- Added new K-components output and plots to
physignal.eigen.
- Updated handling of p > n conditions in
physignal.eigen.
- New function 'extended.pgls' for evaluating within-species trends in a phylogenetic context
- New dataset 'pupfish.ws'
- New function
physignal.eigenfor evaluating the dimensions of phylogenetic signal in multivariate data - Added an option to
gm.prcompto allow the phylogeny to be scaled to unit length - Added
groups.firstargument togm.measurement.error, to optionally include groups in ANOVA table.
- Fixed missing argument in
perm.indexwithinmorphol.disparity. - Ensured proper size-scaling of predicted shapes in
gm.prcomp. - Fixed the missing re-order of data for
anc.BM.
- Improved
anc.BM
- Internal changes for compliance with RRPP and Matrix changes
- Fixed issue with
integration.Vreland phylogeny checks - Fixed issue with unsigned.AI in
bilat.symmetryand removed signed.AI - Fixed issue with
readland.tpsand negNA = TRUE - Fixed issue with
plot.gm.prcompphylo.pardefault
- New function,
gm.measurement.error
- Fixed issue with
estimate.missingfor shapes files and TPS option - Fixed names issue with
bilat.symmetry - Fixed problems with ellipsis use in
readmulti.tps - Fixed issue with
lambda.optinternal function, for use inphysignal.z, which precluded verbose results.
- Reversed order of asymmetry components for internal consistency
- Updated internal code and Rd file formats to match new CRAN policies
- Added a feature to print a table to identify inconsistent landmarking in both
readland.tpsandreadmulti.tps, rather than just return an error.
- Fixed issue with
readland.tpswhenwarnmsg = FALSE - Fixed issue with
bilat.symmetry(updated nested model computations) - Fixed issue with
readland.tpswhen curves exist but are not to be read - Fixed issue with bootstrap CI for
modularity.testandphylo.modularity - Fixed a bug in
logLikhinternal function that requiredmatrixclass objects for calculation. - Fixed a typo bug in
procD.lmthat caused lost results. - Fixed names being dropped from shape components in
bilat.symmetry - Fixed
readland.fcsvto be consistent with SlicerMorph updates.
- Additional error checking in
modularity.testandphylo.modularityrgl - Added better warning for
estimate.missingfor failing withmethod = "Reg"to estimate landmarks. - Added
shape.predictorexamples to PLS functions.
- New function,
physignal.z - New function,
compare.physignal.z
- Updated
plotspecandpicknplot.shapefunctions to accommodate changes inrgl
- New function,
integration.Vrel - New function,
compare.ZVrel - Added a
lambdaargument toprocD.pgls.
- Updated
Cov.projfunction to work withRRPP
- Fixed issue in
compare.CRwhen CR.null = TRUE. - Added catch to
anc.BMfor singleton nodes
- Fixed issue in
compare.CRwhen CR.null = TRUE. - Added catch to
anc.BMfor singleton nodes
- Added a transform argument to
morphol.disparityfor PGLS models, consistent withgm.prcompapproaches. - New function,
module.eigen, plus S3 generic associated functions. - New function,
na.omit.geomorph.data.frame.
- Fixed some
as.matrixnames dropping in support code. - Fixed pairwise Z-scores in
compare.plsandcompare.CRto use box-cox transformed values. - Added Pcov as needed output
phylo.integrationandphylo.modularity. - Fixed small issue with label plotting in
gridPar.r. - Fixed bug in
readmulti.tpsto allow for any kind of tps input and correctly combine them into an array - Fixed typo bug in
integration.test(only affected separate matrices). - Fixed bug in
estimate.missing(only affecting method = "Reg").
- Included calculation of individual asymmetry indices to
bilat.symmetryoutput - Updated
bilat.symmetryto use arguments available with updates toRRPP::lm.rrpp, taking advantage of parallel processing, C++, and turbo-charged (coefficient-suppressed) calculations to maximize speed. - More options for parallel processing.
*
make_ggplot2function for convertinggeomorphplots toggplotobjects, which can be amended.
