NEWS

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transport 0.15-4 (2024-09-16)

OVERVIEW

• CRAN maintenance update. Replace ancient "Calloc"s by "R_Calloc"s (and so on). Remove WSGeometry from suggested packages as it is no longer on CRAN.

transport 0.15-3

OVERVIEW

• Works around a (very) rare infinite loop in the networkflow algorithm that seems to have to do with numerical precision by introducing a (generous) iteration limit and making the loop interruptible by the user.

transport 0.15-2 (2024-05-09)

OVERVIEW

• Bug fix. The function gen_cost0 introduced in the previous version was only designed for 2d scenarios. There is now another function gen_cost0d for the "single thread, more than 2d" case.

transport 0.15-1

OVERVIEW

• Dependence on R version >= 4.1 is now in DESCRIPTION. This R version was required before, but rather than being stated explicitly, installation failed with an obscure error. Reported by Chao Zhang [#1].
• Bug fix in internal function gen_cost used to compute distance matrices. For points at (almost) the same position negative entries of squared cost matrices were possible. Fixed.
• The computation of distance matrices is almost twice as fast now by use of a new internal function gen_cost0 when running functions in a single thread.

transport 0.15-0 (2024-03-26)

OVERVIEW

• unbalanced is now a generic function with methods for class pgrid (corresponding to the previous function unbalanced) and wpp (new functionality).
• plot.ubtrans has been replaced by plot.ut_grid and there is a new method plot.ut_wpp, where ut_grid and ut_wpp are (now) the classes of the outputs of the two unbalanced methods when setting output="all".

transport 0.14-8

OVERVIEW

• Bug fix in function unbalanced. The function returned zero even if only one of the measures was the zero measure (for p=1, after reduction).

transport 0.14-7 (2024-02-18)

OVERVIEW

• Maintenance update to fix a new note in CRAN checks.

transport 0.14-6 (2023-07-02)

OVERVIEW

• Skip new semidiscrete test on CRAN as the special configurations only give slightly perturbed results (which seem random in spite of the seed). Re-reduce the tolerance everywhere else.

transport 0.14-5

OVERVIEW

• Increase tolerance in new semidiscrete test. Previously, it failed for some of the more special configurations, in particular if there was no long double.

transport 0.14-4 (2023-06-25)

OVERVIEW

• Replace broken link.

transport 0.14-3

OVERVIEW

• Bug fix in src/Makevars. Object files in subfolders were not cleaned properly. This had no practical implications for the most usual installation procedures, but has been fixed now.

transport 0.14-2

OVERVIEW

• We thank Peter Jacobs for contributions.
• Bug fixes: The C code underlying the functions computing semidiscrete optimal transport for p=2 resulted in a segmentation fault for certain (not so rare) input combinations. Also there was a memory leak. Both are fixed.

transport 0.14-1 (2023-05-21)

OVERVIEW

• We thank Mauro Ferrante and Oskar Nenoff for contributions.
• Bug fix: The output of 'transport.default' with method="networkflow" was typically wrong if both mass vectors a and b had only one non-zero entry each.
• Bug fix: function 'unbalanced' with output="all" (and sometimes output="rawres") threw an error if one of a and b had only one non-zero entry.

transport 0.14-0

OVERVIEW

• Computation of semidiscrete optimal transport for p=1 did not work with newer versions of CGAL due to conflicting C++ standards. This appears to be fixed completely.
• The colors of the mass points in plots of semidiscrete optimal transport plans can now be controlled via a parameter pcol.

transport 0.13-2

OVERVIEW

• Important bug fix in the recently added function unbalanced. If p=1 and image a has more total mass than image b, then the returned solution was typically wrong if there are pixels with zero mass. In most cases this came with suspicious warning messages and the computed distance was still correct. Fixed.

transport 0.13-1

OVERVIEW

• Add WSGeometry to suggested packages.

transport 0.13-0 (2022-10-30)

OVERVIEW

• New function unbalanced for computing unbalanced transport (and unbalanced Wasserstein distance) between pgrids.
• New function plot.ubtrans for plotting the result from unbalanced.
• Resolves recent R CMD check warnings due to C function declarations without prototypes.

