We use this vignette to reproduce the real world example for local
outlier detection analysed and described in Puchhammer and Filzmoser
(2023). All functions are included in the package
ssMRCD.
Data Preparation
The original data from GeoSphere Austria (2022) is pre-cleaned and
saved in the data frame object weatherAUt2021. Additional
information can be found on the helping page.
data("weatherAUT2021")
head(weatherAUT2021)
#> p s vv t rsum rel name lon lat alt
#> 1 941.35 154.5 2.15 6.15 49.5 77.5 AIGEN/ENNSTAL 14.13833 47.53278 641
#> 2 945.80 172.5 2.95 6.25 39.5 76.0 ALLENTSTEIG 15.36694 48.69083 599
#> 3 985.50 152.0 2.55 8.20 46.5 78.0 AMSTETTEN 14.89500 48.10889 266
#> 4 893.20 123.5 1.85 5.10 66.0 74.5 BAD GASTEIN 13.13333 47.11055 1092
#> 5 984.50 176.0 1.50 8.45 40.5 75.0 BAD GLEICHENBERG 15.90361 46.87222 269
#> 6 992.05 188.5 2.20 8.95 60.5 77.0 BAD RADKERSBURG 15.99333 46.69222 207
To apply the local outlier detection function
local_outliers_ssMRCD we need to specify a structure to
calculate the ssMRCD estimator, meaning we need a neighborhood
assignment and a weight matrix specifying the relative
influence of the neighborhoods on each.
Since a prominent part of Austria is Alpine landscape small sized
neighborhoods might be appropriate. Thus, we construct a grid of the
longitude and latitude values and classify the observations. We
summarize neighborhoods for a very small number of observations.
cut_lon = c(9:16, 18)
cut_lat = c(46, 47, 47.5, 48, 49)
N = ssMRCD::groups_gridbased(weatherAUT2021$lon, weatherAUT2021$lat, cut_lon, cut_lat)
table(N)
#> N
#> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
#> 6 1 1 12 1 1 9 5 9 3 1 8 6 7 8 12 6 5 9 5 7 7 17 7 9 21
N[N == 2] = 1
N[N == 3] = 4
N[N == 5] = 4
N[N == 6] = 7
N[N == 11] = 15
N = as.numeric(as.factor(N))
The final neighborhood structure can be seen in the following plot,
where the neighborhoods are differently colorized.
g1 = ggplot() +
geom_text(data = weatherAUT2021, aes(x = lon, y = lat, col = as.factor(N), label = N)) +
geom_hline(aes(yintercept = cut_lat), lty = "dashed", col = "gray") +
geom_vline(aes(xintercept = cut_lon), lty = "dashed", col = "gray") +
labs(x = "Longitude", y = "Latitude", title = "Austrian Weather Stations: Neighborhood Structure") +
coord_fixed(1.4) +
theme_classic() +
theme(legend.position = "none")
g1
A natural choice for the weight matrix when using a
grid-based neighborhood structure is the geographical inverse-distance
weighting matrix. It is the default value for the
local_outliers_ssMRCD function but can explicitly be
calculated using the function geo_weights. This function
returns also the center of each neighborhood. E.g. for neighborhood 4 we
have the following weights, corresponding to the transparancy of the
arrows.
GW = geo_weights(coordinates = weatherAUT2021[, c("lon", "lat")],
groups = N)
GW$W[4, ]
#> 1 2 3 4 5 6 7
#> 0.02554129 0.03265041 0.06004253 0.00000000 0.19041215 0.09170249 0.08164324
#> 8 9 10 11 12 13 14
#> 0.08849001 0.06215254 0.04767836 0.04370851 0.04285327 0.03754845 0.03340820
#> 15 16 17 18 19 20 21
#> 0.02547782 0.02752795 0.02472584 0.02375660 0.02127099 0.02047626 0.01893310
g1 +
labs(title = "Austrian Weather Stations: Weighting Matrix W") +
geom_segment(aes(x = GW$centersN[4, 1],
y = GW$centersN[4, 2],
xend = GW$centersN[-4, 1]-0.1,
yend = GW$centersN[-4, 2]-0.05,
alpha = GW$W[4, -4]),
arrow = arrow(length = unit(0.25, "cm")),
linewidth = 2,
col = "blue")+
geom_text(aes(x = GW$centersN[, 1], y = GW$centersN[, 2], label = 1:length(GW$centersN[, 2])))
Parameter Tuning
Regarding the parameter settings we have many possibilities. When it
comes to the number of neighbors we want to compare
each observations with there are different possibilities. Either by
specifying a value for k like k = 10 which
gives the number of observations to compare with or the value for
dist (e.g. dist = 1.5) as the radius of a
circle around the observation where all observations inside are compared
to the initial observation. A default value for k that is
used among various local outlier detection methods is 10. However,
depending on the spatial structure of the data it makes sense to use
other values as well.
For the spatial smoothing parameter
lambda the restriction is it has to be in the
interval [0, 1). One can set the values according to some argumentation
based on the spatial distribution but also on underlying structures. A
value of 0.5 is the default value.