- Fixed bug in
plotAllometrywherecrossprodwas used instead oftcrossprod - Fixed typo causing error in
phylo.integration - Fixed issue in
integration.testfor permutations
- Added Box-Cox transformation to
effect.size - Added an argument to flip axes in
plot.gm.prcomp - Added pairwise r, Z, and P-values to
integration.testandphylo.integration
- Fixed bug in
compare.CRso object labels are retained - Fixed bug with
plot.bilat.symmetrythat missed changed object output inbilat.symmetry. - Fixed issue with permutations in multi-module configurations for
integration.testandphylo.integration - Fixed error in
plot.gm.prcomp3D tree plotting with time.plot = TRUE - Fixed error in
compare.evol.ratesfor univariate data and permutations - Fixed plotting parameter arguments for phylo.par in
plot.gm.prcomp. - Made it possible to assign
summary.gm.prcompas an object - Fixed plotting issue in
warpRefMesh - Fixed single variable issue in
compare.evol.ratesrelated to R 4.0.2 changes - Added factor labels to output object CR.mat in
modularity.test&phylo.modularity - Fixed bug in computations of
phylo.modularity - Fixed order consistency for pairwise calculations in
phylo.modularity - Allows single landmarks as slider LM in gpagen
- Fixed labels in
plotRefToTarget, allowing 3d TPS warp grids to show labels and for txt.pos to be passed to 3d plots - Fixed bug in txt.adj argument for
gridPar
- Updated
readmulti.ntsfunction turning it into a wrapper ofreadland.ntsthus allowing also multiple dta files to be read in and compiled
- Fixed non-centering issue in
geomorph:::pls
- A vignette has been added (geomorphPCA) to aid the transition of users to the gm.prcomp family of functions for exploring and visualizing shape space.
- Updates to
gm.prcompto include PaCA. - Added the possibility of a 3D PCA plot with a phylogeny and time on the z-axis to
plot.gm.prcomp. - Added the possibility of controlling plot3d definitions in
plotspec. - New dataset of dorsal views of lizard heads added:
lizards. mshapenow has options (na.actionargument) for missing values.- New function,
readland.fcsvfor importing landmark data from SlicerMorph.fcsvfiles. combine.subsetsupdated to include weighting options for relative centroid size.
- Fixed row order issue for BM simulation in
compare.evol.ratesandcompare.multi.evol.rates - Fixed bug in FA shape components output in
bilat.symmetry - Fixed pGPA issue to use first specimen rather than mean in first iteration
plotGMPhyloMorphospaceandplotTangentSpacenow deprecated- Removed DA.mns and FA.mns from
bilat.symmetry(use DA.component and FA.component) - Option for handling NAs added to mshape and plot.mshape
- Function plotTangentSpace has been deprecated
- Added the possibility of plotting an outline with method = "vector" in plotRefToTarget
- Fixed small bug in plot.mshape par definitions
- Amended specimen name extraction from .tiff files when using imageID in readland.tps
- Function plotGMPhyloMorphoSpace has been deprecated
- New function added:
readmulti.tps
- Fixed small bug in readland.tps to accurately replace negative values with NA when only one specimen has NAs and allow for NAs in the original file
- Effect sizes provided in the output of
compare.evol.rates,compare.multi.evol.rates,integration.test,modularity.test,phylo.integration,phylo.modularity,physignal,two.b.pls
- Adjustment in 'class' statements to be compliant with new handling of objects in R 4.0
- Fixed small bug in plotAllometry that returned spurious RegScore values.
