High-Performance Open-Source Archive
plotly for 3D graphics (was
previously RGL)RGL)shape.predictor and
gm.prcomp to indicate if estimated configurations should be
scaled to unit size.plotOutliers to allow distances from limited
PCs.physignal.eigen.physignal.eigen.physignal.eigen.physignal.eigen for evaluating the
dimensions of phylogenetic signal in multivariate datagm.prcomp to allow the phylogeny to
be scaled to unit lengthgroups.first argument to
gm.measurement.error, to optionally include groups in ANOVA
table.perm.index within
morphol.disparity.gm.prcomp.anc.BM.anc.BMintegration.Vrel and phylogeny
checksbilat.symmetry and
removed signed.AIreadland.tps and negNA = TRUEplot.gm.prcomp phylo.par
defaultgm.measurement.errorestimate.missing for shapes files and
TPS optionbilat.symmetryreadmulti.tpslambda.opt internal function, for use
in physignal.z, which precluded verbose results.readland.tps and
readmulti.tps, rather than just return an error.readland.tps when
warnmsg = FALSEbilat.symmetry (updated nested model
computations)readland.tps when curves exist but are
not to be readmodularity.test and
phylo.modularitylogLikh internal function that required
matrix class objects for calculation.procD.lm that caused lost
results.bilat.symmetryreadland.fcsv to be consistent with SlicerMorph
updates.modularity.test and
phylo.modularity rglestimate.missing for failing
with method = "Reg" to estimate landmarks.shape.predictor examples to PLS functions.physignal.zcompare.physignal.zplotspec and picknplot.shape
functions to accommodate changes in rglintegration.Vrelcompare.ZVrellambda argument to
procD.pgls.Cov.proj function to work with
RRPPcompare.CR when CR.null = TRUE.anc.BM for singleton nodescompare.CR when CR.null = TRUE.anc.BM for singleton nodesmorphol.disparity for
PGLS models, consistent with gm.prcomp approaches.module.eigen, plus S3 generic associated
functions.na.omit.geomorph.data.frame.as.matrix names dropping in support
code.compare.pls and
compare.CR to use box-cox transformed values.phylo.integration and
phylo.modularity.gridPar.r.readmulti.tps to allow for any kind of tps
input and correctly combine them into an arrayintegration.test (only affected
separate matrices).estimate.missing (only affecting method =
“Reg”).bilat.symmetry outputbilat.symmetry to use arguments available with
updates to RRPP::lm.rrpp, taking advantage of parallel
processing, C++, and turbo-charged (coefficient-suppressed) calculations
to maximize speed.make_ggplot2
function for converting geomorph plots to
ggplot objects, which can be amended.plotAllometry where crossprod
was used instead of tcrossprodphylo.integrationintegration.test for permutationseffect.sizeplot.gm.prcompintegration.test
and phylo.integrationcompare.CR so object labels are
retainedplot.bilat.symmetry that missed changed
object output in bilat.symmetry.integration.test and phylo.integrationplot.gm.prcomp 3D tree plotting with
time.plot = TRUEcompare.evol.rates for univariate data
and permutationsplot.gm.prcomp.summary.gm.prcomp as an
objectwarpRefMeshcompare.evol.rates
related to R 4.0.2 changesmodularity.test & phylo.modularityphylo.modularityphylo.modularityplotRefToTarget, allowing 3d TPS warp
grids to show labels and for txt.pos to be passed to 3d plotsgridParreadmulti.nts function turning it into a
wrapper of readland.nts thus allowing also multiple dta
files to be read in and compiledgeomorph:::plsgm.prcomp to include PaCA.plot.gm.prcomp.plotspec.lizards.mshape now has options (na.action
argument) for missing values.readland.fcsv for importing landmark data
from SlicerMorph .fcsv files.combine.subsets updated to include weighting options
for relative centroid size.compare.evol.rates and
compare.multi.evol.ratesbilat.symmetryplotGMPhyloMorphospace and
plotTangentSpace now deprecatedbilat.symmetry (use
DA.component and FA.component)readmulti.tpscompare.evol.rates,
compare.multi.evol.rates,integration.test,
modularity.test, phylo.integration,
phylo.modularity, physignal,
two.b.plscompare.CRreadmulti.tpsmshape inability to distinguish between one p x k
specimen and a n x pk matrix.procD.allometry, advanced.procD.lm and
nested.update through procD.lm and other
