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tidydr 0.0.7

• nk() can now use any clustering method through fun (2026-10-08, Thu)
  • fun defaults to cluster::pam, so the default result is bit-for-bit unchanged
  • stats::kmeans works out of the box; stats::hclust is cut with cutree()
  • a function returning a plain vector of cluster labels is also accepted
  • for non-pam clusterers the silhouette width is computed with cluster::silhouette() and assembled into the same shape pam() produces
• silinfo_widths() exports the fine-grained silhouette widths of one k (2026-10-08, Thu)
  • returns a data.frame with sample, cluster, neighbor and sil_width
  • the per-cluster averages are attached as the "clus.avg.widths" attribute
• autoplot() for a silinfo object gained a silhouette bar plot (2026-10-08, Thu)
  • type = "silhouette" draws the classic per-cluster bar plot
  • type is inferred from k when it is not given, so autoplot(x) is unchanged and autoplot(x, k = 3) still draws the same plot — except that the sample labels are now correct (see the fix below)
  • fixed: autoplot(x, k = ) aligned pam()’s silhouette table to the samples by position, but pam() returns that table sorted by cluster; the labels are now matched by sample name (agreement with the true clustering on iris, k = 3, goes from 84% to 100%)
• added dr_compare() to run several dimensionality reduction methods at once (2026-10-08, Thu)
  • every method is evaluated independently: a method that fails is reported in $summary with its error message instead of aborting the whole call
  • $summary gives method, status, n, k, has_eigenvalue, has_stress and error, so it is visible which methods ran and which did not
  • autoplot() facets the methods that produced plottable coordinates
• DrResult gained a sample_info slot for method-specific, per-sample information (2026-10-08, Thu)
  • a dr_extract() method may return sample_info; fortify() merges its length-n elements into the returned data.frame as columns
  • print() output is unchanged
• the methods advertised by available_methods() are now backed by tests (2026-10-08, Thu)
  • all 14 advertised methods are exercised end-to-end through dr()
  • vegan, smacof, ecodist, ade4, labdsv added to Suggests, together with ape, MASS, Rtsne and uwot, which the tests already used
• available_methods("all") prints its closing note once instead of twice (2026-10-08, Thu)
  • the note is shared by the data and the distance listing but was printed from both branches, so it appeared twice; it is now printed once, after both listings
  • the "data" and "distance" branches are unchanged, and the returned value is unaffected
• dr() now validates its data input and fails early with a tidydr-specific message instead of forwarding an obscure error from the underlying method (2026-10-08, Thu)
  • rejects NULL, bare vectors (hint: use as.dist() for distance vectors), non-numeric data, data.frames with non-numeric columns, and NA/NaN/Inf
  • dist objects remain supported
• nk() now validates data and k (2026-10-08, Thu)
  • k = 1 is rejected: the silhouette width is undefined for a single cluster (previously produced an object that could not be printed)
  • k >= n, non-integer and non-numeric k are rejected with clear messages
  • data may still be a numeric matrix, a numeric data.frame, or a ‘dist’ object
• fortify() no longer mishandles metadata (2026-10-08, Thu)
  • matrix metadata is no longer silently dropped (converted to a data.frame)
  • a list of length n no longer creates n junk .group.* columns
  • atomic vectors (including classed ones such as Date) are used as .group
  • unsupported types raise a warning listing the supported types
• added a dr_extract() fallback for plain numeric matrices (2026-10-08, Thu)
  • makes stats::cmdscale() (and any wrapped method returning a bare matrix) work
  • any function returning a numeric matrix with at least two columns is accepted
  • non-numeric or single-column matrices are rejected
• a hand-written dr_extract() method may return the coordinates as a numeric matrix (2026-10-08, Thu)
  • previously rejected with “length of ‘dimnames’ [2] not equal to array extent”: the Dim1, Dim2, … names were assigned with seq_along(), which counts elements rather than columns on a matrix
  • the matrix is now converted to a data.frame, so fortify() – a ‘ggplot2’ generic – always returns a data.frame
  • a drdata that is neither a data.frame nor a numeric matrix is now rejected with a message pointing at ?dr_extract, instead of a cryptic error
• added a GitHub Actions workflow that runs R CMD check on push and PR (2026-10-08, Thu)

tidydr 0.0.6

• S3 method consistency with ggplot2 (v=4.0.0) (2025-06-21, Sat, #4)
• nk() for choose k (number of clusters) (2023-03-17, Fri)
  • output is a silinfo object with print(), summary() and autoplot() methods

tidydr 0.0.5

• autoplot method for SingleCellExperiment object (2022-11-01, Tue)

tidydr 0.0.4

• added available_methods() to show available DR methods (2022-3-15, Tue)
• update dr_extract to support methods work for distance objects (2022-3-14, Mon)
  • uwot::umap()
  • uwot::tumap()
  • uwot::lvish()
• fixed the error: mapping is missing with no default (2022-3-14, Mon)

tidydr 0.0.3

• update Rd files with return value (2021-12-08, Wed)
• use theme_minimal() as base theme in theme_dr() (2021-12-07, Tue)

tidydr 0.0.2

• add vignette (2021-12-07, Tue)
• print() method for DrResult
• support metadata in fortify(), ggplot() and autoplot()
• update dr_extract to support methods work for distance objects (2021-12-5, Sun)
  • stats::cmdscale
  • MASS::sammon
  • vegan::metaMDS
  • ape::pcoa
  • smacof::mds
  • vegan::wcmdscale
  • ecodist::pco
  • labdsv::pco
  • ade4::dudi.pco
• add new slots eigenvalue and stress to the DrResult class

tidydr 0.0.1

• theme_dr() that add shorten version of x and y axis
• theme_noaxis() to remove axis elements
• autoplot() to plot dr() output
• extend ggplot() to support dr() output
• dr() to unify dimension reduction result
  • supports stats::prcomp and Rtsne::Rtsne
• DrResult class
  • data: original data
  • drdata: Dr result, i.e., point coordinations
  • .call: function call

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