- Adjusted calculations of pairwise effect size in compare.pls and compare.CR to mirror publication equations
- Fixed issue with 3D plotting in plotOutliers with inspect.outliers = T
- New function added:
compare.CR - New function added:
readmulti.tps
- Adjustment to getSurfPCs to allow for more robust surface sliding
- Added a one-tail/two-tailed option to compare.pls
- Fixed
mshapeinability to distinguish between one p x k specimen and a n x pk matrix. - Fixed issue with 3D TPS grids in plotRefToTarget
- Fixed issue with digit.fixed, digitsurface, plotspec, warpRefMesh, build.template, for null ply $material, due to rgl updates
- Updated example in read.ply to not give bad advice for ply $material
- Fixed issue with 3D plotting in plotOutliers with inspect.outliers = T
- Three vignettes have been added: one assists the user in implementing analyses previously included in the deprecated functions
procD.allometry,advanced.procD.lmandnested.updatethroughprocD.lmand otherRRPPtools; the second provides a comprehensive list of main geomorph functions and their use; and the third is a step-by-step demonstration of 3D digitizing procedures readland.tpsnow includes an argument (negNA = FALSE) to define whether negative landmark coordinates should be transformed to NAs (by setting the argument to TRUE)
- Fixed bug with
combine.subsetsfor gpagen objects - Tweaked
procD.lmto work better with missing data frames - Fixed p-value miscalculation in
bilat.symmetry - Added meshColor specification in plotting of 3d meshes (to match RGL change)
- Fixed text plot for 3D (to match RGL changes)
- Added missing gls component in
procD.lmoutput - Fixed missing SS.types for pgls
- Fixed single landmark issue in
readland.shapes - Updated simulator for
compar.evol.ratesto utilize all simulated datasets - Updated rotation in
fixed.angle - Removed code causing warning in
GMfromShapes1
- Permutation computations now performed in
RRPP - New functions added:
plotAllometry,gm.prcomp,picknplot.shape,shape.hulls - Deprecated:
advanced.procD.lm,nested.update,procD.allometry(features of these functions now found usingprocD.lm) - Generalized plotting options
- Reduced dependencies on
geigerandMatrix - Added mean-centering to
compare.evol.ratesfor permutations - Updated
fixed.angleto allow centroids from multiple points to be used as angle points. - Updated
coords.subsetto avoid issue with arrayspecs and naming subsetted data. - Changed the default for sliding to ProcD=FALSE in
gpagen - Added Procrustes distance matrix to
gpagenoutput - Moved
trajectory.analysistoRRPPpackage and updated its arguments - Added partial disparity option to
morphol.disparity
- Fixed ratio call for permutations in
compare.evol.rates - Fixed bug in
phylo.modularitycall when groups > 2 - Fixed scaling default in
combine.subsets - Updated
trajectory.analysisto properly center mean values for PC plotting (now in RRPP) - Added a trap for large distance matrices to
gpagen, to avoid errors - Fixed bug to allow for a single specimen with missing data in
readland.tps - Fixed bug for HOS result mismatching criterion for
procD.allometry
- Computations for
advanced.procD.lmnow performed using RRPP package - Modified output in
bilat.symmetryso output shapes retain order in 'ind' factor - Modified
readland.tpsto identify missing data only when all lm coordinate are <0 and interactively prompt the user to confirm if they are to be treated as NAs
plotOutliersnow allows to plot outlier configurations in order to compare their shape with the consensusplot.mshapefunction added to plot the consensus configuration with numbers and links- New function
gm.prcomp implements raw and weighted PCA and allows S3 generic plotting of its output - New function
readland.shapesallows reading a shapes file produced by StereoMorph, including landmark data and (potentially multiple) curves, and sampling semilandmarks from these curves. - New function
picknplot.shapeallows interactively picking points in geomorph scatterplots to visualize shape variation across morphospace.
- Modified previous addition to
readland.tpsto identify missing data only when all lm dimensions are <0 and interactively prompt the user to confirm if they are to be treated as NAs. - Added ellipsis to
bilat.symmetryandgeomorphShapesoption to allow more flexiblegpagenoptions within - Changed
procD.pglsto use residuals from GLS model for permutations - Added effect type option to
advanced.procD.lm - Added an additional line of summary to ANOVA tables to signal how effect sizes are calculated
- Adjusted ANOVA tables to show from which distributions P-values are estimated
