`distance()`

The `distance()`

function implemented in
`philentropy`

is able to compute 46 different
distances/similarities between probability density functions (see
`?philentropy::distance`

for details).

The `distance()`

function is implemented using the same
*logic* as R’s base function `stats::dist()`

and takes
a `matrix`

or `data.frame`

object as input. The
corresponding `matrix`

or `data.frame`

should
store probability density functions (as rows) for which distance
computations should be performed.

```
# define a probability density function P
P <- 1:10/sum(1:10)
# define a probability density function Q
Q <- 20:29/sum(20:29)
# combine P and Q as matrix object
x <- rbind(P,Q)
```

Please note that when defining a `matrix`

from vectors,
probability vectors should be combined as rows
(`rbind()`

).

```
library(philentropy)
# compute the Euclidean Distance with default parameters
distance(x, method = "euclidean")
```

```
euclidean
0.1280713
```

For this simple case you can compare the results with R’s base
function to compute the euclidean distance
`stats::dist()`

.

```
P
Q 0.1280713
```

However, the R base function `stats::dist()`

only computes
the following distance measures:
`"euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski"`

,
whereas `distance()`

allows you to choose from 46
distance/similarity measures and when selecting the native distance
functions underlying `distance()`

users can speed up their
computations 3-5x.

To find out which `method`

s are implemented in
`distance()`

you can consult the
`getDistMethods()`

function.

```
[1] "euclidean" "manhattan" "minkowski" "chebyshev"
[5] "sorensen" "gower" "soergel" "kulczynski_d"
[9] "canberra" "lorentzian" "intersection" "non-intersection"
[13] "wavehedges" "czekanowski" "motyka" "kulczynski_s"
[17] "tanimoto" "ruzicka" "inner_product" "harmonic_mean"
[21] "cosine" "hassebrook" "jaccard" "dice"
[25] "fidelity" "bhattacharyya" "hellinger" "matusita"
[29] "squared_chord" "squared_euclidean" "pearson" "neyman"
[33] "squared_chi" "prob_symm" "divergence" "clark"
[37] "additive_symm" "kullback-leibler" "jeffreys" "k_divergence"
[41] "topsoe" "jensen-shannon" "jensen_difference" "taneja"
[45] "kumar-johnson" "avg"
```

Now you can choose any distance/similarity `method`

that
serves you.

```
jaccard
0.133869
```

Analogously, in case a probability matrix is specified the following output is generated.

```
# combine three probabilty vectors to a probabilty matrix
ProbMatrix <- rbind(1:10/sum(1:10), 20:29/sum(20:29),30:39/sum(30:39))
rownames(ProbMatrix) <- paste0("Example", 1:3)
# compute the euclidean distance between all
# pairwise comparisons of probability vectors
distance(ProbMatrix, method = "euclidean")
```

```
#> Metric: 'euclidean'; comparing: 3 vectors.
v1 v2 v3
v1 0.0000000 0.12807130 0.13881717
v2 0.1280713 0.00000000 0.01074588
v3 0.1388172 0.01074588 0.00000000
```

Alternatively, users can specify the argument
`use.row.names = TRUE`

to maintain the rownames of the input
matrix and pass them as rownames and colnames to the output distance
matrix.

```
# compute the euclidean distance between all
# pairwise comparisons of probability vectors
distance(ProbMatrix, method = "euclidean", use.row.names = TRUE)
```

```
#> Metric: 'euclidean'; comparing: 3 vectors.
Example1 Example2 Example3
Example1 0.0000000 0.12807130 0.13881717
Example2 0.1280713 0.00000000 0.01074588
Example3 0.1388172 0.01074588 0.00000000
```

This output differs from the output of
`stats::dist()`

.

```
# compute the euclidean distance between all
# pairwise comparisons of probability vectors
# using stats::dist()
stats::dist(ProbMatrix, method = "euclidean")
```

```
1 2
2 0.12807130
3 0.13881717 0.01074588
```

Whereas `distance()`

returns a symmetric distance matrix,
`stats::dist()`

returns only one part of the symmetric
matrix.

However, users can also specify the argument
`as.dist.obj = TRUE`

in `philentropy::distance()`

to retrieve a `philentropy::distance()`

output which is an
object of type `stats::dist()`

.

```
ProbMatrix <- rbind(1:10/sum(1:10), 20:29/sum(20:29),30:39/sum(30:39))
rownames(ProbMatrix) <- paste0("test", 1:3)
distance(ProbMatrix, method = "euclidean", use.row.names = TRUE, as.dist.obj = TRUE)
```

```
Metric: 'euclidean'; comparing: 3 vectors.
test1 test2
test2 0.12807130
test3 0.13881717 0.01074588
```

Now let’s compare the run times of base R and
`philentropy`

. For this purpose you need to install the
`microbenchmark`

package.

Note: Please make sure to insert vector objects (in our example P, Q) when directly running the low-level functions such as

`euclidean()`

etc. Otherwise, computational overheads are produced that significantly slow down computations when using large vectors.

```
# install.packages("microbenchmark")
library(microbenchmark)
microbenchmark(
distance(x,method = "euclidean", test.na = FALSE),
dist(x,method = "euclidean"),
euclidean(P, Q, FALSE)
)
```

```
Unit: microseconds
expr min lq mean median uq max neval
distance(x, method = "euclidean", test.na = FALSE) 26.518 28.3495 29.73174 29.2210 30.1025 62.096 100
dist(x, method = "euclidean") 11.073 12.9375 14.65223 14.3340 15.1710 65.130 100
euclidean(P, Q, FALSE) 4.329 4.9605 5.72378 5.4815 6.1240 22.510 100
```

As you can see, although the `distance()`

function is
quite fast, the internal checks cause it to be 2x slower than the base
`dist()`

function (for the `euclidean`

example).
Nevertheless, in case you need to implement a faster version of the
corresponding distance measure you can type `philentropy::`

and then `TAB`

allowing you to select the base distance
computation functions (written in C++),
e.g. `philentropy::euclidean()`

which is almost 3x faster
than the base `dist()`

function.

The advantage of `distance()`

is that it implements 46
distance measures based on base C++ functions that can be accessed
individually by typing `philentropy::`

and then
`TAB`

. In future versions of `philentropy`

I will
optimize the `distance()`

function so that internal checks
for data type correctness and correct input data will take less
termination time than the base `dist()`

function.