RRPP tools; 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 proceduresreadland.tps now includes an argument (negNA = FALSE)
to define whether negative landmark coordinates should be transformed to
NAs (by setting the argument to TRUE)combine.subsets for gpagen objectsprocD.lm to work better with missing data
framesbilat.symmetryprocD.lm outputreadland.shapescompar.evol.rates to utilize all
simulated datasetsfixed.angleGMfromShapes1RRPPplotAllometry,
gm.prcomp, picknplot.shape,
shape.hullsadvanced.procD.lm,
nested.update, procD.allometry (features of
these functions now found using procD.lm)geiger and
Matrixcompare.evol.rates for
permutationsfixed.angle to allow centroids from multiple
points to be used as angle points.coords.subset to avoid issue with arrayspecs
and naming subsetted data.gpagengpagen outputtrajectory.analysis to RRPP package
and updated its argumentsmorphol.disparitycompare.evol.ratesphylo.modularity call when groups >
2combine.subsetstrajectory.analysis to properly center mean
values for PC plotting (now in RRPP)gpagen, to
avoid errorsreadland.tpsprocD.allometryadvanced.procD.lm now performed using
RRPP packagebilat.symmetry so output shapes
retain order in ‘ind’ factorreadland.tps to identify missing data only
when all lm coordinate are <0 and interactively prompt the user to
confirm if they are to be treated as NAsplotOutliers now allows to plot outlier configurations
in order to compare their shape with the consensusplot.mshape function added to plot the consensus
configuration with numbers and linksgm.prcomp implements raw and weighted PCA
and allows S3 generic plotting of its outputreadland.shapes allows reading a shapes
file produced by StereoMorph, including landmark data and (potentially
multiple) curves, and sampling semilandmarks from these curves.picknplot.shape allows interactively
picking points in geomorph scatterplots to visualize shape variation
across morphospace.readland.tps to 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.bilat.symmetry and
geomorphShapes option to allow more flexible
gpagen options withinprocD.pgls to use residuals from GLS model for
permutationsadvanced.procD.lmplot.procD.allometry to allow direct control
of all plotting arguments by the userplotRefToTarget and tps to use plot.xy instead
of plot, and thus avoid conflicts with plot.mshapereadland.tps, to
identify negative values and recode them as NAsphylo.modularitycompare.evol.rates permutation method
for univariate traitestimate.missing regression
approachphylo.integration where Y-dataset
contained a single variableintegration.test when 3+ partitions
with non-contiguous variablesprocD.lm for
single factor OLS models.procD.fitprocD.allometryprocD.allometryreadland.nts when file
contained a single specimen’s datamorphol.disparity
when phylogeny utilizedreadland.tps to be general to whitespace
delimitationinterlmkdist to calculate linear
distances between landmarks (interlandmark distances)advanced.procD.lmprocD.lm,
procD.pgls)procD.lm and procD.pgls, with limited
outputcompare.evol.ratesplotTangentSpace to pass
arguments to prcomp. Also, adjusted default tolerance to
remove redundant PC dimensions.arrayspecsarrayspecs
and two.d.arrayprocD.lmplotGMPhyloMorphoSpace to center data by
phylogenetic meanread.morphologika now supports lists of file names to
return a single data objectreadland.nts and
readmulti.nts to avoid ambiguity and resolve misinformation
in previous versionsreadland.nts to accept specimen labels with
spaces in nameprocD.fitadvanced.procD.lmplotAllSpecimens if no
colour specifiedintegration.test and
phylo.integrationcompare.pls, coords.subset,
shape.predictordroplevels.geomorph.data.frame added to support
codeprocD.lm and its
allies to choose the computationally fastest algorithms based on design
matrix complexity and data dimensionalityprocD.fit to remove unused levels from
factorsgeomorph.data.frame to drop
unused factor levelsmshape to be used on lists, arrays, or
matricessingle.factor function to properly maintain
factor levels when combining factorsphylo.integrationplot.procD.allometry and plot.plswriteland.tpstwo.b.plsprocD.allometryplot.procD.allometry (method=“PredLine”)plotTangentSpace when groups are
