogLik needs, in order to calculate loglikelihood contributions from individual observations: the design matrices are missing. Therefore, lax provides the function gev_refit, which is a version of gev.fit that adds this information.

The following code fits a GEV regression model in which the location, scale and shape parameters of the GEV distribution vary between Oxford and Worthing. Then alogLik is used to provide adjusted standard errors and an adjusted loglikelihood.

library(lax)
# Column 4 of ow contains 1 for Oxford and -1 for Worthing
large <- gev_refit(ow$temp, ow, mul = 4, sigl = 4, shl = 4, show = FALSE,
                   method = "BFGS")
# Adjust the loglikelihood and standard errors
adj_large <- alogLik(large, cluster = ow$year, cadjust = FALSE)
# MLEs, SEs and adjusted SEs
t(summary(adj_large))
#>             loc locloc  scale scaleloc    shape shapeloc
#> MLE     81.1700 2.6690 3.7290   0.5312 -0.19890 -0.08835
#> SE       0.3282 0.3282 0.2292   0.2292  0.04937  0.04937
#> adj. SE  0.4036 0.2128 0.2425   0.1911  0.03944  0.03625

This reproduces the values in rows 1, 3 and 4 in Table 2 of Chandler and Bate (2007). The estimation of the ‘meat’ of the sandwich adjustment is performed using the sandwich package. In this example, we need to pass cadjust = FALSE to sandwich::meatCL in order that the adjustment is the same as that used in Chandler and Bate (2007). Otherwise, meatCL makes a finite-cluster bias correction.

Confidence intervals

A confint method calculates approximate (95%) confidence intervals for the parameters, based on the adjusted loglikelihood. Chandler and Bate (2007) consider three types of loglikelihood adjustment: one vertical and two horizontal. The type of adjustment is selected by the argument type. The default is type = "vertical" and there is an option to perform no adjustment.

confint(adj_large)
#> Waiting for profiling to be done...
#>               2.5 %     97.5 %
#> loc      80.3729001 81.9602100
#> locloc    2.2437419  3.0831279
#> scale     3.2991896  4.2598984
#> scaleloc  0.1611912  0.9433844
#> shape    -0.2741177 -0.1157069
#> shapeloc -0.1652089 -0.0200268
confint(adj_large, type = "none")
#> Waiting for profiling to be done...
#>                2.5 %       97.5 %
#> loc      80.52440863 81.813160870
#> locloc    2.01969229  3.308352990
#> scale     3.32435238  4.236272757
#> scaleloc  0.09100223  1.020139218
#> shape    -0.28957175 -0.094326264
#> shapeloc -0.18850187  0.008628523

Confidence regions

The conf_region function in the chandwich package can be used to produce confidence regions for pairs of parameters. Here, we consider the ‘central’ (midway between Oxford and Worthing) scale and shape intercept parameters: \(\sigma_0\) and \(\xi_0\) in Chandler and Bate (2007).

library(chandwich)
which_pars <- c("scale", "shape")
gev_none <- conf_region(adj_large, which_pars = which_pars, type = "none")
#> Waiting for profiling to be done...
gev_vertical <- conf_region(adj_large, which_pars = which_pars)
#> Waiting for profiling to be done...
plot(gev_none, gev_vertical, lwd = 2, xlim = c(3.1, 4.5), ylim = c(-0.35, -0.05),
     xlab = expression(sigma[0]), ylab = expression(xi[0]))

Comparing nested models

alogLik also has an anova method, which can be used to perform (adjusted) loglikelihood ratio tests of nested models. To illustrate this we fit, and adjust, a smaller model, in which Oxford and Worthing have a common GEV shape parameter, and then compare this model to the larger one.

