Package **roahd** (**RO**bust **A**nalysis of **H**igh dimensional **D**ata) is an `R`

package meant to gather recently proposed statistical methods to deal with the robust analysis of functional data (Francesca Ieva et al. 2019).

The package contains an implementation of quantitative methods, based on functional depths and indices, on top of which are built some graphical methods (functional boxplot and outliergram) useful to carry out an explorative analysis of a functional dataset and to robustify it by discarding shape and magnitude outliers.

Both univariate and multivariate functional data are supported in the package, whose functions have been implemented with a particular emphasis on computational efficiency, in order to allow the processing of high-dimensional dataset.

The package has been designed to work with a representation of functional data through dedicated, simple and handy `S3`

classes, namely `fData`

for univariate functional data and `mfData`

for multivariate functional data.

The use of `S3`

classes is exploited by suitable `S3`

methods implementing the statistical features of the package, that are able to dispatch the correct method call depending on the class of their functional data argument.

`S3`

class `fData`

implements a representation of univariate functional datasets. They are obtained once specifying, for each observation in the functional dataset, a set of measurements over a discrete grid, representing the dependent variable indexing the functional dataset (e.g. time).

In other words, if we denote by \(T = [t_0, t_1, \ldots, t_{P-1}]\) an evenly spaced grid (\(t_i - t_{i-1} = h > 0\)), and imagine to deal with a dataset \(D_{i,j} = X_i(t_j)\), \(\forall i = 1, \ldots, N\) and \(\forall j=0, \ldots, P-1\), the object `fData`

is built starting from the grid and the values in the following way:

```
library( roahd )
# The number of observations in the functional dataset.
= 5
N # The number of points in the 1D grid where the functional data are measured.
= 1e2
P # The previous two variable names are used consistently throughout the tutorial
# and the package's documentation to indicate the number of observations and the
# grid size.
# The grid over which the functional dataset is defined
= seq( 0, 1, length.out = P )
grid
# Creating the values of the functional dataset
= matrix( c( sin( 2 * pi * grid ),
Data cos( 2 * pi * grid ),
4 * grid * ( 1 - grid ),
tan( grid ),
log( grid ) ),
nrow = N, ncol = P, byrow = TRUE )
# Building an fData object
# The constructor takes a grid and a matrix-like structure for data values
# (see help for more details on how to use the constructor)
= fData( grid, Data )
fD
# Inspecting the structure of an fData object
str( fD )
```

```
## List of 6
## $ t0 : num 0
## $ tP : num 1
## $ h : num 0.0101
## $ P : int 100
## $ N : int 5
## $ values: num [1:5, 1:100] 0 1 0 0 -Inf ...
## - attr(*, "class")= chr "fData"
```

`plot( fD, main = 'Univariate FD', xlab = 'time [s]', ylab = 'values', lwd = 2 )`

Thus, an object `fData`

is a list containing: the fields `t0`

, `tP`

, defining the starting and end point of the one dimensional grid of the `fData`

object, the constant step size `h`

and the number of grid points `P`

and the field `values`

defining the measurements of the dataset over the one dimensional grid.

An `mfData`

object, instead, implements a multivariate functional dataset, i.e. a collection of functions having more than one components, each one depending on the same variable. In practice, we deal with a discrete grid \([t_0, t_1, \ldots, t_{P-1}]\) and a dataset of \(N\) elements, each one having \(L\) components observed over the same discrete grid: \(D_{i,j,k} = X_{i,k}(t_{j})\), \(\forall i = 1, \ldots, N\), \(\forall j = 0, \ldots, P - 1\) and \(\forall k = 1, \ldots, L\).

```
# Creating some values for first component of the dataset
= t( sapply( runif( 10, 0, 4 ),
Data_1 function( phase ) sin( 2 * pi * grid + phase ) ) )
# Creating some values of functions for
= t( sapply( runif( 10, 0, 4 ),
Data_2 function( phase ) log( grid + phase ) ) )
# Building an fData object
# The constructor takes a grid and a list of matrix-like structures for data values,
# each one representing the data values of a single component of the dataset
# (i.e. D_{,,k}, k = 1, ... L ).
# (see help for more details on how to use the constructor)
= mfData( grid, list( Data_1, Data_2 ) )
mfD
str( mfD )
```

```
## List of 6
## $ N : int 10
## $ L : int 2
## $ P : int 100
## $ t0 : num 0
## $ tP : num 1
## $ fDList:List of 2
## ..$ :List of 6
## .. ..$ t0 : num 0
## .. ..$ tP : num 1
## .. ..$ h : num 0.0101
## .. ..$ P : int 100
## .. ..$ N : int 10
## .. ..$ values: num [1:10, 1:100] 0.852 0.843 0.172 0.374 0.881 ...
## .. ..- attr(*, "class")= chr "fData"
## ..$ :List of 6
## .. ..$ t0 : num 0
## .. ..$ tP : num 1
## .. ..$ h : num 0.0101
## .. ..$ P : int 100
## .. ..$ N : int 10
## .. ..$ values: num [1:10, 1:100] 0.32 -0.117 0.421 1.013 -0.581 ...
## .. ..- attr(*, "class")= chr "fData"
## - attr(*, "class")= chr "mfData"
```

```
# Each component of the mfData object is an fData object
sapply( mfD$fDList, class )
```

