######releasing v. 0.23.3 *fixed more docu to comply with CRAN *moved spinimage functions to mesheR *replaced all instances of %dopar% with %do% when function is called from windows ######releasing v. 0.23.2 *disabled all!! parallel functionality to pass R CMD check *set mc.cores=1 for stupid windows in all instances ######releasing v. 0.23.1 *cleaned empty sections in docu and fixed examples. ######releasing v. 0.23 *minor docu fixes *more docu work and added option to project meshes in the workspace with ray2mesh *a lot of new doumentation and minor bug fixes *automatically set cores=1 for mclapply when run on stupid windows *fixed docu of procSym (thanks to Paolo Piras) and option to center mesh in scalemesh according to bbox or vertex mean *Merge branch 'master' of ssh://git.code.sf.net/p/morpho-rpackage/code ######releasing v. 0.22.1 *Merge branch 'master' of ssh://git.code.sf.net/p/morpho-rpackage/code *minor changes *clarified direction of rotation in docu of rotaxis3d ######releasing v. 0.22 *added option 'ask' and 'countbegin' to 'warpmovie3d.mesh3d' *added option circle in Fortran routine 'angcal' to enable calculation of angles without regard of vector direction (i.e. angles rho > pi/2 will be pi - rho). *removed blank in listname of readallTPS *removed workingdir change in warpmovie and fixed readallTPS *added option 'close' to warpmovie and minor improvement in orp *use eigenPCA as backup if try(prcomp) fails in procSym *Merge branch 'master' of ssh://git.code.sf.net/p/morpho-rpackage/code *replaced pcomp with eigenPCA to avoid occational LAPACK error *added method "eigen" and function eigenPCA to avoid La.svd errors *minor fixes *renamed rotaxis to rotaxis3d because it only works for 3D-configs *added legend plot to histGroup *added docu for rotaxis and function meshcube to get cube around a mesh *added rotaxis to rotate around arbitrary axis in 3D *added readallTPS to read outlines and landmarks from tpsdig2 *added option 'col' ins histGroup *removed B as sparseMatrix because unnecessary *Merge branch 'master' of ssh://git.code.sf.net/p/morpho-rpackage/code *added dependency Matrix to gain from sparse matrix support for lots of sliding landmarks *fixed support for landmark arrays in permudist and removed irritating debug print command from name2num *fixed support for landmark arrays in permudist and removed irritating debug print command from name2num *fixed support for landmark arrays in permudist and removed irritating debug print command from name2num *corrected description of procSym ######releasing v. 0.21 *added warpmovie2d - an equivalent to warpmovie3d.matrix for 2D landmark data. *Merge branch 'master' of ssh://git.code.sf.net/p/morpho-rpackage/code *fixed correct ylim value in histGroup *adapted projRead for usage with parallel backend *added option outname in projRead *updated docu for fixLMtps and added checks for small samples. *removed unnecessary return value (only used for debug) in fixLMtps *fixed missing value in fixLMtps if weight=F ######releasing v. 0.20 ######releasing v. 0.20 *fixed error concerning single/double entry groups *removed unnecessary check from groupPCAcrova *fixed weighting in groupPCA *changed weighting in proc.weight to weighting by inverse distance and updated docu *fixed correct lighting of lines in pcaplot3d *added matrix support for place.patch and option to mark entries in checkLM ######releasing v. 0.19 *fixed bug consisting in wrong dimnames for 2D configs in procSym *added r2morphologika export filter for landmark arrays *fix in anonymize, added docu for exVar and added some suggestions to DESCRIPTION file *added exVar.mvr to estimate variance quotient between predicted space and actual space on plsr regression models. *added url to description file *cosmetical change in source code of warpmovie.matrix *fixed missing weighting argument in subfunction of groupPCA *added weighting according to group size to groupPCA and updated docu (added Boulesteix) *fixed docu mismatch in warpmovie3d and changed default color to green. *updated docu for warpmovie3d - including warpmovie3d.matrix *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *added file warpmovie.matrix *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *added warpmovie3d.matrix *added namespace Morpho:: to call of groupPCAcrova in groupPCA to avoid stupid windows error. ######releasing v. 0.18 *fixed docu in rotonto *fixed docu mismatches *fixed handling of single entry groups in CVA and groupPCA *fixed disabeling of cross-validation in groupPCA *added option to load mesh stored as R-object in check.lm. *improved rendering onf pcaplot3d and changed return to invisible in find.outliers *fixed meshDist.matrix *added option "mesh" in relaxLM for reprojection onto a surface already loaded