- Modified
plot.procD.allometryto allow direct control of all plotting arguments by the user - Modified
plotRefToTargetand tps to use plot.xy instead of plot, and thus avoid conflicts withplot.mshape - Added catch for missing data to
readland.tps, to identify negative values and recode them as NAs
- Fixed multi-group output in
phylo.modularity - Fixed issue with
compare.evol.ratespermutation method for univariate trait - Fixed issues with
estimate.missingregression approach - Fixed issues with
phylo.integrationwhere Y-dataset contained a single variable - Fixed issue with
integration.testwhen 3+ partitions with non-contiguous variables - Fixed effect size calculation error in
procD.lmfor single factor OLS models. - Fixed ellipses options in
procD.fit
- Simplified options available in
procD.allometry
- Fixed CAC calculations in
procD.allometry - Fixed dimnames error in
readland.ntswhen file contained a single specimen's data - Fixed PGLS weights for factors in
morphol.disparitywhen phylogeny utilized - Fixed
readland.tpsto be general to whitespace delimitation
- New function:
interlmkdistto calculate linear distances between landmarks (interlandmark distances) - PGLS option for
advanced.procD.lm - An option to use types I, II, or III sums of squares and cross-products for ANOVA analyses (e.g.,
procD.lm,procD.pgls) - An option to choose between SS, F-values, or Cohen's f-squared to calculate effect sizes for ANOVA analyses
- Effect sizes are now centered on mean values from distributions of random statistics. Statistics are also log-transformed in certain cases to normalize distributions
- An option to use only an intercept as a model for
procD.lmandprocD.pgls, with limited output - An option to use permutation tests when comparing net evolutionary rates for
compare.evol.rates
- Added ellipsis programming to
plotTangentSpaceto pass arguments toprcomp. Also, adjusted default tolerance to remove redundant PC dimensions. - Enhanced landmark labeling in
arrayspecs - Created transferability of dimnames between
arrayspecsandtwo.d.array - Updated Rd files for PLS functions to better cross-reference the similar functions
- Added data frame output to
procD.lm - Change to
plotGMPhyloMorphoSpaceto center data by phylogenetic mean read.morphologikanow supports lists of file names to return a single data object- Updated Rd files for
readland.ntsandreadmulti.ntsto avoid ambiguity and resolve misinformation in previous versions - Updated
readland.ntsto accept specimen labels with spaces in name
- Fixed problem with incorporating lm arguments in
procD.fit - Fixed univariate PLS to allow negative correlations
- Fixed permutation issues with
advanced.procD.lm - Fixed links not plotting in
plotAllSpecimensif no colour specified - Added missing random.r output to
integration.testandphylo.integration
- New functions:
compare.pls,coords.subset,shape.predictor droplevels.geomorph.data.frameadded to support code
- Added a sensor to support code for
procD.lmand its allies to choose the computationally fastest algorithms based on design matrix complexity and data dimensionality - Updated
procD.fitto remove unused levels from factors - Updated all functions using
geomorph.data.frameto drop unused factor levels - Updated
mshapeto be used on lists, arrays, or matrices
- Fixed
single.factorfunction to properly maintain factor levels when combining factors - Fixed plotting issues with
phylo.integration
- Added return of min/max shape matrices to
plot.procD.allometryandplot.pls - Added option to save specimen ID to ID= line in
writeland.tps
- Optimized analytical functions for faster computations
- Added force match of specimen order between blocks in
two.b.pls - Updated A, Ahat, ref, p and k outputs when 2D matrix is used in
procD.allometry - Added option to plot group labels in
plot.procD.allometry(method="PredLine") - Added legend option to
plotTangentSpacewhen groups are specified - Removed 'verbose' from
plotTangentSpace; function now returns PC scores automatically when assigned to object - Updated
plotTangentSpaceto return min and max shapes for all PC axes in $pc.shapes
- Fixed label output issue with
bilat.symmetryshape components - Fixed error plotting TPS grids when groups were included in
plot.procD.allometry - Fixed error in
digit.curveswhere open outline would be treated as closed if starting point was the end point - Fixed reading of ape::chronos phylogenies in 'phylo' functions
- Fixed error in reading names in
readland.tpsfor some tps files
- Removed dependency on
phytools - Small addition to outputs in
procD.pgls - Added reading polygons in