`## [1] "fData" "fData"`

```
plot( mfD, lwd = 2, main = 'Multivariate FD',
xlab = 'time', ylab = list( 'Values 1', 'Values 2' ))
```

The fact that `mfData`

components are `fData`

objects is indeed conceptually very natural, but also allows for a seamless application of `S3`

methods meant for `fData`

on multivariate functional data components, making the exploration and manipulation of multivariate datasets rather easy:

```
plot( mfD$fDList[[ 1 ]], main = 'First component',
xlab = 'time', ylab = 'Values', lwd = 2 )
```

Moreover, `mfData`

objects can be obtained also from a set of homogeneous `fData`

objects, i.e. of equal sample size and defined on the same grid:

```
= fData( grid, Data_1 )
fD_1
= fData( grid, Data_2 )
fD_2
= as.mfData( list( fD_1, fD_2 ) )
mfD
= as.mfData( lapply( 1 : 10, function( i )( fD_1 ) ) ) mfD
```

`fData`

objects can be subset using a suitably overloaded operator `[.fData`

, that allows for the use of standard slices of `matrix`

and `array`

classes also for `fData`

.

```
# Subsetting fData and returning result in matrix form
1 , 1, as_fData = FALSE ]
fD[
1, , as_fData = FALSE ]
fD[
2, 10 : 20, as_fData = FALSE ]
fD[
10, as_fData = FALSE ]
fD[ ,
# As default behavior the subset is returned in fData form
<- par(mfrow = c(1, 1))
oldpar par(mfrow = c(1, 2))
plot(fD, main = "Original dataset", lwd = 2)
plot(fD[, 1:20], main = "Zooming in", lwd = 2)
par(oldpar)
```

An algebra of `fData`

objects is also implemented, making it easy to sum, subtract, multiply and divide these objects by meaningful and compliant structures.

**Sums** and **subtractions**, available through `+`

and `-`

operators (see help at `+-.fData`

), allow to sum an `fData`

on the left hand side and a compliant structure on the right hand side. This can be either another `fData`

of the same sample size and defined over the same grid, or a 1D/2D data structure with a number of columns equal `fData`

’s grid length (i.e. `P`

), and number of rows equal to `fData`

’s sample size (i.e. `N`

) or equal to one (in this case the only observation available is recycled `N`

times). The operations are then performed element-wise between the lhs and rhs.

```
+ fD
fD
+ matrix( 1, nrow = N, ncol = P )
fD
+ array( 2, dim = c( N, P ) )
fD
+ 1 : P fD
```

**Multiplication** and **division**, instead, is implemented only for an `fData`

left hand side and a numeric variable or numeric vector right hand side. In the first case, each function in the functional dataset is multiplied/divided by the specified quantity; in the second case, specifying a vector of length `N`

, the multiplication/division of each functional observation is carried out by the corresponding quantity in the vector, in an element-wise way:

```
* 2
fD
/ 3
fD
* ( 1 : N )
fD
/ ( 1 : N ) fD
```

`fData`

and `mfData`

objects can be visualized thanks to specific `S3`

plotting methods, `plot.fData`

and `plot.mfData`

.