into R. *removed option output from render.meshdist -> invisible() handles things much smoother *corrected docu for slider3d *fixed wrong variable name in render.meshDist *added option centerweight and weights to proc.rot and ProcGPA for testing purposes. *added centerweight to rotonto allowing to center the data according to the weights. *removed wrong brackets in docu *removed unnecessary scaling from rotonmat *added weighting option to rotonto *made warpmovie more consistent by adding an overall bounding box *forgot to commit meshDist *fixed erroneous coloring in mesh2ply added material check in rmVertex and fixed wrong normals in warpmovie3d and fixed material$color dimensions in meshDist *added ... in warpmovie *added import for meshlab pickpoint files *added fix in mcNNindex for single core *added anglecheck in gauss_displace.f90 ######releasing v. 0.17 *Monstous cleanup and adding heap docu file for yet to document/deprecated/internal functions *changed line endings to unix *fixed NaN for negative distances due to rounding error. *added check for zero length normals in matr_meshKD *fixed typprob and fixed missing output in adnormals. *added distance option to pt_upmesh and added fix for CVA for groups containing only one observation. *added code for within group covariance matrix *added option for pooled covariance in typprob *added typprob and typprobClass to perform calculation of typicality probabilities. *made closemeshKD equivalent to vcgClost from Rvcg *moved gaussDisplace and icp to package mesheR and speed up rotmesh.onto *fixed wrongly placed parenthesis. *added function smoothMesh3d - a wrapper for the cli app trismooth. made gaussDisplace and icp multicore functions. *fixed ply2mesh with readnormals=F and pointclouds, renamed relaxSym to gaussDisplace and added nn2 wrapper using multicores. renamed relax_sym.f90 to gauss_displace.f90 and added option "tol" to only take into account displacements below a defined threshold. *minor change in relaxSymtest *added check for face normal floats *speed up ply2mesh even more by replacing "read.table" with "scan". *removed unnecessary apply call, and added colClasses statements to spped up ply2mesh *added option "reflection" to icp, rotmesh.onto and rotonmat. *added functions icp and angcheck (fortran) *added check for zero unref vertices in rmUnrefVertex *added docu for vertex helper functions *added checks for division by zero for adnormals, angcalc and crossp *moved barycenter.f90 to face_helper.f90 and added routine for checking invalid faces. added a lot of stuff to remove (unreferenced) vertices from meshes. *improved relaxSym by using option searchtype in subroutine nn2 (from RANN package) *added option sign to mesh2mesh to get signed distances. *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *fixed division by zero in adnormals.f90 *added option for restricting neighbourhood in relax_sym.f90 by using closest points for gaussian smoothing only - uses kd-trees *fixes of variable reset to zero in relaxSym (r and fortran code) *fixed wrongly initialized variable outpoint2 in relax_sym.f90 *fixed missing scale entry in rotmesh.onto *added relax_sym to start checking for displacement *added option angweight in adnormals.f90 *removed obsolete functions in mc.closemat *added signed distances to closematKD, closemeshKD *added signed distances to closematKD, closemeshKD *changed dependency to RANN because it is faster than FNN *added closemeshKD *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *added Fortran routine matr_meshKD to search preselected faces by kd-tree search of barycenter distances (also added barycenter.r and barycenter.f90) also added crossp as separate subroutine ######releasing v. 0.16 *renamed deformGrid3d and added documentation *changed name of deform.grid to deformGrid and fixed mistake in meshDist preventing distvec to work *updated documentation *added option "sign" to render.matrix *added sign in render.meshDist to enable different visualisations without reprojection. *added lineplot for 2D and 3D wireframe plotting. *fixed mirroring matrix for 2D. *added option add in check.lm *added correct parameters for option ray in meshDist *added options displace to show colored residual vector between origin and closest point. *changed specular="black" in render.meshDist *turned meshDist into generic S3 function and added meshDist.matrix for 3D point-cloud to mesh distance visualisation. *minor code cleaning *minor docu changes in meshDist. *added option distvec in meshDist to provide custom distance vectors. *fixed tol for unsigned distances and added ... for additional rendering parameters. *fixed wrong tol evaluation *fixed correct color charts for render.meshDist and updated documentation. *added option tol to meshDist