transport 0.12-5

OVERVIEW

• Bug fix: transport.pgrid with method "networkflow" and a non-square grid was typically wrong. Seems to be correct now.
• Bug fix: transport.pgrid with method "shielding" caused an error if the grid had fewer than 200 points in total (e.g. 14x14). Largely fixed (a problem may remain for very small grids (e.g. below 4x4), but this is clearly not an application case for the shielding method anyway).
• Bug fixes: some non-standard parameter combinations caused errors in the transport function. Fixed.
• pgrid.plot has a new option "angle" to make the heads of the arrows wider for very small transport problems

transport 0.12-4 (2022-08-12)

OVERVIEW

• Minor changes in the internal code for easier maintenance.
• Minor fixes in NEWS and man files to make the newest package check happy.

transport 0.12-3

OVERVIEW

• We thank Jiahua Chen, Michel Groppe and Heather Turner for contributions.
• Several bugs in connection with mass/weight vectors not being ordered or containing zeroes have been fixed.
• The function wasserstein1d is considerably faster now for large datasets.

SIGNIFICANT CHANGES

• Speed improvement for function wasserstein1d due to a more efficient counting procedure.

BUG FIXES

• Function wasserstein1d. In previous versions the result was typically wrong if locations were not ordered *and* varying weights were specified. Fixed.
• Function wasserstein1d. There was an uncaught error if one or several of the (inner) weights were zero. This is fixed and the function works with general non-negative weights (with positive sum) now.
• Function transport.default and wasserstein. For the default networkflow method the from and to indices in the returned transport plan referred to the vectors of positive entries in a and b (rather than the full vectors a and b). In particular this typically led to wrong distance computations in the function wasserstein if entries with mass 0 were present (the Wasserstein distance / cost returned by the function transport with option fullreturn = TRUE was correct). Fixed.
• Function transport.default. There was an uncaught error if in one of the vectors only one of the masses was non-zero. Fixed.

transport 0.12-2 (2020-03-11)

OVERVIEW

• We thank Christoph Weitkamp for contributions.
• Fixes a serious bug in the main transport function. For method = "networkflow" and mass vectors a, b containing zeroes, the results were typically wrong before.
• Function transport_track now uses argument fps (frames per second) instead of delay.time for generation of animated gifs. This argument is used consistently.

transport 0.12-1 (2019-08-19)

OVERVIEW

• Fixes a compilation error under Solaris.
• Returns to using a Makevars file instead of the configure script for the same openmp functionality as in the previous version.
• We thank Brian Ripley for pertinent hints on both.

transport 0.12-0 (2019-08-06)

OVERVIEW

• We thank Nicolas Bonneel for contributions.
• The main workhorse function transport has a new method "networkflow". This is currently the recommended method for solving the discrete optimal transport problems directly via a simplex algorithm (it is fastest unless special structure is known, e.g. p=2). The method is available for objects of classes pp, wpp, pgrid. The code is based on the modified version of the Lemon Library provided by Nicolas Bonneel. https://github.com/nbonneel/network_simplex
• A new configure script checks for openmp support at install time. If supported the installed version allows the user to run a multithreaded version of the "networkflow" method via a new argument "threads" in the appropriate transport functions.
• Fixes a bug in the transport.track function which could cause an error when trying to generate a gif using this function. Also adds some minor customization options to this function.

transport 0.11-2 (2019-07-06)

OVERVIEW

• We thank Luc Lehericy for contributions.
• A bug in the function transport.wpp was fixed which for strongly unbalanced weights created sometimes an infinite loop.

transport 0.11-1 (2019-04-17)

OVERVIEW

• We thank Samuel Ackerman for contributions.
• The functions subwasserstein and transport.pp are faster now. Depending on the example the speed increase can be very substantial.

SIGNIFICANT CHANGES

• Function subwasserstein is much faster now for large objects because distance matrixes are not precomputed anymore. Set the new argument precompute=TRUE if you must reproduce the old behaviour.

BUG FIXES

• Due to the misplacement of a line of code, epsilon-scaling in the auction algorithm was not working properly for the function transport.pp. In some simple pathological examples the algorithm took very long. Reported by Samuel Ackerman. Fixed.

transport 0.11-0 (2019-02-04)

OVERVIEW

• Several improvements regarding exact and approximate computations of Wasserstein distances, including a bug fix.