The graphical parameters of these functions have been suitably customized in order to enhance the visualization of functions. In particular, elements are plotted by default with continuous lines and an ad-hoc palette that helps differentiating them. As default x- and y-axis labels, as well as titles, are dropped so that plot’s arguments calls are not displayed when no value is provided.

In case of `mfData`

the graphical window is split into a rectangular lattice to plot single dimensions. The rectangular frame has `floor( sqrt( L ) )`

rows and `ceiling( x$L / floor( sqrt( x$L ) ) )`

columns. If custom labels/titles are desired, they must be provided in the following way: since the grid is the same for all the dimensions, just one string is expected for x-axis (e.g. `xlab = 'grid'`

), while either a single string or a list of `L`

strings (one for each dimension) is expected for both the y-axis label(s) and title(s). In case just one string is passed to `plot.mfData`

, the same value is used for all the dimensions.

`roahd`

provides a number of depth definitions, that are exploited by the visualization functions but can also be used by themselves. These are based on the notion of **Band Depth** (López-Pintado and Romo 2007, 2009).

**Band Depth** and **Modified Band Depth** are implemented in the functions `BD`

and `MBD`

. Both of them can work with either an `fData`

object, specifying the univariate functional dataset whose depths must be computed, or a matrix of data values (e.g. in the form of `fData$values`

output). `MBD`

can be called with the additional parameters `manage_ties`

(defaulting to `FALSE`

), specifying whether a check for the presence of tied data must be made prior to computing depths, and therefore a suitable computing strategy must be used. The implementation of `MBD`

exploits the recommendations of (Sun, Genton, and Nychka 2012), but extends them in order to accommodate for the possible presence of ties.

```
BD( fD )
BD( fD$values )
MBD( fD )
MBD( fD$values )
MBD( fD, manage_ties = TRUE )
MBD( fD$values, manage_ties = TRUE )
```

Another definition available is the **Half Region Depth** (along with its modified version), that is built on top of the **Epigraph** and **Hypograph** indexes (see López-Pintado and Romo 2011):

```
HRD( fD )
HRD( fD$values )
MHRD( fD )
MHRD( fD$values )
```

A generalization of MBD to multivariate functional data, implementing the ideas of F. Ieva and Paganoni (2013), is also available through the functions `multiBD`

and `multiMBD`

. These functions accept either a `mfData`

object, specifying the multivariate functional dataset whose depths have to be computed, or a list of matrices of data values (see example below).

The function computes the BD or MBD for each component of the multivariate functional dataset and then averages them according to a set of weights. These can be specified in two ways: either with the flag `uniform`

, that is turned into `rep( 1/L, L )`

(where `L`

stands for the number of components in the multivariate dataset), or by providing the actual set of weights to be used. The latter option allows to use ad-hoc set of weights, like in (Tarabelloni et al. 2015).

```
multiBD( mfD, weights = 'uniform' )
multiMBD( mfD, weights = 'uniform', manage_ties = FALSE )
multiBD( mfD, weights = c( 0.6, 0.4) )
multiMBD( mfD, weights = c( 0.7, 0.3 ), manage_ties = FALSE )
multiBD( list( fD_1$values, fD_2$values ), weights = c( 0.6, 0.4) )
multiMBD( list( fD_1$values, fD_2$values ), weights = c( 0.7, 0.3 ), manage_ties = FALSE )
```

Suitable `S3`

extensions to the functions for the computation of mean function and median of functional datasets are also present.

The sample mean of a functional dataset coincides with the *cross-sectional* mean function, i.e. the function obtained by computing the mean across the whole dataset point-by-point along the grid where functional data are defined:

\[ \widehat{\mu}( t_j ) = \dfrac{1}{N} \sum_{i=1}^{N} X_i(t_j), \qquad \forall j = 0, \ldots, P-1 \]

for a univariate functional dataset, while in the multivariate case is:

\[ \widehat{\mu}_k(t_j) = \dfrac{1}{N} \sum_{i=1}^{N} X_{i,k}(t_j), \qquad \forall j = 0, \ldots, P-1, \qquad \forall k = 1, \ldots, L. \]