rendering distances within this threshold green. *fixed color management for meshDist when sign=T *merged files for projRead and projBack and added option --sign to return signed distances; also added option sign in meshDist ######releasing v. 0.15.99 *speed up for meshDist and render.meshDist *added grey conversion for colored meshes (mesh2grey); added writing of material3d$color to mesh2ply and speed up color calculation in ply2mesh. *cleaned some documentation *added option readcol to file2mesh *adapted place.patch and ray2mesh to work with the new --angmax feature of rayproject *added option readcol in ply2mesh to import vertex colors. *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *tried to improve memory management in check.lm *removed flag from Makevars *fixed docu of render.meshDist *more cleaning of obsolete functions and obeiing to R CMD checklog *tried to make package compliant with official R package rules *added option mindist to find the closest point (if the ray hits the target in both directions) *mention minimisation criterion in docu of slider3d and added BEdetect, that quantifies non-affine deformation for each landmark. *updated bone2skin added input option for lists in check.lm ; mesh2mesh now supports links to files as well as meshes from workspace; name2xxx allows vectors as input. *fixed missing parameter "ramp" in meshDist *added generic plot and export function for meshDist *added docu for meshDist *added rgl rendering option in meshDist *mesh2Dist returns a vector of specified colors, *added description for meshDist and option to search along rays; fixed cleanup in ray2mesh *added meshDist, that calculates distances between meshes and saves colored ply file and suiting png with colorramp. *added distance to output of minClost *added coloring support for mesh2ply *set mmahalanobis to FALSE in proc.weight and formatted fortran source of minClost subroutine *added fortran routine and R wrapper to find closest point for 3d-matrices. fixed error in relaxLM. *fixed missing description in find.outliers docu and added distance report to output *added option mahalanobis to find.outliers and updated documentation *fixed bug in NNshapeReg (sum instead of mean as weights sum to one) *added NNshapeReg (nearest neighbour estimation) and added euclidean option in proc.weight *added docu for plotNormals *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *replaced %do% with %dopar% ######releasing v. 0.15 *added automatic creation of destination folder in anonymize *replaced GPA/OPA subroutines in Semislide with the ones from Morpho instead of shapes package *added dataslide info in man/procSym.Rd *fixed wrong declaration in Semislide *formatting in map.mesh *procSym: option center.part set to FALSE; name2*: also working for matrices and vectors. warpRestrict: fixed double used variable *added relaxLM + docu to slide one config against another. fixed issue in warpRestrict *added Morpho-deprecated to successivly renaming functions with dots in their names. *readded accidentally removed output of pairedLM in procSym. *added automatical setting of mc.cores=1 in CVA on windows systems *added option to select cores manually in functions using multicore features *removed instance of mclapply for initial reprojection in slider3d *removed unnecessary file mc.procSym *added option to manually select cores in slider3d *updated man for find.outliers *merged win and *nix versions by using the packages "parallel" and "doParallel" available since R v2.14 *unified mc.find.outliers and find.outliers and made color selection possible for functions using collapsed triangle meshes for fast normal rendering *optimized anonymize for complete replacement of strings and adding suffixes and prefixes *improved anonymize to check for same entries and allowed vector of string as input *added function spinimageLM, and spinimageMesh for calculating spinimages of landmarks and/or complete meshes (very slow) *changed License in DESCRIPTION file to standardised expression "GPL-2" *forgot to commit manual for relWarps ######releasing v. 0.14 *unified slider3d and mc.slider3d *added option "silent" to sc.procGPA to suppress output of time elapsed. Finished relWarps, wrote documentation and crosschecked results with output from othe software. *fixed uniform component for relWarps *added uniform comp in relWarps *renamed relwarps to relWarps to avoid naming conflict with the shapes package. *inserted OS -switch in mc.slider3d; changed mc.relwarps to relwarps; removed alias for mc.CVA from doku *minor adaption in documentation files. *slight correction for crossvalidation of CVA and additional option "breaks" in histGroup *added crossvalidation for groupPCA *unified CVA and mc.CVA by adding OS switch and corrected calculation of