NEW FUNCTIONS

• subwasserstein Allow for approximate computation of Wasserstein distances via subsampling. Code by Jörn Schrieber

SIGNIFICANT CHANGES

• Function wasserstein can now also compute Wasserstein distances in the vanilla case of two mass vectors with cost matrix.

BUG FIXES

• The result was incorrectly normed when applying function wasserstein to objects of class "wpp" with prob=TRUE. Fixed.

transport 0.10-0 (2019-01-02)

OVERVIEW

• Semidiscrete optimal transport can now also be computed for p=1 (in addition to p=2) if CGAL is available. Adapt then src/Makevars and install this package from source. This functionality is based on stand-alone C++ code by Valentin Hartmann
• Easier extraction of the Wasserstein distance from semidiscrete optimal transport results

NEW FUNCTIONS

• semidiscrete1 The workhorse function for computing semidiscrete optimal transport for p=1. This is called by the function transport (if first input object has class pgrid, second input object has class wpp and p=1) and by the function semidiscrete (if p=1). Calling semidiscrete1 directly offers finer control of the algorithm.
• plot_apollonius The workhorse function for plotting the semidiscrete optimal transport plan for p=1. This is called by the function plot.pgrid (if the second input object has class wpp and p=1). Calling plot_apollonius directly allows to plot arbitrary Apollonius diagrams (a.k.a. weighted Voronoi tesselations) based on a two-column matrix of centers and a vector of weights. It allows offers finer control over plotting.

SIGNIFICANT CHANGES

• Functions transport and plot.pgrid can now compute and plot semidiscrete optimal transport plans also for p=1 (in addition to p=2) using an object of class pgrid and an object of class wpp. The result of the plot is an Apollonius diagram (a.k.a. weighted Voronoi tesselations) consisting of hyperbola segments.
• The object returned by semidiscrete now always contains a component giving the Wasserstein distance between the input objects. The function wasserstein simply extracts this component.

transport 0.9-4 (2017-10-03)

OVERVIEW

• Compilation with the most recent version of clang resulted in an error. Fixed.

transport 0.9-3 (2017-09-29)

OVERVIEW

• Minor change to remove a compiler warning

transport 0.9-2

OVERVIEW

• Minor changes in Makevars to enable compilation under Windows and pass CRAN checks

transport 0.9-1

OVERVIEW

• Minor bug fixes

transport 0.9-0

OVERVIEW

• Fixed serious bug, introduced in version 0.7-0, by which the algorithm hanged for pgrid-objects if p>1 method="revsimplex" (the default) if masses are not integer valued
• New method "shielding" for pgrid-objects if p=2 that is considerably faster than the existing methods. Option to link package against CPLEX makes this combination even much faster and enables computation for 128x128 grids within a few seconds. C++ code by Bernhard Schmitzer

transport 0.8-2 (2017-03-09)

OVERVIEW

• New function wasserstein1d to compute the Wasserstein distance between two univariate samples (with weights)

transport 0.8-1 (2016-12-08)

OVERVIEW

• We thank Atreju Tauschinsky for contributions
• The wasserstein function supports now the wpp class
• Several minor bug fixes

transport 0.8-0

OVERVIEW

• We thank Florian Heinemann and Timo Wilm for contributions
• New class weighted point patterns with full functionality
• Optimal transport between pgrid and wpp that returns transport tesselation
• Dynamic optimal transport (displacement interpolation)

NEW CLASSES

• wpp The class wpp describes general discrete measures with finite support, i.e. patterns of finitely many "weighted" points (without specific structure for the locations or weights). There are constructors for this class, as well as plot, print and summary functions. The function 'transport' can deal with this class. We thank Timo Wilm for help with creating this class.