The sample median of a functional dataset, instead, is defined as the element of the functional dataset fulfilling the maximum depths, given a certain definition of depth. For instance, for MBD:

\[ \widehat{m}( t_j ) = \left(\text{arg}\max_{i=1, \ldots, N} MBD( X_i )\right)( t_j), \qquad j = 0, \ldots, P-1. \]

The sample mean is implemented in the `S3`

methods `mean.fData( x, ... )`

and `mean.mfData( x, ... )`

, that can be invoked directly on `fData`

and `mfData`

objects. These methods can be called directly without the `.fData`

or `.mfData`

suffix, due to their `S3`

nature and call, that allows them to be dispatched from the standard `mean`

function. The sample median, instead, is implemented in the functions `median_fData( fData, type = 'MBD', ... )`

and `median_mfData( mfData, type = 'multiMBD', ... )`

. Here, the `type`

flag can take any name of functions (available in the caller’s environment) that can be used to compute the depths defining the sample median, taking respectively a 2D matrix of data values and a list of 2D matrix of data values as argument (plus, optionally, the dots arguments).

```
# Exploiting the S3 nature of these functions and the dispatching from the
# standard `mean` function
mean( fD )
mean( mfD)
median_fData( fD, type = 'MBD' )
median_fData( fD, type = 'MHRD' )
<- par(mfrow = c(1, 1))
oldpar par(mfrow = c(1, 2))
plot(fD, main = "Mean", lwd = 2)
plot(mean(fD), add = TRUE, lwd = 2, col = "black", lty = 2)
plot(fD, main = "Median", lwd = 2)
plot(median_fData(fD, type = "MBD"), add = TRUE, lwd = 2, lty = 2, col = "black")
par(oldpar)
```

The computation of covariance functions and cross-covariance functions for univariate and multivariate functional datasets is provided through the function `cov_fun( X, Y = NULL )`

.

Given a univariate functional dataset, \(X_1, X_2, \ldots, X_N\), defined over the grid \([t_0, t_1, \ldots, t_P] \subset I\), its covariance function (evaluated over the grid) is \(C(t_i,t_j) = Cov(X(t_i),X(t_j))\) for \(i,j=1,\ldots,P\). Given another univariate functional dataset \(Y_1, Y_2, \ldots, Y_N\), the cross-covariance function is \(C_{X,Y}(t_i,t_j) = Cov(X(t_i),Y(t_j))\).

Given a multivariate functional dataset with observations of \(L\) components, \(X_1, X_2,\ldots, X_N\), the covariance function has the following block structure: \(C^{k,l} = [ Cov(X_k(t_i),X_l(t_j))]_{i,j=1}^{P}\), for \(k,l = 1, \ldots, L\). Of course, it is \(C^{k,l} = [C^{l,k}]^T\). Analogously, the cross-covariance between two multivariate datasets is given by the cross covariances of the components.

When `X`

is a univariate functional dataset, and if `Y`

is `NULL`

, `cov_fun`

returns the sample covariance function of the functional dataset, defined over the tensorized grid where `X`

is defined. If `Y`

is a univariate functional dataset (in form of `fData`

object), the method returns the cross-covariance function of `X`

and `Y`

.

When `X`

is a multivariate dataset, `Y`

can be `NULL`

, an `fData`

or a `mfData`

object. In the first case the method returns the covariance function of `X`

, in form of a list of *only* the upper-triangular blocks. The blocks are sorted in the list by row, therefore the first is the covariance of the first component, then the cross-covariance of the first component with the second, etc. In the second case, the method returns the list of cross-covariances between `X`

’s components and `Y`

. In the third case, the method returns the list of upper-triangular blocks of cross-covariances between `X`

’s and `Y`

’s components.

```
# Simple covariance function
= cov_fun( fD )
C1
# Cross-covariance function of first and second component of mfD
= cov_fun( mfD$fDList[[1]], mfD$fDList[[2]] )
CC
# Block-covariance function of mfD
= cov_fun( mfD ) BC
```

Each covariance function estimate (the elements of the list in the multivariate case, too) is returned as an instance of the `S3`

class `Cov`

, that stores the values of the covariance matrix as well as the grid parameters.

`plot.Cov`

, an `S3`

specialization of `plot`

is available as plotting method for `Cov`

objects. It is built around `graphics::image`

, hence all the additional parameters of `image`

can be used to customize it.

