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

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)

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

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

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'

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

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

0.25-1

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

0.25

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)