small <- gev_refit(ow$temp, ow, mul = 4, sigl = 4, show = FALSE, 
                   method = "BFGS")
adj_small <- alogLik(small, cluster = ow$year, cadjust = FALSE)
summary(adj_small)
#>              MLE     SE adj. SE
#> loc      81.1200 0.3260 0.40640
#> locloc    2.4540 0.3047 0.20370
#> scale     3.7230 0.2232 0.24020
#> scaleloc  0.3537 0.2096 0.16840
#> shape    -0.1845 0.0488 0.04028
anova(adj_large, adj_small)
#> Analysis of (Adjusted) Deviance Table
#> 
#>           Model.Df Df  ALRTS Pr(>ALRTS)  
#> adj_large        6                       
#> adj_small        5  1 6.3572    0.01169 *
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(adj_large, adj_small, type = "none")
#> Analysis of (Adjusted) Deviance Table
#> 
#>           Model.Df Df  ALRTS Pr(>ALRTS)  
#> adj_large        6                       
#> adj_small        5  1 3.1876     0.0742 .
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

We see that the adjustment of the loglikelihood for clustering makes enough of a difference to matter: if we perform a test at the 5% significance level then we choose the larger model when we adjust but the smaller model if we do not.

texmex

library(texmex, quietly = TRUE)
# Note: phi = log(scale)
evm_fit <- evm(temp, ow, gev, mu = ~ loc, phi = ~ loc, xi = ~loc)
adj_evm_fit <- alogLik(evm_fit, cluster = ow$year)
summary(adj_evm_fit)
#>                       MLE      SE adj. SE
#> mu: (Intercept)  81.17000 0.32820 0.40620
#> mu: loc           2.66800 0.32820 0.21420
#> phi: (Intercept)  1.30600 0.06091 0.06531
#> phi: loc          0.14330 0.06091 0.05106
#> xi: (Intercept)  -0.19900 0.04937 0.03968
#> xi: loc          -0.08821 0.04937 0.03647

evd

The fgev() function in evd fits GEV regression models, but it only allows covariate effects in the location parameter.

library(evd, quietly = TRUE)
fgev_fit <- fgev(ow$temp, nsloc = ow[, "loc"])
adj_fgev_fit <- alogLik(fgev_fit, cluster = ow$year)
summary(adj_fgev_fit)
#>              MLE      SE adj. SE
#> loc      81.1600 0.32980 0.40830
#> loctrend  2.5040 0.31080 0.19910
#> scale     3.7900 0.22810 0.25230
#> shape    -0.2097 0.04765 0.04063

extRemes

library(extRemes, quietly = TRUE)
fevd_fit <- fevd(temp, ow, location.fun = ~ ow$loc, scale.fun = ~ ow$loc,
                 shape.fun = ~ ow$loc)
adj_fevd_fit <- alogLik(fevd_fit, cluster = ow$year)
summary(adj_fevd_fit)
#>             MLE      SE adj. SE
#> mu0    81.17000 0.32820 0.40620
#> mu1     2.66800 0.32820 0.21420
#> sigma0  3.72900 0.22930 0.24410
#> sigma1  0.53090 0.22930 0.19230
#> xi0    -0.19890 0.04938 0.03969
#> xi1    -0.08828 0.04938 0.03648

eva

library(eva, quietly = TRUE)
gevr_fit <- gevrFit(ow$temp, information = "observed",
                    locvars = ow, locform = ~ ow$loc, 
                    scalevars = ow, scaleform = ~ ow$loc,
                    shapevars = ow, shapeform = ~ ow$loc)
adj_gevr_fit <- alogLik(gevr_fit, cluster = ow$year)
summary(adj_gevr_fit)
#>                          MLE      SE adj. SE
#> Location (Intercept) 81.1700 0.32810 0.40620
#> Location ow$loc       2.6680 0.32810 0.21420
#> Scale (Intercept)     3.7290 0.22920 0.24400
#> Scale ow$loc          0.5307 0.22920 0.19230
#> Shape (Intercept)    -0.1989 0.04936 0.03968
#> Shape ow$loc         -0.0882 0.04936 0.03647

evir

The gev() function in evir only fits stationary GEV models.