`plot( C1, main = 'Covariance function', xlab = 'time', ylab = 'time' ) `

`roahd`

collects the implementation of some useful indexes that can be used to describe and summarize functional datasets.

`EI`

and `MEI`

implement the **Epigraph Index** and the **Modified Epigraph Index**, while `HI`

and `MHI`

implement the **Hypograph Index** and the **Modified Hypograph Index** (see López-Pintado and Romo 2011; Arribas-Gil and Romo 2014). These indexes can be used to sort data in a top-down and bottom-up fashion, and are used to define the HRD/MHRD and to build the outliergram.

These `S3`

methods can be called on univariate functional datasets, provided either in form of a `fData`

object or a 2D matrix of values.

```
# Calling on fData objects
EI( fD )
MEI( fD )
HI( fD )
MHI( fD )
# Calling on 2D matrix type objects
EI( fD$values )
EI( matrix( rnorm( 20 ), nrow = 4, ncol = 5 ) )
```

When dealing with multivariate functional data, in particular in case of **bivariate** data, it is possible to compute correlation coefficients between data components that generalize the Kendall’s tau and Spearman’s coefficients (Valencia, Romo, and Lillo 2015a, 2015b).

The function `cor_kendall( mfD, ordering = 'max' )`

allows to compute the Kendall’s tau correlation coefficient between components of a bivariate dataset. The function accepts a `mfData`

object and a criterion to perform the ordering of functional data (this ordering is used to determine the concordances and discordances between pairs in the definition of the coefficient).

Two criteria are available so far, that directly reflect those proposed in the reference paper: `max`

, for the ordering between maxima of functions, and `area`

, for the ordering between area-under-the-curve of functions.

```
= 10
N = 1e3
P
= seq( 0, 1, length.out = P )
grid
= t( sapply( 1 : N, function( i )( sin( 2 * pi * grid ) + i ) ) )
Data_1
# Monotone nonlinear transformation of data
= Data_1^3
Data_2
= mfData( grid, list( Data_1, Data_2 ) )
mfD
plot( mfD, main = list( 'Comp. 1', 'Comp. 2') )
```

```
# Kendall correlation of monotonically dependent data is exactly 1
cor_kendall( mfD, ordering = 'max' )
```

`## [1] 1`

`cor_kendall( mfD, ordering = 'area' ) `

`## [1] 1`

The function `cor_spearman( mfD, ordering = 'MEI', ... )`

can be used to compute the Spearman correlation coefficient for a bivariate `mfData`

object, tuning the ordering policy specified by `ordering`

(defaulting to `MEI`

) to rank univariate components and then compute the correlation coefficient. Besides `MEI`

, also `MHI`

can be used to rank univariate components.

```
# Spearman correlation of monotonically dependent data is exactly 1
cor_spearman( mfD, ordering = 'MEI' )
## [1] 1
cor_spearman( mfD, ordering = 'MHI' )
## [1] 1
```

`roahd`

contains also some functions that can be used to simulate artificial data sets of functional data, both univariate and multivariate. These are used in the adjustment procedure of the outliergram and functional boxplot, but can also be used to help the development of new methodologies and help their testing.

Artificial univariate data are obtained simulating realizations of a gaussian process over a discrete grid with a specific covariance function and center (e.g. mean or median). Given a covariance function, \(C(s,t)\) and a centerline \(m(t)\), the model generating data is: \[X_i(t) = m(t) + \epsilon(t), \quad Cov(\epsilon(s),\epsilon(t)) = C(s,t), \quad i = 1, \ldots, N.\]

The function `generate_gauss_fdata(N, centerline, Cov = NULL, CholCov = NULL)`

can be used to simulate a population of such gaussian functional data. The required arguments are: `N`

the number of elements to be generated; `centerline`

, the center of the distribution (mean or median); `Cov`

, a matrix representation of the desired covariance function, intended as the measurements of such function over a tensor grid whose marginal must be the grid where the functional data will be defined (i.e. the argument `grid`

in `fData`

); `CholCov`

the Cholesky factor of the discrete representation of the covariance function over the tensor grid (optional and alternative to the argument `Cov`

). The inner procedure to generate the synthetic population of gaussian functional data makes use of the Cholesky factor of `Cov`

, hence by providing its Cholesky factor, if already present in the caller’s scope, can save computing time.

