Spatstat

analysing spatial point patterns

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RELEASE NOTES

spatstat 1.39-0

23 October 2014

We thank Shane Frank, Shaaban Ghalandarayeshi, Ute Hahn, Mahdieh Khanmohammadi, Nicoletta Nava, Jens Randel Nyengaard, Sebastian Schutte, Rasmus Waagepetersen and Carl G. Witthoft for contributions.

OVERVIEW

• ANOVA extended to Gibbs models.

• Improved algorithm for locally-scaled K-function.

• Leave-one-out calculation of fitted values in ppm objects.

• New dataset: presynaptic vesicles.

• Geometrical operations with windows and images.

• More edge corrections for K-function.

• Improved handling and plotting of ‘fv’ objects.

• Utilities for perspective views of surfaces.

• New classes ‘anylist’, ‘solist’ will ultimately replace ‘listof’.

• Bug fixes.

• Version nickname: ‘Smoke and Mirrors’

NEW DATASETS

• vesicles
  Synaptic vesicles
  (includes raw data files for training purposes)

NEW CLASSES

• anylist
  List of objects.
  (A replacement for ‘listof’)

• solist
  List of two-dimensional spatial objects.
  (A replacement for some uses of ‘listof’)

NEW FUNCTIONS

• perspPoints, perspLines, perspSegments, perspContour
  Draw points and lines on a surface, as seen in perspective view.

• hopskel.test
  Hopkins-Skellam test of CSR

• project2set
  For each data point in a point pattern X, find the nearest
  spatial location in a given window W.

• stienen, stienenset
  Stienen diagrams

• dirichlet.vertices
  Vertices of the Dirichlet tessellation

• discs
  Union of discs.
  Given a point pattern dataset recording the locations and diameters
  of objects, find the region covered by the objects.

• increment.fv
  Increments of a summary function: g(x) = f(x+h)-f(x-h).

• rotmean
  Rotational average of pixel values in an image

• fardist
  Distance from each pixel/data point to farthest part of window boundary

• circumradius.owin
  Circumradius of a window

• rmax.Trans, rmax.Ripley
  Compute the maximum distance ‘r’ for which the
  translation edge correction and isotropic edge correction
  are valid.

• is.grey
  Determines whether a colour value is a shade of grey.

• harmonise
  Convert several objects of the same class to a common format.
  (New generic function with existing methods harmonise.im and harmonise.fv)

• area
  New generic function, with methods for ‘owin’ and ‘default’.

• Fhazard
  Hazard rate of empty space function

• anylist, as.anylist, [.anylist, [<-.anylist, print.anylist, summary.anylist
  Support for new class ‘anylist’

• solist, as.solist, [.solist, [<-.solist, print.solist, summary.solist
  Support for new class ‘solist’

• plot.anylist, plot.solist
  Plot methods for the classes ‘anylist’ and ‘solist’
  (Currently identical to ‘plot.listof’)

SIGNIFICANT USER-VISIBLE CHANGES

• anova.ppm
  Now applies to Gibbs models as well as Poisson models,
  using adjusted composite likelihood ratio test statistic.

• persp.im
  If visible=TRUE, the algorithm will also calculate which pixels of x
  are visible in the perspective view. This is useful for drawing
  points or lines on a perspective surface.

• Kest
  New option: correction=”rigid” computes the rigid motion correction.

• pairwise interactions
  Fitted parameters and other calculations for pairwise interaction models
  DiggleGatesStibbard, DiggleGratton, Fiksel, Geyer, Strauss
  may change slightly due to a change in handling numerical rounding effects.

• eval.fv
  Functions no longer need to have exactly the same sequence of ‘r’ values.
  They will now be made compatible using ‘harmonise.fv’.

• fitted.ppm
  New argument ‘leaveoneout’ allows leave-one-out calculation
  of fitted intensity at original data points.

• Kinhom, Linhom
  New argument ‘leaveoneout’ specifies whether the leave-one-out rule
  should be applied when calculating the fitted intensities.

• crosspaircounts
  Results may change slightly due to a change in handling numerical
  rounding effects.

• Fest, Gest
  New argument ‘domain’ supports bootstrap methods.