read.morphologika - Plots of 3D shapes now plotted in pairs in single rgl window for:
plotTangentSpace,plot.bilat.symmetry,plot.procD.allometry,plot.pls - Functions performing warping of 3D meshes now present progress bar
- Added option pt.col to
plot.procD.allometryto designate plotting colors
- Fixed error in output order in
plotOutliers - Fixed error in calculation slope distances in
advanced.procD.lm - Fixed 2D data input error for
phylo.modularity - Fixed centering error for CAC scores in
procD.Allometry - Fixed deformation plot issue with
phylo.integration(viaplot.pls) - Fixed two small issues with
plot.pls, regarding best fit line and matrix reduction. - Fixed three small issues with
gpagensource files: indexing errors, arbitrary PC rotations for surface points, maximum iteration disparity. - Fixed
digitize2Dscaling issue when different scales used in each image - Fixed
phylo.integrationerror when 3+ partitions examined - Fixed typo in
modularity.testfor CI intervals into matrix input - Updated permutation procedure in
phylo.integrationso that prob(A,B|phy)~prob(B,A|phy) - Fixed typo in
plotAllSpecimenswhere links were not being plotted
- New functions:
modularity.test,integration.test,phylo.modularity,phylo.integration,procD.allometry,nested.update,geomorph.data.frame - Seed option added for most analytical functions
- Major overhaul of underlying support code for analytics
- Output from analytical functions provided in lists
- Added 'summary' option to most analytical functions
- Plotting for most analytical functions as 'plot(res)' if res is output from function
- Diagnostic plots for anova/regression added
- Nested ANOVA via
nested.updateofprocD.lmobjects
- Deprecated:
compare.modular.partitions,morphol.integr,phylo.pls, andplotAllometry - Removed internal C-code for
gpagen - Removed automatic plots for most analytical functions
- Removed method="" parameter from
physignal. Only Kmult used - Removed verbose option for most functions: all output provided in lists
- Added option to pre-multiply coordinates by scale in
digitize2d - Added plotting options to
plotAllSpecimens
- Fixed
morphol.disparity$Prob.Dispdisplaying NAs
- Fixed small change in C-code for
gpagen
- New function
compare.multi.evol.ratesfor comparing rates of evolution among traits plotGMPhyloMorphoSpacenow plots 3D phylomorphospaces and chronophylomorphospaces- Added ShowPlot option to
bilat.symmetry,compare.modular.partitions,globalIntegration,morphol.integr, andphylo.pls
- Updated Imports packages as per new CRAN policies
- Small change to C-code for
gpagen(added additional checks on alignment) - Package ape now full Import for geomorph (no longer ImportsFrom)
- Enhanced input flexibility for
advanced.ProcD.lm: for single-factor analyses and matrix/variable input - Enhanced
readland.ntsflexibility with specimen labels; now supports spaces in labels - Generalized
read.plyto allow reading meshes with many properties - Generalized input for
physignalandcompare.evol.rates: univariate data accepted as named vector - Enhanced input for
define.links: read and append links to existing links matrix
- Corrected error in
warpRefMeshwhere normals were incorrectly assigned to new mesh3d object - Corrected error in
readland.tpswhich read in a file containing a single specimen returned a 2D matrix rather than 3D array; this fixes the issue withdigitize2dnot working for a single file - Corrected error in
morphol.integrwhere warpgrids = F did not work for 3D datasets - Corrected issue with
globalIntegrationfor use with 3D data - Corrected bug in
plotRefToTargetmethod = "TPS" where the wrong options from gridPars were being passed
- New globalIntegration` function for evaluating integration vs. self-similarity of shape variation
- Coordinates returned by digitize2d` are now unscaled, and SCALE= returns the scale
- Phylogenetic simulation procedure in
compare.evol.ratesgeneralized to use a single evolutionary rate matrix pairwiseD.testandpairwise.slope.test now defunctdefine.sliders.2danddefine.sliders.3dnow defunctread.morphologikacan read files with missing data- Ability to not show plot added to
physignalandcompare.evol.rates
- Corrected error in defining starting point in
digit.curves
- ability to include pre-digitized landmarks added to
build.templateanddigitsurface - new
gridParis a new function to customize plots ofplotRefToTarget - new
digit.curvesis a new function to calculate equidistant semilandmarks along 2D and 3D curves define.slidersis new interactive function for defining sliding semilandmarks for 2D and 3D curves, plus an automatic mode when given a sequence of semilandmarks along a curve
