We modified the function dist_make() to pass along
additional arguments to the distance function. This helps with distance
functions that take extra parameters. We removed the method
keyword argument from dist_make() because we found it not
to be useful in practice.
We added a new function, dist_multi_centroid(), to
produce a distance matrix between multiple centroid positions.
We fixed an error in dist_groups() that will pop up in
future versions of R. In R 4.0.0, the data.frame() function
will have a new default value, stringsAsFactors = FALSE.
This update caused one column in the output from
dist_groups() to change from a factor to a character
vector, which broke one of our tests. We updated the code to
deliberately make this column a factor. The function’s behavior will be
preserved when R 4.0.0 is released.
We’ve made two major updates for this release.
The centroid functions have gained a keyword argument,
squared. The final step in computing distance to group
centroids involves taking a square root. Sometimes, we end up with a
negative number inside the square root. Normally, this produces
NaN as a result. However, if squared is set to
TRUE, we don’t take the square root and the result is
always a real number. The default setting is
squared = FALSE, which gives the distance as you’d expect.
Thanks to Sam Ross for helpful advice on this topic.
We added a new function, pivot_to_numeric_matrix(). This
function takes a data frame in long format and converts to a matrix
suitable for distance calculations. Long-format data frames are commonly
used with functions in the tidyverse, and proper conversion
to a matrix requires a few non-obvious steps. The packages
dplyr, tidyr, and tibble are
needed to run the function, and have been added as suggested packages
for usedist.
During development, we had implemented an additional function to
create a distance matrix directly from a data frame in long format.
However, we found that it was nearly as convenient to use
pivot_to_numeric_matrix() and dist_make()
together to achieve the same result. We added an example to the README
file to illustrate this.
Initial release!
For the first release, we’ve moved over all the distance
matrix-related functions from the qiimer package. Utility
functions dist_setNames and dist_make were
added to the existing functions dist_subset,
dist_get, and dist_groups.
The other area of focus for our initial release was a set of distance-to-centroid functions. These functions operate on a set of items that are placed into several groups, and they apply algebraic formulas to find the group centroid distances based on the distance matrix. If you had a set of points in normal Euclidean space, you could easily find the centroid positions and compute the distances from there. The centroid functions included in the package are more useful for non-Euclidean distances, where it is less straightforward to locate the centroids in space. The centroid functions were inspired by work in microbial ecology, where it is typical to work with non-Euclidean distances between samples.