0.2-04 - 2013-05-06 * A new method : clust, to perform hierarchical clustering ; so far it should be considered as a preliminary version. * Momocs now requires the ape package. 0.2-03 - 2013-02-26 * Some emergency fixes but the maintainer do not have time not contract to work on until a few months. * Due to deprecated packages handling images, only black and white images are supported so far. 0.2-02 - 2012-10-02 * Corrected some minor bugs * Some additions to help files 0.2-01 - 2012-10-17 * Lot of changes for this version, including: * Coe class replaces former Nef and now handles eFourier, rFourier and tFourier methods. * hqual, hquant, hpow and hcontrib (formerly harm.qual, harm.quant, etc.), morpho.space, dudi.plot, etc. now handles efourier, tfourier and rfourier through the "method" argument. * Worked a lot on helpfiles. * A vignette called "A graphical introduction to Momocs". 0.1-04 + 0.1-05 (Not released) * hquant now has a dist.method argument. * show(Coe) improved * (e, r, t)fourier ("", .i) now do some checks. * new tfourier/t.fourier.i components $x1 et $y1 are used to fit the orig/reco shapes. * hist(Coe) and boxplot(Coe) now handles all three methods * boxplot(Coe). New argument "vencenter0" to center vertically y=0. * coo.perim. New function. Returns coo perimeter. * coo.perim.pts. New function. Returns curv. abscissa for all points of a coo. * coo.force2close. New function. Like it says. * edi. New function. Calculates euclidean intermediates. * coo.sample.int. Given a coo, calculates intermediates on the true curv. abscissa* * meanShapes. Calculates average shapes on Coe objects. * New function. morpho.space. Calculates morphological spaces with many options. * dudi.plot. Plotting shapes is now handled by morpho.space. * pca2shp and dudi.plot. Added the argument "rotate.shp" to rotate shapes when plotting the morphological space. * pca. Changed "subset" for "subset.fac" and "subset.lev" and corrected a minor bug. * PC.contrib. New function. * pix2chc. New function. Converts "pixel" coordinates to chain-coded coordinates. * chc2pix. New function. The opposite operation. * Coo2chc. New function. Writes a .chc file from a Coo object (e.g. to use with SHAPE suite). * chc2Coo. New function. The opposite operation. * Nef2nef. New function. Writes a .nef file from a Nef object (to use with SHAPE suite). * nef2Nef. New function. The opposite operation. * coo.plot. Added a "centroid", "lwd" and default arguments. * coo.draw. Added "lwd" and "lty" argument. * Coo-class. Corrected some minor bugs. * Coo-class. Removed slot @scale from Coo class. * Coo-class. Added setters "[<-". * Coo-class. Now Coo objects can be passed to Coo builder. * Datasets. Resaved hearts and bot accordingly. * slide(Coo). Corrected a bug. * coo.scale. Corrected a minor bug ; and if scale is missing the centroid size is used. * coo.centpost. New function. Returns the centroid position of the coo. * coo.centsize. New function. Returns the centroid size of the coo. * Coo-class. Added slot @coo.closed. Changed the show(Coo) accordingly. * is.closed. New function. Checks if outlines are closed or not. * coo.unclose. New function. Unclose an outline (if it is closed). * Coo-class. New methods: close(Coo) & unclose(Coo), like it says. * efourier. Now accepts (nb.h=-1), which sets nb.h to the highest possible value and has a "silent" argument. * coo.ldk. New function. Used to define landmarks on a single coo. * defLandmarks. New method. To define landmarks on Coo objects. * ed. New function. Returns euclidean distance. * edm.nearest2. New function. Given two matrices returns the shortest distance for every point of m1 to any point of m2 and the corresponding row index for m2. * edm.nearest. New function. Same as edm.nearest2, but only returns shortest distances found. * plot(Coo) and stack(Coo) are now the former plot(Coo, met="stack"). * diapo(Coo) is now the former plot(Coo, met="single"). * panel(Coo) is now the former plot(Coo, met="panel"). * Added landmarks plotting in plot methods for Coo. * Added names support in panel(Coo). * dev.segments. New function. Draw segments when passed as a matrix and with a color argument for every segment. * Started utilities for arrays with A.mshape, returns the mean shape of an array of landmarks coordinates. * A.plot. Plots an array with options (Momocs' equivalent to plotshapes{shapes}). * A.draw. Add segments corresponding to shapes. A.plot and A.draw are landmarks equivalent of coo.plot and coo.draw. * A.points. Add points, typically landmarks, given as an array, on an existing plot. * defLandmarks(Coo). New method. Provides an user interface to defines landmarks. * cooLandmarks(Coo). New method. Retrieve landmarks coordinates (if defined) from a Coo object. * vecs.param. New function. Returns ratio of norms and signed angle between two vectors provided as four numeric. * coo.baseline. New function. Returns a coo aligned on a baseline, e.g. c(-0.5, 0) ; c(0.5; 0) for Bookstein's * baseline(Coo). Coo method for defining a baseline when landmarks have been defined. * procGPAalign. Use procGPA{shapes} to perform a Procrustes alignment on a Coo object. * Consequently, shapes package is now required. * coo.rotate.center. New function. Rotates a coo with a given center of rotation. * show(Coo). Corrected a small bug for plotting shapes with less than 10 points. * a2l. New function. Converts an array to a list. * Coo builder. Now accepts arrays. * coo.list.panel. Corrected a bug when dim[1] == 1 0.1-03 - 2012-09-04 (Not released) * coo.plot. New argument: "first.point = TRUE". Whether to draw the first point. * coo.plot. Corrected a very minor bug when met="stack". * coo.draw. New function. Adds a shape on the active plot * Coo.plot. Corrected some minor bugs. * efourier. Corrected a (very small) bug * coo.list.panel. Added "density = NULL" and "angle = 45" parameters. * manova.nef. Corrected one bug concerning the selection of the number of harmonics to retain. * dudi.plot. Removed the obsolete "lwd.star=0.25". * dudi.plot. Corrected bugs for arguments "cex.points, clabel". * Coo builder. If "names" of the coo provided is NULL, then create these names. * import.img.Conte. Added "auto=TRUE, plot=TRUE" parameters. * import.multi1.jpg. New function to help to extract outlines from images with more than one mask. * Coo. Changed slot @ldk from 'numeric' to 'list' * coo.oscillo. Added two arguments "ref=TRUE, ref.nb=8" to add some reference points on the oscillo curves and on the shape. * New method: slide on Coo. * Corrected bugs on the align, scale, sample, center, align methods for Coo objects. * eFourier. Corrected a bug when EFA performed without normalization. * coo.scale. Slight change on code, no visible change. * New function. l2a, converts a list to an array. * New dataset. hearts: 450 outline of hand-drawn hearts by 15 different persons. 0.1-02 - 2012-08-21 * Package almost entirely rewritten 0.1 & 0.1-01 - 2012-05-01 * Initial release