NEWS.md
In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

CHANGES IN GEOMORPH VERSION 4.0.8

Improved anc.BM

Internal changes for compliance with RRPP and Matrix changes

Fixed issue with integration.Vrel and phylogeny checks
Fixed issue with unsigned.AI in bilat.symmetry and removed signed.AI
Fixed issue with readland.tps and negNA = TRUE
Fixed issue with plot.gm.prcomp phylo.par default

CHANGES IN GEOMORPH VERSION 4.0.7

New function, gm.measurement.error

Fixed issue with estimate.missing for shapes files and TPS option
Fixed names issue with bilat.symmetry
Fixed problems with ellipsis use in readmulti.tps
Fixed issue with lambda.opt internal function, for use in physignal.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.tps and readmulti.tps, rather than just return an error.

CHANGES IN GEOMORPH VERSION 4.0.6

Fixed issue with readland.tps when warnmsg = FALSE
Fixed issue with bilat.symmetry (updated nested model computations)
Fixed issue with readland.tps when curves exist but are not to be read
Fixed issue with bootstrap CI for modularity.test and phylo.modularity
Fixed a bug in logLikh internal function that required matrix class objects for calculation.
Fixed a typo bug in procD.lm that caused lost results.
Fixed names being dropped from shape components in bilat.symmetry
Fixed readland.fcsv to be consistent with SlicerMorph updates.

Additional error checking in modularity.test and phylo.modularity rgl
Added better warning for estimate.missing for failing with method = "Reg" to estimate landmarks.
Added shape.predictor examples to PLS functions.

CHANGES IN GEOMORPH VERSION 4.0.5

New function, physignal.z
New function, compare.physignal.z

Updated plotspec and picknplot.shape functions to accommodate changes in rgl

CHANGES IN GEOMORPH VERSION 4.0.4

New function, integration.Vrel
New function, compare.ZVrel
Added a lambda argument to procD.pgls.

CHANGES IN GEOMORPH VERSION 4.0.3

Updated Cov.proj function to work with RRPP

CHANGES IN GEOMORPH VERSION 4.0.2

Fixed issue in compare.CR when CR.null = TRUE.
Added catch to anc.BM for singleton nodes

CHANGES IN GEOMORPH VERSION 4.0.1

Fixed issue in compare.CR when CR.null = TRUE.
Added catch to anc.BM for singleton nodes

CHANGES IN GEOMORPH VERSION 4.0.1

Added a transform argument to morphol.disparity for PGLS models, consistent with gm.prcomp approaches.
New function, module.eigen, plus S3 generic associated functions.
New function, na.omit.geomorph.data.frame.

Fixed some as.matrix names dropping in support code.
Fixed pairwise Z-scores in compare.pls and compare.CR to use box-cox transformed values.
Added Pcov as needed output phylo.integration and phylo.modularity.
Fixed small issue with label plotting in gridPar.r.
Fixed bug in readmulti.tps to 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").

CHANGES IN GEOMORPH VERSION 4.0.0

Included calculation of individual asymmetry indices to bilat.symmetry output
Updated bilat.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.
More options for parallel processing. *make_ggplot2 function for converting geomorph plots to ggplot objects, which can be amended.

Fixed bug in plotAllometry where crossprod was used instead of tcrossprod
Fixed typo causing error in phylo.integration
Fixed issue in integration.test for permutations

CHANGES IN GEOMORPH VERSION 3.3.2 (Minor Release)

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.test and phylo.integration

Fixed bug in compare.CR so object labels are retained
Fixed bug with plot.bilat.symmetry that missed changed object output in bilat.symmetry.
Fixed issue with permutations in multi-module configurations for integration.test and phylo.integration
Fixed error in plot.gm.prcomp 3D tree plotting with time.plot = TRUE
Fixed error in compare.evol.rates for univariate data and permutations
Fixed plotting parameter arguments for phylo.par in plot.gm.prcomp.
Made it possible to assign summary.gm.prcomp as an object
Fixed plotting issue in warpRefMesh
Fixed single variable issue in compare.evol.rates related 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.nts function turning it into a wrapper of readland.nts thus allowing also multiple dta files to be read in and compiled

CHANGES IN GEOMORPH VERSION 3.3.1 (Patch Release)

Fixed non-centering issue in geomorph:::pls

CHANGES IN GEOMORPH VERSION 3.3.0 (Minor Release)

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.prcomp to 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.
mshape now has options (na.action argument) for missing values.
New function, readland.fcsv for importing landmark data from SlicerMorph .fcsv files.
combine.subsets updated to include weighting options for relative centroid size.

