Morpho - Morpho 2.0.3-1

Windows version OSX version Linux version (source code)

Changes in Morpho version 2.0.3 (2014-05-13) - added support for objects stored in a list in bindArr - made rotreverse an S3 function for matrices and mesh3d - fixed bug in slider3d if pairedLM != 0 - fixed pooled within covariance matrix (covW) for single group entries - speed up rotonto, rotonmat by vectorizing - removed junk comments - added fix for weighted Grandmean in CVA (thanks to Anne-Beatrice Defour) - added check for empty patches and curves in cExtract (thanks to M. Friess for pointing that out) - added 'cutMeshPlane' and 'cutSpace' to cut a pointcloud into upper and lower part - added function 'solutionSpace' to calculate the basis of the solution space for Ax=b, with det(A)=0 - minor changes in asymPermute (docu and table naming) - enabled multigroup support in asymPermute - added groupmean output in asymPermute - updateNormals: if no faces are present, mesh will be returned unchanged now. quadric faces are converted to triangular ones - add new function 'quad2trimesh' for converting quadric meshes into triangular meshes. - made code in pcaplot3d easier to maintain by creating .pcaplot3d - assigned additional attributes to output of procSym

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Published by zarquon42b about 12 years ago

Morpho - Morpho 2.0.2

Windows version OSX version Linux version (source code)

Changes in Morpho version 2.0.2 (2013-02-24) - added function 'fixLMmirror' to estimate missing bilateral landmarks - wrote C++ versions of some subroutines to speed up Procrustes registration. - added function arrMean3 to calculate fast average of 3D-array - reprojection onto surface in 'slider3d' now can run in parallel (only OS X and Linux)

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Published by zarquon42b over 12 years ago

Morpho - Morpho 2.0.1

Windows version OSX version Linux version (source code)

Changes in Morpho version 2.0.1 (2013-02-07) - 'createAtlas' has new option "keep.fix" to specifiy landmarks that should be kept from sliding in case corrCurves are defined. - wrote C++ implementation of 'covPCA' (much faster) and added bootstrapping option to compute confidence intervals for PC-scores (removed obsolete options "mc.cores" and "scores") - all functions calling trimesh-tools are now wrappers for much faster implementations from Rvcg - placePatch now runs in parallel - warpmovie3d now allows make movie of deformed mesh AND landmarks

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Published by zarquon42b over 12 years ago

Morpho - Morpho 1.99 - codename "Morphodillo"

Windows version OSX version Linux version (source code)

Changes in Morpho version 1.99 (2013-12-18) All FORTRAN code is now replaced by C++ code using Rcpp/RcppArmadillo!! - renamed 'adnormals' to 'updateNormals' - 'permudist' is now massively faster by using C++ code for permutation. It can handle more than 2 groups now. - as the new 'permudist' is now implemented in 'groupPCA', it gets a boost, too. - added function 'RegScore' to calculate Regression scores as described in Drake & Klingenberg(2008) - added 'CAC' (common allometric component) - added functions 'asymPermute' (assessing directional asymmetry) and 'meanMat' (fast Matrix averaging) - covPCA now returns the distances instead of squared distances - added option to revert vecx to translate a matrix back into an array containing landmarks - adapted 'ray2mesh' to work in parallel calls and added option "mc.cores" in 'placePatch' - even in Windows - added option "add" in "meshDist" and "render" to add to existing rgl window. - fixed error in in 'placePatch' in case "data" is a matrix

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Published by zarquon42b over 12 years ago

Morpho - Morpho 1.0-2

Windows version OSX version Linux version (source code)

Caution: the latest version of rgl (>= 0.93.963) and doParallel (>= 1.0.6) is required