A more sophisticated approach is to introduce outliers to the data
set and examine how well the parameter setting is able to find those.
The function parameter_tuning can be used to analyse
different combinations of k (or dist) and
lambda (see also help page).
Observations are switched and thus, this should introduce outliers
that we know of. Nevertheless you should keep in mind that the
observations are switched entirely randomly. If unlucky we might switch
similar observations and thus, the measured performance of the detection
method might suffer. However, since we want to compare the different
parameter settings on the same contaminated data sets this should not
affect the fine tuning itself.
Moreover, we implicitly assume that the original data set has no
outliers. This is in general not the case. Thus, the false-negative rate
(FNR) is not the true FNR regarding all outliers. Nevertheless, the
parameter tuning is a way to see the effects of the parameter setting on
the FNR and the false-positive rate (FPR) which is represented by the
total number of found outliers.
set.seed(123)
parameter_tuning(data = weatherAUT2021[, 1:6],
coords = weatherAUT2021[, c("lon", "lat")],
groups = N,
repetitions = 3,
k = c(5, 10, 15),
lambda = c(0, 0.25, 0.5, 0.75))$plot
It is apparent that some parameter settings are non-optimal compared
to others. In general the final choice of the best parameter setting
based on the output above depends on the overall goal. We choose
lambda = 0.5 and k = 10. Although
k = 10 is not the optimal choice here, the difference in
performance is quite small and thus, we prefer to use the default
value.
Outlier Detection and Covariance Estimation
If we are only interested in the covariance estimation we can use the
function ssMRCD. A more convenient way if we are interested
in local outlier detection is to use the function
local_outliers_ssMRCD, which already embeds the covariance
estimation.
res = local_outliers_ssMRCD(data = weatherAUT2021[, 1:6],
coords = weatherAUT2021[, c("lon", "lat")],
groups = N,
lambda = 0.5,
k = 10)
summary(res)
#> Local outliers: 11 of 183 observations (6.01%).
#> Used cut-off value: 14.50966.
#> Observations are compared to their k=10 neighbors.
The found outliers can be accessed by the list element
outliers.
cat(weatherAUT2021$name[res$outliers], sep = ",\n")
#> OBERGURGL,
#> RUDOLFSHUETTE,
#> SCHOECKL,
#> PATSCHERKOFEL,
#> FEUERKOGEL,
#> LOIBL/TUNNEL,
#> SONNBLICK (TAWES),
#> WIEN-JUBILAEUMSWARTE,
#> RAX/SEILBAHNBERGSTATION,
#> GALZIG,
#> VILLACHER ALPE
Diagnostics: Covariance Estimation
For the covariance estimation there are two diagnostic plots
implemented for the S3-object "ssMRCD", which can be
specified by type. For type "convergence" the
convergence property for this specific data set is shown. For
"ellipses"the estimated covariance matrices are shown in
the first two eigenvectors fo the overall data set. The
colour_scheme parameter yields even more insight into the
covariances (see also ?plot.ssMRCD for more details).
covariance_res = res$ssMRCD
plot(covariance_res,
centersN = res$centersN,
manual_rescale = 0.5,
type = c("convergence", "ellipses"),
colour_scheme = "regularity",
legend = TRUE,
xlim = c(9, 19))
For completeness the global biplot based on the global covariance
matrix is also plotted:
biplot(stats:: princomp(weatherAUT2021[, 1:6],
cor = TRUE,
covmat = robustbase::covMcd(weatherAUT2021[, 1:6])),
col = c("grey", "black"))
Diagnostics: Local Outlier Detection
For the local outlier detection method there are several plots
regarding diagnostics available (see ?plot.locOuts). The
histogram shows all next distances and the cut-off value. The spatial
plot shows the outliers on the map, the 3D-plot as well, but with an
additional axis for the next-distance/next-distance divided by cut-off
value. The line plot shows the scaled values and the specified area in
the map. Orange-coloured lines are other outliers on the map, the
darkred colored line is the selected observation
(focus).
plot(res, type = "hist", pos = 4)
plot(res, type = "spatial", colour = "outScore", xlim = c(9.5, 19))
# SCHOECKL
plot(res, type = "lines", focus = res$outliers[3])
plot(res, type = "3D", colour = "outScore", theta = 0, phi = 10)
If you want a fancy GIF you can also use the following code making
use of the package animation. You should have ImageMagick
installed.
library(animation)
# fineness of movement
n = 90
param = rbind(cbind(rep(0, 2*n + n/2), c(seq(90, 0, length.out = n), seq(0, 90, length.out = n), seq(90, 30, length.out = n/2))),
cbind(c(seq(0, 90, length.out = n), seq(90, 0, length.out = n)), rep(30, 2*n)),
cbind(rep(0, n/2), seq(30, 90, length.out = n/2)))
# use function saveGIF
saveGIF(interval = 0.2,
movie.name = "local_outliers_3D.gif",
expr = {
for (i in 1:dim(param)[1]) {
plot(outs, type = "3D", colour = "outScore", theta = param[i, 1], phi = param[i, 2])
}}
)