specifiedplotTangentSpace; function now
returns PC scores automatically when assigned to objectplotTangentSpace to return min and max shapes
for all PC axes in $pc.shapesbilat.symmetry shape
componentsplot.procD.allometrydigit.curves where open outline would be
treated as closed if starting point was the end pointreadland.tps for some
tps filesphytoolsprocD.pglsread.morphologikaplotTangentSpace, plot.bilat.symmetry,
plot.procD.allometry, plot.plsplot.procD.allometry to
designate plotting colorsplotOutliersadvanced.procD.lmphylo.modularityprocD.Allometryphylo.integration
(via plot.pls)plot.pls, regarding best
fit line and matrix reduction.gpagen source files:
indexing errors, arbitrary PC rotations for surface points, maximum
iteration disparity.digitize2D scaling issue when different scales
used in each imagephylo.integration error when 3+ partitions
examinedmodularity.test for CI intervals into
matrix inputphylo.integration so
that prob(A,B|phy)~prob(B,A|phy)plotAllSpecimens where links were not
being plottedmodularity.test,
integration.test, phylo.modularity,
phylo.integration, procD.allometry,
nested.update, geomorph.data.framenested.update of procD.lm
objectscompare.modular.partitions,
morphol.integr, phylo.pls, and
plotAllometrygpagenphysignal. Only Kmult
useddigitize2dplotAllSpecimensmorphol.disparity$Prob.Disp displaying NAsgpagencompare.multi.evol.rates for comparing
rates of evolution among traitsplotGMPhyloMorphoSpace now plots 3D phylomorphospaces
and chronophylomorphospacesbilat.symmetry,
compare.modular.partitions, globalIntegration,
morphol.integr, and phylo.plsgpagen (added additional
checks on alignment)advanced.ProcD.lm: for
single-factor analyses and matrix/variable inputreadland.nts flexibility with specimen labels;
now supports spaces in labelsread.ply to allow reading meshes with many
propertiesphysignal and
compare.evol.rates: univariate data accepted as named
vectordefine.links: read and append links
to existing links matrixwarpRefMesh where normals were
incorrectly assigned to new mesh3d objectreadland.tps which read in a file
containing a single specimen returned a 2D matrix rather than 3D array;
this fixes the issue with digitize2d not working for a
single filemorphol.integr where warpgrids = F
did not work for 3D datasetsglobalIntegration for use with 3D
dataplotRefToTarget method = “TPS” where
the wrong options from gridPars were being passedcompare.evol.rates
generalized to use a single evolutionary rate matrixpairwiseD.test and pairwise.slope.test now
defunctdefine.sliders.2d and define.sliders.3d
now defunctread.morphologika can read files with missing dataphysignal and
compare.evol.ratesdigit.curvesbuild.template and digitsurfacegridPar is a new function to customize plots of
plotRefToTargetdigit.curves is a new function to calculate
equidistant semilandmarks along 2D and 3D curvesdefine.sliders is new interactive function for defining
sliding semilandmarks for 2D and 3D curves, plus an automatic mode when
given a sequence of semilandmarks along a curvepairwiseD.test and pairwise.slope.test
deprecateddefine.sliders.2d and define.sliders.3d
deprecated (replaced by define.sliders)plotAllometry where verbose=T did
not returnwarpRefMesh generalized - now takes a mesh3d object
(i.e. made from read.ply) rather than calling
read.ply directlyread.morphologika now reads [groups] option and adds
these data to the $labels matrixplotOutliers now has option groups to plot outliers by
levels(groups) using group meansmorphol.disparity help file updated to correctly
indicate that group shape residuals, rather than shape values,
themselves, are randomized in the permutation proceduregpagenreadland.tpstrajectory.analysisgpagen that flipped principal
axesread.morphologika with reading
[wireframe] in some morphologika filesplotOutliers function to identify potential
outliersdefine.links function for enhanced plotting of
shapespairwiseD.test and
pairwise.slope.testphysignal, compare.evol.rates,
procD.pgls and phylo.plsbuild.template,
define.modules, define.sliders.3d,
digit.fixed, digitsurface, and
editTemplate )plotAllometry input can be 2D matrix or 3D arrayread.ply reads normals for enhanced downstream
