- the
`distance()`

function receives a new argument`mute.message`

allowing users to mute message printing when running large-scale distance computations. Example:

- adding
`markdown`

dependency to`DESCRIPTION`

(find details here)

the

`distance()`

function receives a new argument`use.row.names`

to enable passing the row names from the input probability or count matrix to the output distance matrixthe

`distance()`

function can now handle`data.table`

and`tibble`

input #16adding new functionality and arguments

`as.dist.obj`

,`diag`

, and`upper`

to`philentropy::distance()`

to allow users to retrieve a`stats::dist()`

object when working with`philentropy::distance()`

(Many thanks to Hugo Tavares #18 - see also #13) When using`philentropy::distance(..., as.dist.obj = TRUE)`

users can now directly pass the`distance()`

output into`hclust`

:

Before:

```
ProbMatrix <- rbind(1:10/sum(1:10), 20:29/sum(20:29),30:39/sum(30:39))
dist.mat <- distance(ProbMatrix, method = "jaccard")
true.dist.mat <- as.dist(dist.mat)
clust.res <- hclust(true.dist.mat, method = "complete")
clust.res
```

```
Call:
hclust(d = true.dist.mat, method = "complete")
Cluster method : complete
Number of objects: 3
```

Now:

```
ProbMatrix <- rbind(1:10/sum(1:10), 20:29/sum(20:29),30:39/sum(30:39))
dist.mat <- distance(ProbMatrix, method = "jaccard", as.dist.obj = TRUE)
clust.res <- hclust(true.dist.mat, method = "complete")
clust.res
```

```
Call:
hclust(d = true.dist.mat, method = "complete")
Cluster method : complete
Number of objects: 3
```

- fixing a bug in
`gJSD()`

which tested transposed matrix rows rather than transposed matrix columns for sum > 1 (see issue #17 ; many thanks to @wkc1986)

- exporting all Rcpp distance measure functions individually (see issue #9), this enables access to much faster computations (see micro benchmarks at https://hajkd.github.io/philentropy/articles/Distances.html)

fixing bug which caused that KL distance returns NaN when P == 0 (see issue #10; Many thanks to @KaiserDominici)

fixing bug which caused stack overflow when computing distance matrices with many rows (see issue #7; Many thanks to @wkc1986 and @elbamos)

fixing bug in

`gJSD()`

where an`rbind()`

input matrix is not properly transposed (Many thanks to @vrodriguezf; see issue #14)

`gJSD()`

receives new argument`est.prob`

to enable empirical estimation of probability vectors from input count vectors (non-probabilistic vectors)Jaccard and Tanimoto similarity measures now return

`0`

instead of`NAN`

when probability vectors contain zeros (Many thanks to @JonasMandel; see issue #15)

- Fixing bug that caused
`jensen-shannon`

computations to compute wrong values when`0 values`

were present in the input vectors (see issue #4 ; Many thanks to @wkc1986) - Fixing bug that caused
`jensen-difference`

computations to compute wrong values when`0 values`

were present in the input vectors - Fixing bugs in all distance metrics when handing 0/0, 0/x or x/0 cases

- new message system
- extending documentation

- Fixing bug that caused that
`JSD()`

gives NaN when any probability is 0 - see https://github.com/HajkD/philentropy/issues/1 (Thanks to William Kurtis Chang)

- Fixing C++ memory leaks in
`dist.diversity()`

and`distance()`

when check for`colSums(x) > 1.001`

was peformed (leak was found with`rhub::check_with_valgrind()`

)

Initial submission version.