the Grandmean in groupPCA and CVA *created placeDowels for soft tissue marker placement *added cylinder to create and place cylinder representing soft-tissue thicknesses. *fixed bug in plotNormals and tanplan (added normalisation in a case) *added option square to qqmat and fixed wrong number of zeros for estimating bendingenergy outliers in relax.mesh *updated version *forgot to commit CVA (unsaved file) *added histGroup to plot histogram for multiple groups *added histGroup to plot histogram for multiple groups *updated documentation for (mc.)slider3d *removed meshres from wrong folder *removed debug output from groupPCA *added function groupPCA to perform PCA based on group means covariance matrix. fixed slightly wrong calculated p-value in (mc.)CVA,CVA,permudist,permuvec *remove accidentally staged folder *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage ######releasing v. 0.13.1 *renamed files and documentation c.xxx and proj.xxx *renamed files c.xxx and proj.xxx *updated documentation and increased S3 compatibility. *renamed mc.fixLMtps to fixLMtps because mc.procGPA is replaced by sc.procGPA. *added example data for warp.mesh and warpmovie3d and updated documentation. Also renamed mc.fixLMtps to fixLMtps because mc.procGPA is replaced by sc.procGPA. *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *renamed function warpmovie to warpmovie3d *chmod 644 *removed deprecated man-pages *added manual for permudist *version 0.13 released *changed mc.permudist and mc.permuvec to permudist and permuvec and made it working for windows *fixed bug in mc.permuvec and added Documentation *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *adapted arguments of procSym to those in mc.procSym *changed minimum required R version to 2.10. *changed deprectated function in example code of CVA *added dependency "foreach" and "doMC" for Linux Version *correct estimation of scale factor in restricted *fixed typo in man rotonto *fixed bugs and added options 'nPC' to limit nr of PCs in warp.restrict and option stop.prob to try a optimum match even when the threshold is reached. also the option 'scaling' in "rotonto" is replaced by 'scale' for consistency *fixed bug in warp.restrict and restrict *added meshres to estimate meshresolution *got spinimage working *added function (Fortran based) for estimation of mesh resolution, angle comparison and modified plotspin *renamed plotmat to plotspin (only file) *get spinimage working/ added plotspin and ang.r *added spinimage function and fortran code *added spinimage (also Fortran code) to generate spinmaps *added option in calcTang_U_s to give weights to the normal lengths, and passed this option to mc.slider3d *fixed wrong calculation of rmsrho in (mc.)procSym *minor bug in (mc.)procSym ######release version 0.12 *updated manual for procSym *added option for using only a subset of landmarks for Procrustes registration. *cleaned code of mc.procSym, procSym added single-core version of mc.procGPA and replaced vec1 by t(vecx) in scaleproc to remove depends from "shapes" package *Merge branch 'master' into tps *relax.mesh *modified relax.mesh *added warp.restrict to add deformation based on training dataset to get probabilistic estimates *changed pcaplot to the generic function pcaplot3d working on the output of (mc.)procSym *added anonymize to replace names stored in row names or dimnames with numbers *added find.face, del.face and add.face for manual defining and deleting faces from a surface mesh. added get.obj.size to show information of how much space all objects in the current workspace occupy. added option "clean" tp file2mesh to suppress removing unreferences vertices during import. *added rendering option in check.lm bugfix in mc.pls2B *added permutation testing to mc.pls2B *added option reflect to rotonto *fixed bug in procAOV and orp (scale all configs according to mshape) *added plot.normals to plot normals of a mesh added explained variance to each factor in procAOV *pimped deform.grid and difplot (lines are drawn as triangles) added rownames in output of procAOV *added pls_2B for 2-Block partial least square analysis fixed bug in r2morphoj *changed procAOV (added asym mean to overall SS) added function r2morphoj to export array to morphoj readable text format *corrected degrees of freedom in procAOV *added procAOV which performs Procrustes ANOVA sensu Klingenberg added p-value in mc.permudist assign different classes to results from mc.procSym *added possibility not to adress surfaces in check.lm *added option add, and colouring to deform.grid *moved all functions related to crestlines to file "crestlines.r" *added read.curves and plot.curvature to read & plot output text of setCurvature *fixed bug in mesh2ply2 giving now processable output for commandline tool