• plot.fv
  New argument ‘mathfont’ determines the font (e.g. plain, italic, bold)
  for mathematical expressions on the axes and in the legend.
  Defaults to italic.

• scanpp
  Upgraded to handle multiple columns of mark data.

• circumradius
  The function ‘circumradius’ is now generic, with methods
  for the classes ‘owin’ and ‘linnet’.

• edge.Trans
  New argument ‘give.rmax’

• fvnames, plot.fv
  The symbol ‘.a’ is now recognised. It stands for ‘all function values’.

• as.function.fv
  Argument ‘extrapolate’ can have length 1 or 2.

• varblock
  New argument ‘confidence’ determines the confidence level.

• $<-.fv
  This can now be used to add an extra column to an ‘fv’ object
  (previously it refused).

• minnndist, maxnndist
  New argument ‘positive’. If TRUE, coincident points are ignored:
  the nearest-neighbour distance of a point is the distance to the
  nearest point that does not coincide with the current point.

• plot.fv
  Improved handling of ‘shade’ argument.

• Kmeasure
  Now passes ‘…’ arguments to as.mask()

• Ksector
  Now allows start < 0.
  New arguments ‘units’ and ‘domain’.

• pairorient
  New arguments ‘units’ and ‘domain’.

• eroded.areas
  New argument ‘subset’

• disc
  New argument ‘delta’

• plot.plotppm
  New argument ‘pppargs’

• harmonise.fv, harmonise.im
  These are now methods for the new generic ‘harmonise’

• Fest, Gest
  These functions now also compute the theoretical value of hazard
  for a Poisson process, if correction = “km”.

• with.fv
  Improved mathematical labels.

• Gfox, Jfox
  Improved mathematical labels.

• area.owin
  This function is now a method for the new generic ‘area’

• edges
  Default for argument ‘check’ changed to FALSE.

BUG FIXES

1. varblock
   Calculations were incorrect if more than one column of
   edge corrections was computed.
   [Bug introduced in spatstat 1.21-1, november 2010.]
   Fixed.

2. varblock
   Crashed if one of the quadrats contained no data points.
   Fixed.

3. lohboot
   Interval was calculated wrongly when global=TRUE and fun=”Lest” or “Linhom”.
   Fixed.

4. nnmark
   Crashed when at=”points” if there was only a single column of marks.
   [Spotted by Shane Frank.]
   Fixed.

5. plot.msr
   Some elements of the plot were omitted or cut off.
   Fixed.

6. plot.msr
   Did not work with ‘equal.scales=TRUE’.
   Fixed.

7. plot.msr, augment.msr
   Crashed if every data point was duplicated.
   Fixed.

8. as.im.owin
   Crashed if X was a 1 x 1 pixel array.
   Fixed.

9. owin
   Coordinates of polygon data were altered slightly when fix=TRUE.
   [Spotted by Carl Witthoft.]
   Fixed.

10. objects of class ‘fv’
    Assigning a new value to names(x) or colnames(x) or dimnames(x)
    would cause the internal data format to become corrupted.
    Fixed.

11. to.grey, complementarycolour
    Did not work properly on ‘colourmap’ objects.
    Fixed.

12. Kest
    Ignored argument ‘var.approx’ if the window was a rectangle.
    Fixed.

13. rmh.ppm, rmhmodel.ppm
    Ignored the argument ‘new.coef’.
    [Spotted by Sebastian Schutte]
    Fixed.

14. as.function.fv
    The meanings of ‘extrapolate=TRUE’ and ‘extrapolate=FALSE’ were swapped.
    Fixed.

15. varblock
    Handled the case ‘fun=Lest’ incorrectly.
    Fixed.

16. [.fv
    Sometimes garbled the internal data format, causing plot.fv to crash.
    Fixed.

17. range.fv
    Sometimes returned NA even when na.rm=TRUE.
    Fixed.

18. Fest
    Argument ‘eps’ was not interpreted correctly.
    Fixed.

19. plot.fv
    Argument ‘lwd’ was not passed to legend()

20. flipxy.owin
    Sometimes deleted the name of the unit of length.
    Fixed.

Release notes are available in raw text format here.