library(evir, quietly = TRUE)
gev_fit <- gev(ow$temp)
adj_gev_fit <- alogLik(gev_fit)
summary(adj_gev_fit)
#>           MLE      SE adj. SE
#> xi    -0.1801 0.06051  0.0509
#> sigma  4.3980 0.28180  0.2558
#> mu    80.7800 0.39240  0.4128

fExtremes

The gevFit() function in fExtremes only fits stationary GEV models.

library(fExtremes, quietly = TRUE)
gevFit_fit <- gevFit(ow$temp)
adj_gevFit_fit <- alogLik(gevFit_fit)
summary(adj_gevFit_fit)
#>          MLE      SE adj. SE
#> xi   -0.1802 0.06047 0.05087
#> mu   80.7900 0.39240 0.41290
#> beta  4.3980 0.28170 0.25570

mev

The fit.gev() function in mev only fits stationary GEV models.

library(mev, quietly = TRUE)
gfit <- fit.gev(ow$temp)
adj_gfit <- alogLik(gfit)
summary(adj_gfit)
#>           MLE     SE adj. SE
#> loc   80.7800 0.3924 0.41290
#> scale  4.3980 0.2818 0.25580
#> shape -0.1801 0.0605 0.05089

POT

Among other things, the fitgpd() function in the POT package can fit a GP distribution to threshold excesses using maximum likelihood estimation. We illustrate alogLik using an example from the fitgpd documentation. There is no cluster dependence here. However, there may be interest in using a sandwich estimator of covariance if we are concerned about model misspecification. In this case, where we simulate from the correct model, we expect the adjustment to make little difference, and so it proves.

library(POT, quietly = TRUE)
set.seed(24082019)
x <- POT::rgpd(200, 1, 2, 0.25)
fit <- fitgpd(x, 1, "mle")
adj_fit <- alogLik(fit)
summary(adj_fit)
#>          MLE      SE adj. SE
#> scale 1.8670 0.20930 0.19260
#> shape 0.2573 0.08887 0.07121

References

Bader, B., and J. Yan. 2020. Eva: Extreme Value Analysis with Goodness-of-Fit Testing. https://CRAN.R-project.org/package=eva.

Belzile, L., J. L. Wadsworth, P. J. Northrop, S. D. Grimshaw, and R. Huser. 2019. mev: Multivariate Extreme Value Distributions. https://github.com/lbelzile/mev/.

Chandler, R. E., and S. Bate. 2007. “Inference for Clustered Data Using the Independence Loglikelihood.” Biometrika 94 (1): 167–83. https://doi.org/10.1093/biomet/asm015.

Gilleland, E., and R. W. Katz. 2016. “extRemes 2.0: An Extreme Value Analysis Package in R.” Journal of Statistical Software 72 (8): 1–39. https://doi.org/10.18637/jss.v072.i08.

Heffernan, J. E., and A. G. Stephenson. 2018. ismev: An Introduction to Statistical Modeling of Extreme Values. https://CRAN.R-project.org/package=ismev.

Pfaff, B., and A. McNeil. 2018. evir: Extreme Values in r. https://CRAN.R-project.org/package=evir.

Ribatet, M., and C. Dutang. 2016. POT: Generalized Pareto Distribution and Peaks over Threshold. https://CRAN.R-project.org/package=POT.

Southworth, H., J. E. Heffernan, and P. D. Metcalfe. 2017. texmex: Statistical Modelling of Extreme Values. https://CRAN.R-project.org/package=texmex.

Stephenson, A. G. 2002. “evd: Extreme Value Distributions.” R News 2 (2): 0. https://CRAN.R-project.org/doc/Rnews/.

Wuertz, D., T. Setz, and Y. Yohan Chalabi. 2017. fExtremes: Rmetrics - Modelling Extreme Events in Finance. https://CRAN.R-project.org/package=fExtremes.