setCurvature added support for vectors in mc.permudist; added output options of MahaD2 distances in qqmat *added permutation test to mc.CVA over Euclidean distances in case the input is a matrix. added option to ruedell specific file2ply2. *added mc.permudist for permutation testing distances between two groups. *added qqmat to plot multivariate qq-plots for checking mv-normal distribution *added function pred.PCmult for prediction of multiple shapes based on PCs. *added exVar to naively calculating variance explained by mulitvariate model *removed unnecessary loop in (mc.)procSym and added missing parenthesis in ray2mesh *adde name2... to extract information from array dimension names and convert them to factors/numeric *added option ignore.stdout to proj.read,proj.back & ray2mesh to supress console output of system calls, improved fq (linux kill R) *added ask option to fq *renamed qf -> fq *added qf - a custom exit command forcing quit R on Linux *dimnames[[3]] of input is added as rownames to output of vecx *modified: R/map.mesh.r: fixed bug in option subset *modified: R/map.mesh.r fixed bug in option subset & added option fix to keep original target landmarks ######released v0.10 *updated and cleaned documentation *fixed bug in place.patch, ray2mesh and warpmovie *Merge branch 'tps'; resolved conflit in R/map.mesh.r *awsome finished (hopefully) map.mesh including interactiv region selecting *improved code in map.mesh *added optionin map.mesh *added option select3d to map.mesh *added option subset *pimped map.mesh *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *improved map.mesh and fixed typos in ray2mesh & replace NaN with "0" in relax.mesh *added check for diverging normals in place.patch *bug fix in place.patch *fixed bug in (mc.)procSym, concerning projection into tangent space *fixed bug in (mc.)procSym, concerning projection into tangent space *improvements in deform.grid, mc.procSym and proc.weight *added option to calculate weigts based on (regularizable) Mahalanobisdistance *changed subfunction slido to avoid spawning of two many children by the mclapply function. *added export for ply2 format (only for Ms. Ruedell) *added support for automatic placement of curves in place.patch *fixed bug in place.patch *added option smooth=false to proj.read and place.patch *Revert "Revert "Revert "Revert "improvements in check.lm"""" *Revert "Revert "Revert "improvements in check.lm""" *Revert "Revert "improvements in check.lm"" *Revert "improvements in check.lm" *Merge branch 'tps' into tmp *improvements in check.lm *Revert "some improvements in check.lm" *some improvements in check.lm *Merge branch 'tps' *Merge branch 'tps' into tmp *added cca *replace rgl.clear with rgl.pop *replaced eigen() with svd() in CVA.crova to evade casual lapack errors *added check.lm to control automatic placement of semilandmarks *saved ray2mesh *added place.patch to check visually, if automatic patch application was succesful *added option inbound and strict to ray2mesh added inflate option to place.patch to evade thin walled mesh problems *added tools for semiautomatic patch placement *cleaned Fortran section before merge *bugfix in read.csv.folder *cleaned code relax.mesh *added rayprojection add end of relax.mesh *added autoestimation of tol (for relax.mesh) *working relax.mesh, ray2mesh *minor change in relax.mesh *a lot of changes and a working version of relax.mesh *added relax.mesh *added mc.mesh_mesh *eod *wochendende *eod *slight changes and removed obsolete r-code *finally projection is working *eod - atleast ang_calc is working *mittagessen *cleaned code *added vertex search *working fortran version of closest point search. *fortran closest on mesh *added map.mesh for mapping patches onto larger surface *fix for files with no landmarks *added vecx (converts array to matrix) *added correct kernel for 3d tps :U(r)=-|r| *heavy cleaning after pimping tps3d, fx and tpsfx.f90 *test tps *changed computation in mc.relwarps for 3d-matrixes using a negative version of Lsubk to render it positive-semidefinite added option for orthogonal projection into tangent space before performing PCA. *fixed pseudoinverse *added 3d support for mc.relwarp (hopefully it works) *bugfixes *minor changes in mc.procGPA & mc.relwarps *added mc.relwarp for relative warp analysis. *changed scaling in mc.procGPA to mshape of 1 for CSinit=T *improved mc.fixLMtps to get weighted estimates *weekend build *added docu for mc.fixLMtps *bug fixes in fx.r and mc.tps3d concerning 2D configs. Added mc.fixLMtps. *changed distances in mc.permuvec to Mahalanobisdistance (of pooled WGcov) *changes in permu* *renamed permuvar to mc.permuvar *added permuvar to test differences in shape variation using permutation testing *removed debug "print" command from