digitizing from ply filesreadland.tps reads curves from tps files and convert
them to landmarks (semilandmarks)plotTangentSpace has enhanced plotting flexibility with
labels and colorsbilat.symmetryphylo.plsadvanced.procD.lm for statistically
comparing two or explanatory modelsplotRefToTargetwarpRefOutlineprocD.pglsprocD.lm,
procD.pgls pairwiseD.test and
pairwise.slope.testarrayspecsphylo.plsplotAllometryprocD.lm when verbose=TRUEgpagengpagen
with option to disablefastAnc (phytools)procD.lm,
pairwise.D.test and pairwise.slope.testreadland.tpsplotTangentSpaceplotAllometryprocD.pgls added to assess high-dimensional ANOVA and
regression models in a phylogenetic contextpairwise.slope.test added to compare slopes of
regression linesprocD.lm and
pairwise.d.testdigitize2d. Function now reads
multiple images and outputs TPS file, can be used with missing data, and
digitizing session can be restarted where previous session stoppedtwo.b.pls,
morphol.integr, and phylo.plsbilat.symmetryplotAllometry and plotTangentSpaceplotGMPhyloMorphoSpacedigitize2dgpagenphylo.pls for assessing the multivariate
association between two blocks of variables in a phylogenetic
contexttwo.b.pls for assessing the multivariate
association between two blocks of variablesmorphol.disparity to compare Procrustes
variance disparity among groupsProcD.lmplotRefToTarget, plotTangentSpace,
plotAllometry, and bilat.symmetrywarpRefMesh to create a mesh3d
surface that represents the mean shape, findMeanSpec to
assist in choosing a template ply file for use with
warpRefMesh that identifies specimen closest to the mean
shape, and defline.modules to interactively assign
landmarks to modular partitions [currently 2D only]compare.evol.rates,
phylo.pls, morphol.integr,
two.b.pls, physignal, and
plotGMPhyloMorphoSpacecompare.evol.rates and physignalbilat.symmetry, phylo.pls,
two.b.pls, morphol.integr,
plotAllometry, plotTangentSpace,
physignalcompare.evol.ratesmorphol.integrarrayspecs has been removedplotAllometry (method = “CAC”)plotAllometry outputbuild.Template, digit.fixed,
digitsurface, and plotSpecread.vrml now defunctarrayspecs, readland.tps,
readland.nts, readmulti.nts,
two.d.array, plotTangentSpace,
trajectory.analysis, bilat.symmetry,
gpagenbilat.symmetrydigitize2D and updated
flexibility of the functionreadmulti.ntsdefine.sliders.3d to allow
sliders to be in any orderpPsup (original code from J. Claude) to not
include size re-scaling by beta (underlying function used in
trajectory.analysis only)compare.evol.ratescompare.evol.rates for comparing
multivariate evolutionary rates on phylogeniesdefine.sliders.2d and define.sliders.3d
replace curves2d and digit.curvesplotTangentSpace and PlotAllometrymorphol.integrcurves2d and digit.curves deprecatedplotAllometryread.plydigitsurface, buildtemplate,
plotspec, digitfixed, and
digitcurves now support ply file inputplotRefToTartgetread.vrml code for additional file
formatspairwiseD.test function addedbilat.symmetry output includes symmetric and asymmetric
shape componentsmorphol.integr to be
compatible with new CRAN guidelinesbilat.symmetry to be
compatible with new CRAN guidelinesphysignalPlotGMPhyloMorphoSpacereadland.tps to allow for non-numeric ID and
reading a single specimen per filecurves2Ddigitize2Dread.morphologikafixed.angleplotTangentSpacephysignal and
PlotGMPhyloMorphoSpacephysignal on
getAncStates from geiger, which is no longer
supportedplotGMPhyloMorphoSpace on
getAncStates from geiger, which is no longer
supportedbilat.symmetry function addedwriteland.tps function addedfixed.angle function addedcompare.modular.partitions generalized to allow 2 or
more partitionsmorphol.integr generalized to allow 2 or more
partitionstrajectory.analysis re-written to accept formulas,
allowing greater flexibility for motion analysismorphol.integrphysignalplotAllometryplotTangentSpaceplotTangentSpaceplotTangentSpaceread.morphologika accepts greater variety of input file
formatsbuildtemplate positional error in plot between
template and scan corrected
digit.curves error with passing objects to internal
function corrected
gpgen occasional reflection issue corrected
Added a NEWS.md file to track changes to the
package.
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