News

princurve 2.1.3 (2018-09-10)

• Removed extra dependencies in princurve by removing vignettes; fixes #28.

• Fully deprecated principal.curve() function.

princurve 2.1.2 (2018-07-24)

• DOCUMENTATION: Use the magick package to generate animated GIFs in the vignette, instead of the animation package, because animation uses ffmpeg which is not installed on all CRAN systems.

• DEPRECATION: Added deprecation which will be triggered starting from 2018-08-01 upon calling principal.curve() or get.lam().

princurve 2.1.1 (2018-07-23)

• DOCUMENTATION: Added vignettes on the algorithm behind princurve and on benchmarking results between princurve 1.1 and 2.1.

• BUG FIX principal_curve(): Don't apply rownames to curve as approx_points could be set to a different value other than nrow(x).

• TESTING: Skip comparison unit test between princurve 1.1 and 2.1 on CRAN.

• MINOR CHANGE project_to_curve(): Attempt to fix rchk warnings by not using x(i, j) = v notation but instead x[j * x.nrow() + i] = v.

• DOCUMENTATION: Fix in README documentation.

princurve 2.1.0 (2018-07-14)

• BUG FIX principal_curve(): avoid division by zero when the initial principal curve has already converged.

• BUG FIX project_to_curve(): set dimension names of outputted s correctly.

• DOCUMENTATION: Added cran-comments.md and revdep to repository.

• MINOR CHANGE: Removed adjust_range(); use grDevices::extendrange() instead.

• TESTING start_circle(): Added unit tests.

• BUG FIX start_circle(): Make sure circle is centered and scaled correctly.

• MINOR CHANGE: Move smoother functions from inside principal_curve() to a list smoother_functions.

• TESTING smoother_functions: Added tests to ensure each of the smoother functions work correctly.

• SPEED UP project_to_curve(): Significantly speed up this function by not allocation objects that don't need allocation, and pre-allocating objects that do.

• SPEED UP principal_curve(): Added approx_points parameter. This allows approximation of the curve between smoothing and projection, to ensure principal_curve() scales well to higher numbers of samples.

princurve 2.0.4 (2018-07-09)

• BUG FIX: Fixed issues with legacy principal.curve() and get.lam() (#8).

• TESTING: Perform direct comparison between the current princurve and princurve 1.1-12 to check whether principal.curve() and get.lam() produce output with exactly the same format and almost exactly the same values.

• SIGNIFICANT CHANGE: Remove the ord parameter from project_to_curve(), in order to reduce the amount of Rcpp code a little bit.

• DOCUMENTATION: Improved citations (#10).

• DOCUMENTATION: Improved news (#11).

• SPEED UP project_to_curve(): Do not compute lambda accurately as it is only used to order the points in x.

• MINOR CHANGE: Added ... argument to whiskers().

• DOCUMENTATION: Minor fix in output documentation of principal_curve().

• DOCUMENTATION: Added more information to the README.

• MINOR CHANGE: Support both news() and markdown news on GitHub.

princurve 2.0.3 (2018-07-04)

• SIGNIFICANT CHANGES: Reimplemented project_to_curve() completely in Rcpp, thereby completely removing all Fortran code from princurve.

• TESTING: test both on linux and osx.

• TESTING: Added tests to ensure project_to_curve() works similar to legacy get.lam().

princurve 2.0.2 (2018-06-12)

• MAINTAINER: Changed the maintainer from Andreas Weingessel to Robrecht Cannoodt.

• SIGNIFICANT CHANGES: Added functions principal_curve() and project_to_curve() with a slightly different interface than principal.curve() and get.lam().

• DEPRECATION: Prepare get.lam() and principal.curve() for deprecation planned on 2018-07-01. Will contact maintainers of reverse depending packages.

• BUG FIX: Allow start_circle() to work when the number of dimensions is larger than 2.

• DOCUMENTATION: Rewrite the README in markdown.

• DOCUMENTATION: Use roxygen2 for the documentation.

• MINOR CHANGES: Clean up code to ensure consistent code formatting.

• TESTING: Added tests for principal_curve() and project_to_curve().

• TESTING: Enabled continuous integration using https://travis-ci.org/dynverse/princurve and https://ci.appveyor.com/project/dynverse/princurve.

princurve 1.1-12 (2013-04-25)

• BUG FIX: src/sortdi.f (sortdi): Fix Fortran array bounds problem.

princurve 1.1-11 (2011-09-18)

• MINOR CHANGES: Update for R 2.0.

• DEPRECATION: Removed whiskers()

princurve 1.1-10 (2009-10-04)

• BENCHMARKING: For larger data sets, most of the time is spent in get.lam().

• BUG FIX: smooth.spline(x,y) will only use and return values for "unique" {x}:s. This means that the fitted {y}:s maybe be fewer than the input vector. In order to control for this, we use predict().

• NEW FEATURE: Now smoother can also be a function taking arguments lambda, xj and ... and return y of the same length as lambda and xj.

• NEW FEATURE principal.curve(): Arguments start and stretch can be NULL, which behaves the same as if they are "missing" [which is hard to emulate with for instance do.call()].

• NEW FEATURE: Added converged and nbrOfIterations to return structure.

• SPEED UP/MEMORY OPTIMIZATION: Now the nxp matrix 's' is allocated only once. Before it was built up using cbind() once per iteration.

• SPEED UP: Now the smoother function is identified/created before starting the algorithm, and not once per dimension and iteration.

• MEMORY OPTIMISATION principal.curve(): Now the result matrix allocated as doubles, not logicals (as NA is), in order to prevent a coersion.

• BUG FIX: An error was thrown if smoother was a function.

• MINOR CHANGES: Cleaned up source code (removed comments).

princurve 1.1-9 (2007-07-12)

• MINOR CHANGE: Clarify license.

princurve 1.1-8 (2006-10-04)

• MINOR CHANGE: Update license and add depending packages.

princurve 1.1-7 (2004-11-04)

• MINOR CHANGE: Depend on R >= 1.9.0

• MINOR CHANGE: Changed license to GPL version 2 or newer, as granted by Trevor Hastie.

• MINOR CHANGE: Don't require defunct modreg.

princurve 1.1-6 (2004-01-31)

• MINOR CHANGE: Removed INDEX.

princurve 1.1-5 (2002-07-03)

• MINOR CHANGE: Added PACKAGE to Fortran calls.

princurve 1.1-4 (2002-07-02)

• MINOR CHANGES: Change all T to TRUE.

princurve 1.1-2 (2001-06-10)

• MINOR CHANGE plot.principal.curve(): Rename argument object to x.

• MINOR CHANGE lines.principal.curve(): Rename argument object to x.

• MINOR CHANGE points.principal.curve(): Rename argument object to x.

• MINOR CHANGE: Rename internal functionstart.circle() to startCircle().

princurve 1.1-0 (2000-12-27)

• DESCRIPTION: Added Title and Maintainer field.

• MINOR CHANGES: Changed F to FALSE.

• DOCUMENTATION: Added keywords to get.lam().

• DOCUMENTATION: Expanded documentation of principal.curve(): added default values to usage, description, keywords and aliases.

• MINOR CHANGES: Changed precision in getlam.f from v(2,10) to v(2,p).

Reference manual