Changes in Morpho version 1.0-2 (2013-11-05) - added option "barycoords" in 'closemeshKD' and added normal weighting - made reprojection ind 'slider3d' using multiple cores in case "meshlist" is specified - added option "blockdiag" in 'CreateL' to supress returning blockdiagonal matrix containin Lsubk - significant speedup in calcGamma (responsible for sliding) - added option "meshlist" in 'slider3d' and fixed memory allocation problem for orthogonal projection with large amounts of landmarks in 'procSym' (underlying routine 'orp') - added autonaming of output in write.pts - 'mergeMeshes' now allows a list of meshes to merge - fixed error in 'mcNNindex' in case k=1 - added landmark matrix to output of 'cExtract' - set pointsize to 10 in 'deformGrid3d' in case "type="p"" - added options "silent"/"ignore.stdout" to 'ply2mesh', 'projRead', 'ray2mesh', 'slider3d' and 'warp.mesh' to supress terminal output - added option "pt.size" instead of "radius" in 'checkLM' and 'plotAtlas' to control point/sphere size. - added option "fixRepro" in 'slider3d' and 'relaxLM' to supress reprojection of fix landmarks onto the surface. This can be useful when some fix landmarks are in "thin air". - added support for point cloud export in 'mesh2ply' and 'mesh2obj' - added option "silent" in 'rmUnrefVertex' - fixed error in 'relWarps' preventing it to work for 2D configs - added function 'checkLM'. Useful to visualize if projection by 'placePatch' was successful by browsing through sample. - added functions 'placePatch', 'createAtlas' and 'plotAtlas' for defining templates and functions to project (semi-) landmarks from an atlas onto all specimen in a given sample - fixed missing '-1' subtraction in 'covW' - added function 'mergeMeshes' to concatenate multiple triangular meshes. - made function 'procAOVsym' (procrustes Anova for object symmetry) public. - made functions 'cSize', 'mcNNindex', 'meshcube', 'meshres', 'ProcGPA' public. - added option 'info' in 'read.mpp' - merged 'CreateL' and 'CreateL2D' - rewrote large parts of 'CVA', 'groupPCA' and 'permudist' to make the code more efficient - 'covPCA' now allows permutation tests to check if pairwise distances between covariance matrices are significant and reports rownames for two-group case - removed unnecessary complicated check for empty groups by simply using function 'factor' in 'covW' and 'typprobClass' - white space formatting in code - added option "mshape" to function 'orp' to specify a custom pole for projection - made function 'fx', 'PCAcrova' and 'calcTang_U' interntal-only by prefixing function name with '.' - removed unnecessary sinus calculation in 'angle.calc'

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Published by zarquon42b over 12 years ago

Morpho - Morpho 1.0beta2 (a.k.a. 0.99.1)

Windows version OSX version Linux version (source code)

Caution: the latest version of rgl (>= 0.93.963) is required

Changes in Morpho version 0.99.1 (2013-10-07) - added option "fixRepro" in 'slider3d' and 'relaxLM' to supress reprojection of fix landmarks onto the surface. This can be useful when some fix landmarks are in "thin air". - added support for point cloud export in 'mesh2ply' and 'mesh2obj' - added option "silent" in 'rmUnrefVertex' - fixed error in 'relWarps' preventing it to work for 2D configs - added function 'checkLM'. Useful to visualize if projection by 'placePatch' was successful by browsing through sample. - added functions 'placePatch', 'createAtlas' and 'plotAtlas' for defining templates and functions to project (semi-) landmarks from an atlas onto all specimen in a given sample - fixed missing '-1' subtraction in 'covW' - added function 'mergeMeshes' to concatenate multiple triangular meshes. - made function 'procAOVsym' (procrustes Anova for object symmetry) public. - made functions 'cSize', 'mcNNindex', 'meshcube', 'meshres', 'ProcGPA' public. - added option 'info' in 'read.mpp' - merged 'CreateL' and 'CreateL2D' - rewrote large parts of 'CVA', 'groupPCA' and 'permudist' to make the code more efficient - 'covPCA' now allows permutation tests to check if pairwise distances between covariance matrices are significant and reports rownames for two-group case - removed unnecessary complicated check for empty groups by simply using function 'factor' in 'covW' and 'typprobClass' - white space formatting in code - added option "mshape" to function 'orp' to specify a custom pole for projection - made function 'fx', 'PCAcrova' and 'calcTang_U' interntal-only by prefixing function name with '.' - removed unnecessary sinus calculation in 'angle.calc' - added docu and examples for all newly exposed functions (see above) - added examples for 'find.outliers' - added more examples for covPCA, performing permutation tests - added docu for function 'barycenter' - added a lot of examples to docu and documented data(nose) - added documentation for 'angle.calc' - added example in 'relaxLM' - added section "details" in procSym, added example in slider3d - added example for procAOVsym - changed parameters in examples for 'pls2B' and 'relaxLM' to decrease completion time - removed obsolete Fortran code - added minimum version for imported package 'Matrix'(>= 1.0-1) - changed foreach, parallel and rgl (needs rgl version >= 0.93.963) from 'Depends' to 'Imports' (affecting DESCRIPTION and NAMESPACE) - massive NAMESPACE editing by switching to manual export instead of regular expression export