pairwiseD.testandpairwise.slope.testdeprecated- 'read' functions now allow both tab and space delimited files
define.sliders.2danddefine.sliders.3ddeprecated (replaced by define.sliders)
- Corrected an error in
plotAllometrywhere verbose=T did not return
warpRefMeshgeneralized - now takes a mesh3d object (i.e. made fromread.ply) rather than callingread.plydirectlyread.morphologikanow reads [groups] option and adds these data to the $labels matrixplotOutliersnow has option groups to plot outliers by levels(groups) using group meansmorphol.disparityhelp file updated to correctly indicate that group shape residuals, rather than shape values, themselves, are randomized in the permutation procedure- Internal changes to support functions for compatibility with R 3.1.3
- Generalized plot inputs in
gpagen
- Corrected error
readland.tps - Corrected errors
trajectory.analysis - Corrected an issue with
gpagenthat flipped principal axes - Fixed error in
read.morphologikawith reading [wireframe] in some morphologika files
- new
plotOutliersfunction to identify potential outliers - new
define.linksfunction for enhanced plotting of shapes
- Additional input options added to
pairwiseD.testandpairwise.slope.test - Ability to accommodate singular phylogenetic covariance matrices in:
physignal,compare.evol.rates,procD.pglsandphylo.pls - Enhanced digitizing capability in:
build.template,define.modules,define.sliders.3d,digit.fixed,digitsurface, andeditTemplate) plotAllometryinput can be 2D matrix or 3D arrayread.plyreads normals for enhanced downstream digitizing from ply filesreadland.tpsreads curves from tps files and convert them to landmarks (semilandmarks)plotTangentSpacehas enhanced plotting flexibility with labels and colors
- Corrected error printing output of ANOVA table of
bilat.symmetry - Removed redundant permutation loop in
phylo.pls
- New function
advanced.procD.lmfor statistically comparing two or explanatory models - Added warping of outline in
plotRefToTarget - New function to warp a specimen outline to the reference:
warpRefOutline - Added ShowPlot option to `two.b.pls
- Added RRPP option to
procD.pgls - New dataset pupfish
- Enhanced underlying code in
procD.lm,procD.pglspairwiseD.testandpairwise.slope.test - Removed k>3 restriction in
arrayspecs - Added is.numeric check to
phylo.pls - Removed arrows from plots when groups included in
plotAllometry
- Fixed output of
procD.lmwhen verbose=TRUE - Fixed reflections of aligned coordinate axes when PrinAxes=TRUE in
gpagen
- Specimens rotated to their principal axes in
gpagenwith option to disable
- Underlying code for ancestral state estimation changed to use
fastAnc(phytools)
- Fixed concatenated SSCP matrix issue in
procD.lm,pairwise.D.testandpairwise.slope.test - Corrected issue reading specimen names in
readland.tps - Corrected color options for plotting groups in
plotTangentSpace - Corrected test for slope:group interaction in
plotAllometry
procD.pglsadded to assess high-dimensional ANOVA and regression models in a phylogenetic contextpairwise.slope.testadded to compare slopes of regression lines- Residual randomization options added to
procD.lmandpairwise.d.test - Enhanced capabilities of
digitize2d. Function now reads multiple images and outputs TPS file, can be used with missing data, and digitizing session can be restarted where previous session stopped
- Ability to plot specimen labels added to
two.b.pls,morphol.integr, andphylo.pls - Slight ANOVA table output adjustment in
bilat.symmetry - Vector of labels can be added for plotting in
plotAllometryandplotTangentSpace - Labels for ancestral states added to
plotGMPhyloMorphoSpace
- Fixed scale issue in
digitize2d
- Small change to C-code for
gpagen
- New function
phylo.plsfor assessing the multivariate association between two blocks of variables in a phylogenetic context - New function
two.b.plsfor assessing the multivariate association between two blocks of variables - New function
morphol.disparityto compare Procrustes variance disparity among groups - F-ratios and R-squared values added to output of
ProcD.lm - 3D Visualizations now include "surface" option to view shape deformation as warped mesh3d surfaces in the following:
plotRefToTarget,plotTangentSpace,plotAllometry, andbilat.symmetry - New I/O functions:
warpRefMeshto create a mesh3d surface that represents the mean shape,findMeanSpecto assist in choosing a template ply file for use withwarpRefMeshthat identifies specimen closest to the mean shape, anddefline.modulesto interactively assign landmarks to modular partitions [currently 2D only] - Generalized data input to allow 3D array or 2D matrix of data added to the following analysis functions:
compare.evol.rates,phylo.pls,morphol.integr,two.b.pls,physignal, andplotGMPhyloMorphoSpace - Ability to input univariate data added to
compare.evol.ratesandphysignal - Verbose output = T/F added to the following functions:
bilat.symmetry,phylo.pls,two.b.pls,morphol.integr,plotAllometry,plotTangentSpace,physignal
- Added calculation of pairwise Pvalues, and the option to assess a single group in function
compare.evol.rates - Additional graphical output added to
morphol.integr - Missing data handling altered (now NA is used)
- byLand option in
arrayspecshas been removed - Residual shape component (RSC) plot added and scores returned for
plotAllometry(method = "CAC") - Procrustes ANOVA added to
plotAllometryoutput - Centering = T/F option added to following 3D digitizing functions:
build.Template,digit.fixed,digitsurface, andplotSpec read.vrmlnow defunct- Major re-organization of underlying R code structure and format
- Optimized code to improve speed and performance in following functions:
arrayspecs,readland.tps,readland.nts,readmulti.nts,two.d.array,plotTangentSpace,trajectory.analysis,bilat.symmetry,gpagen - Simplified plotting options in
bilat.symmetry
- Corrected small coding error in
digitize2Dand updated flexibility of the function
- Minor I/O enhancements in
readmulti.nts - Minor I/O enhancements in
define.sliders.3dto allow sliders to be in any order - Simplified
pPsup(original code from J. Claude) to not include size re-scaling by beta (underlying function used intrajectory.analysisonly) - Added name.check for groups in
compare.evol.rates
- New function
compare.evol.ratesfor comparing multivariate evolutionary rates on phylogenies define.sliders.2danddefine.sliders.3dreplacecurves2danddigit.curves- Option allowing specimens to be colored by group added to
plotTangentSpaceandPlotAllometry
- Simplified options in
morphol.integr curves2danddigit.curvesdeprecated
- Corrected parameter estimates when groups specified for Regression Score option in
plotAllometry
- Enhanced plotting of ply files in
read.ply digitsurface,buildtemplate,plotspec,digitfixed, anddigitcurvesnow support ply file input
- Minor changes to plot window options in plotting functions
- Change to magnification factor usage in
plotRefToTartget
- Improved NAMESPACE file and package usage
- Generalized
read.vrmlcode for additional file formats
pairwiseD.testfunction addedbilat.symmetryoutput includes symmetric and asymmetric shape components
- Adjusted plotting routines in
morphol.integrto be compatible with new CRAN guidelines - Adjusted plotting routines in
bilat.symmetryto be compatible with new CRAN guidelines - Alternative ancestral state reconstruction and tests for bifurcating tree implemented in
physignal - Alternative ancestral state reconstruction and tests for bifurcating tree implemented in
PlotGMPhyloMorphoSpace
- Corrected
readland.tpsto allow for non-numeric ID and reading a single specimen per file - Corrected landmark plotting issue and added greater directory flexibility in
curves2D - Added greater directory flexibility and fixed header output in
digitize2D - Added greater flexibility in reading distinct file formats in
read.morphologika - Corrected angle calculations in
fixed.angle - Corrected plotting of deformations grids in
plotTangentSpace - Corrected ancestral state output in
physignalandPlotGMPhyloMorphoSpace
- Removed dependency in
physignalongetAncStatesfromgeiger, which is no longer supported - Removed dependency in
plotGMPhyloMorphoSpaceongetAncStatesfromgeiger, which is no longer supported
bilat.symmetryfunction addedwriteland.tpsfunction addedfixed.anglefunction addedcompare.modular.partitionsgeneralized to allow 2 or more partitionsmorphol.integrgeneralized to allow 2 or more partitionstrajectory.analysisre-written to accept formulas, allowing greater flexibility for motion analysis- PLS scores added to output
morphol.integr - Ancestral states added to output
physignal - Centroid size and allometry scores added as output in
plotAllometry - PC scores added to output of
plotTangentSpace - Option added to select PC axes for plot in
plotTangentSpace - Option added to include specimen numbers to
plotTangentSpace
read.morphologikaaccepts greater variety of input file formats
-
buildtemplatepositional error in plot between template and scan corrected -
digit.curveserror with passing objects to internal function corrected -
gpgenoccasional reflection issue corrected -
Added a
NEWS.mdfile to track changes to the package.