CRAN release 0.1.15

New features

• New function: optimize_graph_layout. Use this to produce optimized output coordinates that
  reflect an input similarity graph (such as that produced by the similarity_graph function.
  similarity_graph followed by optimize_graph_layout is the same as running umap, so the
  purpose of these functions is to allow for more flexibility and decoupling between generating the
  nearest neighbor graph and optimizing the low-dimensional approximation to it. Based on a request
  by user Chengwei94 (#98).
• New functions: simplicial_set_union and simplicial_set_intersect. These allow for the
  combination of different fuzzy graph representations of a dataset into a single fuzzy graph using
  the UMAP simplicial set operations. Based on a request in the Python UMAP issues tracker by user
  Dhar xion.
• New parameter for umap_transform: ret_extra. This works like the equivalent parameter for
  umap, and should be a character vector specifying the extra information you would like returned
  in addition to the embedding, in which case a list will be returned with an embedding member
  containing the optimized coordinates. Supported values are "fgraph", "nn", "sigma" and
  "localr". Based on a request by user PedroMilanezAlmeida (#104).
• New parameter from umap, tumap and umap_transform: seed. This will do the equivalent of
  calling set.seed internally, and hence will help with reproducibility. The chosen seed is
  exported if ret_model = TRUE and umap_transform will use that seed if present, so you only
  need to specify it in umap_transform if you want to change the seed. The default behavior remains
  to not modify the random number state. Based on a request by
  SuhasSrinivasan (#110).

Bug fixes and minor improvements

• A new setting for init_sdev: set init_sdev = "range" and initial coordinates will be
  range-scaled so each column takes values between 0-10. This pre-processing was added to the Python
  UMAP package at some point after uwot began development and so should probably always be used
  with the default init = "spectral" setting. However, it is not set by default to maintain
  backwards compatibility with older versions of uwot.
• ret_extra = c("sigma") is now supported by lvish. The Gaussian bandwidths are returned in a
  sigma vector. In addition, a vector of intrinsic dimensionalities estimated for each point using
  an analytical expression of the finite difference method given by
  Lee and co-workers is returned in the dint vector.
• The min_dist and spread parameters are now returned in the model when umap is run with
  ret_model = TRUE. This is just for documentation purposes, these values are not used directly by
  the model in umap_transform. If the parameters a and b are set directly when invoking umap,
  then both min_dist and spread will be set to NULL in the returned model. This feature was
  added in response to a question from kjiang18 (#95).
• Some new checks for NA values in input data have been added. Also a warning will be emitted if
  n_components seems to have been set too high.
• If n_components was greater than n_neighbors then umap_transform would crash the R session.
  Thank you to ChVav for reporting this (#102).
• Using umap_transform with a model where dens_scale was set could cause a segmentation fault,
  destroying the session. Even if it didn't it could give an entirely artifactual "ring" structure.
  Thank you FemkeSmit for reporting this and providing
  assistance in diagnosing the underlying cause (#103).
• If you set binary_edge_weights = TRUE, this setting was not exported when ret_model = TRUE,
  and was therefore not respected by umap_transform. This has now been fixed, but you will need to
  regenerate any models that used binary edge weights.
• The rdoc for the init param said that if there were multiple disconnected components, a
  spectral initialization would attempt to merge multiple sub-graphs. Not true: actually, spectral
  initialization is abandoned in favor of PCA. The documentation has been updated to reflect the true
  state of affairs. No idea what I was thinking of there.
• load_model and save_model didn't work on Windows 7 due to how the version of tar there
  handles drive letters. Thank you mytarmail for the report (#109).
• Warn if the initial coordinates have a very large scale (a standard deviation > 10.0), because
  this can lead to small gradients and poor optimization. Thank you SuhasSrinivasan for the
  report (#110).
• A change to accommodate a forthcoming version of RcppAnnoy. Thank you Dirk Eddelbuettel for
  the PR (#111).
• A test was failing on Arm architectures. Problem has been "solved" by removing the test, but it
  was testing a floating point value resulting from a failure due to numerical issues, so it's a bit
  of a corner case. Thank you Lucas Kanashiro for reporting (#100).