A built-in function can be used to generate exponential-like covariance functions, namely `exp_cov_function( grid, alpha, beta )`

, generating the discretized version of a covariance of the form \(C(s,t) = \alpha e^{-\beta | s - t | }\) over a lattice given by the tensorization of grid in `grid`

.

A comprehensive example is the following:

```
= 50
N = 1e3
P
= seq( 0, 1, length.out = P )
grid
= exp_cov_function( grid, alpha = 0.2, beta = 0.3 )
Cov
= generate_gauss_fdata( N, centerline = sin( 2 * pi * grid ), Cov = Cov )
Data
= fData( grid, Data )
fD
plot( fD, main = 'Gaussian fData', xlab = 'grid', lwd = 2)
```

The function `generate_gauss_mfdata( N, L, centerline, correlations, listCov = NULL, listCholCov = NULL)`

can be used to generate a gaussian dataset of multivariate functional data. The model generating data is the following:

\[ X_{i,k} = m_k(t) + \epsilon_k(t), \quad Cov(\epsilon_k(s),\epsilon_k(t))=C(s,t), \quad \forall i = 1, \ldots, N, \quad \forall k = 1, \ldots, L,\]

where \(Cor( \epsilon_j(t),\epsilon_l(t))=\rho_{j,l}\) specifies a (*synchronous*) correlation structure among the components of the functional dataset.

In order to use the function one should provide: `N`

, the number of elements to simulate; `L`

, the number of components of the multivariate functional data; `centerline`

, a matrix containing (by rows) the centerline for each component; `correlations`

, a vector of length `1/2 * L * ( L - 1 )`

, containing all the correlation coefficients among the components; either `listCov`

or `listCholCov`

, a list containing either the discretized covariance functions over the tensorized grid where functional data will be defined), or their Cholesky factor.

A comprehensive example is the following:

```
= 10
N = 1e3
P
= seq( 0, 1, length.out = P )
grid
= exp_cov_function( grid, alpha = 0.1, beta = 0.5 )
Cov_1 = exp_cov_function( grid, alpha = 0.5, beta = 0.1)
Cov_2
= matrix( c( sin( 2 * pi * grid ),
centerline cos( 2 * pi * grid ) ), nrow = 2, byrow = TRUE )
= generate_gauss_mfdata( N, 2, centerline, 0.8, list( Cov, Cov ) )
Data
= mfData( grid, Data )
mfD
plot( mfD, main = list( 'Comp.1', 'Comp. 2'), xlab = 'grid', lwd = 2)
```

An implementation of the functional boxplot, through the `S3`

method `fbplot`

, allows for the detection of *amplitude* outliers in univariate and multivariate functional datasets (see Sun and Genton 2011).

`fbplot`

can be used to compute the set of indices of observations marking outlying signals. If used in graphical way (default behavior), it also plots the functional boxplot of the dataset under study

The functional boxplot is obtained by ranking functions from the center of the distribution outwards thanks to a depth definition, computing the region of 50% most central functions and inflating such region by a factor `F`

. Any function crossing these boundaries is flagged as outlier. The default value for `F`

is `1.5`

, otherwise it can be set with the argument `Fvalue`

.

The argument `Depths`

can take either the name of the function to call in order to compute the depths (default is `MBD`

), or a vector containing the depth values for the provided dataset.

An example is:

```
set.seed(1618)
= 1e2
N = 1e2
P
= seq( 0, 1, length.out = P )
grid
= exp_cov_function( grid, alpha = 0.2, beta = 0.3 )
Cov
= generate_gauss_fdata( N, sin( 2 * pi * grid ), Cov )
Data
= fData( grid, Data )
fD
= generate_gauss_mfdata( N, 2, matrix( sin( 2 * pi * grid ), nrow = 2, ncol = P, byrow = TRUE ), 0.6, listCov = list( Cov, Cov ) )
Data
= mfData( grid, Data )
mfD
fbplot( fD, main = 'Fbplot', Fvalue = 3.5 )
```

`fbplot( mfD, main = list( 'Comp. 1', 'Comp. 2' ), Fvalue = 3.5 ) `