NEW FUNCTIONS

• semidiscrete Computes the transport map (in the form of a power diagram) for the semidiscrete transport problem from a pgrid to a wpp object for the case p=2. This function is not usually called by the user because the function transport offers the same flexibility now.
• plot_pgrid_wpp Plots a representation of a transport map (available as a power diagram) between a pgrid and a wpp object. This function gets called when using the generic plot function with a pgrid and a wpp object (in that order), but a direct call to plot_pgrid_wpp by the user offers more possibilites for customizing the plot.
• transport_track Computes a dynamic version of a given transference plan by interpolating in time. The linear interpolation of the projections of the transference plan is computed, which in many important cases corresponds to the displacement interpolation. The result can be either returned as an array or is saved as an animated gif. We thank Florian Heinemann for contributing large parts of this function.

SIGNIFICANT CHANGES

• transport Can now deal with two wpp objects and in the case p=2 also with one pgrid and one wpp object as inputs (in that order).
• aha It is now possible to return the parameters for the optimal power diagram, rather than the (approximative) optimal transference plan in terms of the pixel centers of the source measure. For this, use the new option powerdiag.

OTHER USER-VISIBLE CHANGES

• pgrid If no information is provided on the positions of the pixels, it is now assumed that we have square pixels and the boundary points in the first dimension are 0 and 1 (previous behaviour: boundary points in every dimension are 0 and 1, leading to non-square pixels if the pgrid is non-square).
• pgrid A pgrid object has two additional components 'totmass' giving the sum of pixel values, and 'totcontmass' giving the sum of pixel values divided by pixel areas. The former may be interpreted as totol mass of pgrid if interpreted as a discrete measure on the grid of pixel centers. The latter may be interpreted as total mass of pgrid if interpreted as a continuous measure with constant density on each pixel (seen as small contiguous rectangles).

BUG FIXES

• Various smaller bug fixes for special input.

transport 0.7-5

OVERVIEW

• We thank Ramon Diaz-Uriarte for contributions
• aha can return optimal power diagram now
• Several minor bug fixes

SIGNIFICANT CHANGES

• aha It is now possible to return the parameters for the optimal power diagram, rather than the (approximative) optimal transference plan in terms of the pixel centers of the source measure. For this, use the new option powerdiag.

BUG FIXES

• transport.pp, transport.default Computing the optimal transport from a mass distribution to itself resulted in an error. Fixed.

transport 0.7-4

OVERVIEW

• We thank Yann Abraham and Stefan Kain for contributions
• Several unnecessary outputs are now suppressed by default (timing information, warnings about degenerate bases that did not affect the result)
• Several minor bug fixes

BUG FIXES

• transport.pgrid For p=1 computing the optimal transport from a mass distribution to itself resulted in a segfault or an error (depending on the method used). Fixed.
• transport.pgrid Having a mass distribution of integers and at least one zero could cause an integer overflow. Fixed.

transport 0.7-3 (2016-02-25)

OVERVIEW

• We thank Ludo Daemen and Stefan Kain for contributions
• Minor changes in the documentation and a bug fix

BUG FIXES

• transport.default Using transport.default with the shortlist method gave an error message if no shortlist parameters were set. Fixed.

transport 0.7-0 (2015-10-22)

OVERVIEW

• There are two new ways for computing starting solutions in transport.default and transport.pgrid with method="revsimplex", which lead to substantial speed improvements (mainly in transport.pgrid)
• Several minor bugfixes

SIGNIFICANT CHANGES

• transport.pgrid, transport.default When method="revsimplex" is chosen, transport.pgrid can now start from a solution that is based on the optimal transport between two coarsened problems. This "multiscale" behaviour is invoked automatically if p>1, the grid is 2-dimensional, of a certain minimal size, and has an even number of vertices in each direction (for p=1 use the control parameter nscales as in previous versions). Both transport.pgrid and transport.default can also be started from a solution based on the "Modified Row Minimum Rule" (newly implemented in C Code). This is the default behaviour now for transport.default, and also for transport.pgrid if the multiscale starting solution described above cannot be computed. To get the behaviour of older versions, say control=list(start="nwcorner") in the transport function.

transport 0.6-3 (2014-10-16)

OVERVIEW

• Minor changes in the documentation

transport 0.6-2 (2014-06-22)

OVERVIEW

• Minor changes in the documentation and a bug fix

BUG FIXES

• aha In the underlying C code integer overflows were possible (usually without noticable effects on the result). Fixed.

transport 0.6-1 (2014-05-31)

OVERVIEW

• First public release