CVA *Merge branches 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *minor docu change *Release 0.8.2 *more fixes *more bugs fixed in (mc.)CVA and updated docu *bug fix in (mc.)CVA removed imaginary numbers after eigenanalysis, leading to nonsense. *added support for matrix input in mc.permuvec *renamed file permuved to mc.permuvec *updated package and added bugfix for (mc.)CVA dealing with empty groups, due to factors. *added permuvec to permute distances and angles between two subgroups of two populations *updated proj.back to fit the new version of trimesh_project *removed bugs in mc.unify.list & warpmovie *made mc.unify.list more RAM friendly and added output option; bugfix in ply2mesh. *added estShapeFull *added bone2skin and modified mc.findoutliers *added warpmovie *fixed bug in rotonmat. *docu *added documentation *new version *added (mc.)patch2surf *fixed bug in ply2mesh and added cleaning otion in proj.read. *set updateNormals to FALSE if ray = TRUE in mc.unify.mesh *mittagspause: added support for meshunification alon ray *added manual for mc.unify.list *added manuals and added support for reading normals from ply files without face information. *fixed bug in mc.unify.list *code cleaning and removal of unify.list until a nice version of procGPA is written added fucntion scalemesh ot scale meshes. *mc.unify.list now unifys from files on HDD. *added updatenormals *added some helper functions *added estShape to calculate weighted surfaces, with weights estimated by proc.weight *removed duplicte line in rot.proc and rotonto *added report for singular matrix in CreateL & calcGamma *bugfix in (mc.)procSym concerning Asymmetrie *minor typo *documentation for proc.weight *fixed typo in (mc.)procSym and pimped c.extract *minor changes *added: proc.weight for weighting closest shapes *enable clean up *New version *wrote createL in Fortran, bugfix in mc.slider3d, added sourcfourge adress in manual *some minor fixes and addo (copy of shape's add) added. *cosmetic change *fixed bug in mc.slider3d (forgot list in in subfunction slido) *massive speedup for (mc.)procSym, parallelizing of reprojection in mc.slider3d *speed up for subroutine calcGamma (30% faster using crossprod. *Merge branches 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *only minor file rename *replaced the function centroid.size by c.size (much faster) and changed it (hopefully) in all dependent functions. *Merge branches 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *gone to next level: Fortran routines speed up the whole thing :) *changed procOPA to the faster rotonto in mc.slider3d *little bugfix in mc.slider3d *mc.slider3d first slides configurations (mc speedup) *fixed rotmesh onto *coerce data to matrix. *Added regularization parameter (lambda) to mc versions of some tps applicacions ######release 0.6.5.9 *improved NA declaration. *CreateL,CreateL2D: added check for singular tps matrices and applying gen. inv. added: (mc.)unify.mesh,proj.read removed unnecessary calculation of inverse in tps3d added: documentation *fixed write.table! *changed : mesh2ply round values to 6 digits. *updated documentation. *minor changes in mc.fx, mc.tps3d added mesh2mesh *fixed mc.find.outliers;deform.grid; plot in (mc.)CVA *changed calculation of mahal dist (grandmean-centered groupmeans). *applied meancentering to CVA. *Merge branch 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *Added pred.PC changed mc.CVA (meancentering Data). *Merge branches 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *Weekend build. *hopefully CVA fixed now!! added scale option to rotonmat *Hopefully fixed now! *big bug fix!! for CVA - Crossvalidation issue solved. *heavily speed up for CVA functions *added: calculation of Procrustes Distance to (mc.)CVA (in case of LM) *added: calculation of Procrustes Distance to (mc.)CVA (in case of LM) *speed uo mc.procSym, mc.find.outliers added/updated documentation *fix error that came by accidental renaming of function CVA.crova *Merge branches 'master', 'master', 'master', 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *improved CVA & added mc.CVA *Merge branches 'master', 'master', 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *More improvements to (mc.)find.outliers *added 2D support to (mc.)find.outliers *improved (mc.)find.outliers *improved & fixed (mc).findoutliers *Merge branches 'master', 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *minor bug fix *added: funcions find.outliers and mc.find.outliers as improved replacement of difplot.proc improved: read.csv.folder. added: some documentation. *Merge branches 'master' and 'master' of ssh://morpho-rpackage.git.sourceforge.net/gitroot/morpho-rpackage/morpho-rpackage *update to 0.6.5.2 *read.csv.change *Added csv import *Added DESCRIPTION