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Published by zarquon42b over 12 years ago

Morpho - releasing v. 0.99 (1.0-alpha)

Windows version OSX version Linux version (source code)

Caution: the latest version of rgl (>= 0.93.963) is required

Changes in Morpho version 0.99 (2013-09-20) - added function 'checkLM'. Useful to visualize if projection by 'placePatch' was successful by browsing through sample. - added functions 'placePatch', 'createAtlas' and 'plotAtlas' for defining templates and functions to project (semi-) landmarks from an atlas onto all specimen in a given sample. - fixed missing '-1' subtraction in 'covW' - added function 'mergeMeshes' to concatenate multiple triangular meshes. - made function 'procAOVsym' (procrustes Anova for object symmetry) public. - made functions 'cSize', 'mcNNindex', 'meshcube', 'meshres', 'ProcGPA' public. - added option 'info' in 'read.mpp' - merged 'CreateL' and 'CreateL2D' - rewrote large parts of 'CVA', 'groupPCA' and 'permudist' to make the code more efficient. - 'covPCA' now allows permutation tests to check if pairwise distances between covariance matrices are significant and reports rownames for two-group case. - removed unnecessary complicated check for empty groups by simply using function 'factor' in 'covW' and 'typprobClass' - white space formatting in code - added option "mshape" to function 'orp' to specify a custom pole for projection - made function 'fx', 'PCAcrova' and 'calcTang_U' interntal-only by prefixing function name with '.' - removed unnecessary sinus calculation in 'angle.calc - changed foreach, parallel and rgl (needs rgl version >= 0.93.963) from 'Depends' to 'Imports' (affecting DESCRIPTION and NAMESPACE) - massive NAMESPACE editing by switching to manual export instead of regular expression export

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Published by zarquon42b almost 13 years ago

Morpho -

Windows version OSX version Linux version (source code)

Changes in Morpho version 0.25 (2013-07-24) - added docu for new data set "boneData" - added examples in procSym - replaced abind with bindArr in fixLMtps and procSym (fixes bug introduced in 0.25) - added additional example data (landmarks and a bone surface mesh) - added example in tps3d.Rd - updated DESCRIPTION and README - updated README added sourceforge and github download links - moved Distance calculation in CVA to .CVAdists and radically cleaned code; removal of redundant variables in groupPCA - added README.Rd - added option reflect to procSym (and underlying functions) and added copyright note for code copied from shapes package - added NEWS.Rd

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Published by zarquon42b almost 13 years ago

Morpho -

Windows version OSX version Linux version (source code)

Changes in Morpho version 0.25 (2013-07-24) - updated COPYRIGHT file - simplified code in CVA and CVA.crova and finally mentioned Marta Rufino for providing all examples in docu for CVA (sorry Marta, I simply forgot) - fixed issue when n-groups > n variables in CVA and CVA.crova - replaced nn2 (RANN) with ann (yaImpute) because RANN got (temporarily) banned from CRAN because of violation of policy - added readLandmarks.csv and docu to read landmarks stored in spreadsheet text files (e.g. comma separated) - added check for empty groups in typprobClass and covW - fixed some docu and added examples in pcaplot3d and rotonmat - changed cube creation in deformGrid3d (much faster now). - added options weights and centerweight in rotonmat - added confirmation for plotting spheres in deformGrid when n > 1000 (can be slow) - pcaplot3d now works if data has only 1 PC - removed useless code remains - added docu for anonymize, r2morphoj, r2morphologika, NNshapeReg, kendalldist - added bindArr to concatenate matrices/arrays - switched from depends to import for colorRamps, MASS, RANN - changed default core value in closemeshKD from detectCores() to 1. - added option 'keep' in rmVertex - changed default method in meshDist.mesh3d from vcglib to morpho - renamed regdist.raw to regdist and removed original regdist (too prone to user error)

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Published by zarquon42b almost 13 years ago