Fixed row order issue for BM simulation in compare.evol.rates and compare.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

plotGMPhyloMorphospace and plotTangentSpace now 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

CHANGES IN GEOMORPH VERSION 3.2.1.0900 (Minor Release)

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

CHANGES IN GEOMORPH VERSION 3.2.1

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

CHANGES IN GEOMORPH VERSION 3.2.0 (Minor Release)

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

CHANGES IN GEOMORPH VERSION 3.1.3 (Patch Release)

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 mshape inability 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

CHANGES IN GEOMORPH VERSION 3.1.2 (Patch Release)

Three vignettes have been added: one assists the user in implementing analyses previously included in the deprecated functions 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 procedures
readland.tps now 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.subsets for gpagen objects
Tweaked procD.lm to 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.lm output
Fixed missing SS.types for pgls

CHANGES IN GEOMORPH VERSION 3.1.1 (Patch Release)

Fixed single landmark issue in readland.shapes
Updated simulator for compar.evol.rates to utilize all simulated datasets
Updated rotation in fixed.angle
Removed code causing warning in GMfromShapes1

CHANGES IN GEOMORPH VERSION 3.1.0 (Minor Release)

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 using procD.lm)
Generalized plotting options
Reduced dependencies on geiger and Matrix
Added mean-centering to compare.evol.rates for permutations
Updated fixed.angle to allow centroids from multiple points to be used as angle points.
Updated coords.subset to avoid issue with arrayspecs and naming subsetted data.
Changed the default for sliding to ProcD=FALSE in gpagen
Added Procrustes distance matrix to gpagen output
Moved trajectory.analysis to RRPP package and updated its arguments
Added partial disparity option to morphol.disparity

Fixed ratio call for permutations in compare.evol.rates
Fixed bug in phylo.modularity call when groups > 2
Fixed scaling default in combine.subsets
Updated trajectory.analysis to 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

CHANGES IN GEOMORPH VERSION 3.0.7 (Patch Release)

Computations for advanced.procD.lm now performed using RRPP package
Modified output in bilat.symmetry so output shapes retain order in 'ind' factor
Modified readland.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 NAs

CHANGES IN GEOMORPH VERSION 3.0.6 (Patch Release)

plotOutliers now allows to plot outlier configurations in order to compare their shape with the consensus
plot.mshape function 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.shapes allows reading a shapes file produced by StereoMorph, including landmark data and (potentially multiple) curves, and sampling semilandmarks from these curves.
New function picknplot.shape allows interactively picking points in geomorph scatterplots to visualize shape variation across morphospace.

Modified previous addition to 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.
Added ellipsis to bilat.symmetry and geomorphShapes option to allow more flexible gpagen options within
Changed procD.pgls to 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.allometry to allow direct control of all plotting arguments by the user
Modified plotRefToTarget and tps to use plot.xy instead of plot, and thus avoid conflicts with plot.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.rates permutation method for univariate trait
Fixed issues with estimate.missing regression approach
Fixed issues with phylo.integration where Y-dataset contained a single variable
Fixed issue with integration.test when 3+ partitions with non-contiguous variables
Fixed effect size calculation error in procD.lm for single factor OLS models.
Fixed ellipses options in procD.fit

CHANGES IN GEOMORPH VERSION 3.0.5 (Patch Release)

Simplified options available in procD.allometry

Fixed CAC calculations in procD.allometry
Fixed dimnames error in readland.nts when file contained a single specimen's data
Fixed PGLS weights for factors in morphol.disparity when phylogeny utilized
Fixed readland.tps to be general to whitespace delimitation

CHANGES IN GEOMORPH VERSION 3.0.4

New function: interlmkdist to 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.lm and procD.pgls, with limited output
An option to use permutation tests when comparing net evolutionary rates for compare.evol.rates

Added ellipsis programming to plotTangentSpace to pass arguments to prcomp. Also, adjusted default tolerance to remove redundant PC dimensions.
Enhanced landmark labeling in arrayspecs
Created transferability of dimnames between arrayspecs and two.d.array
Updated Rd files for PLS functions to better cross-reference the similar functions
Added data frame output to procD.lm
Change to plotGMPhyloMorphoSpace to center data by phylogenetic mean
read.morphologika now supports lists of file names to return a single data object
Updated Rd files for readland.nts and readmulti.nts to avoid ambiguity and resolve misinformation in previous versions
Updated readland.nts to 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 plotAllSpecimens if no colour specified
Added missing random.r output to integration.test and phylo.integration

CHANGES IN GEOMORPH VERSION 3.0.3 (Patch Release)

New functions: compare.pls, coords.subset, shape.predictor
droplevels.geomorph.data.frame added to support code

Added a sensor to support code for procD.lm and its allies to choose the computationally fastest algorithms based on design matrix complexity and data dimensionality
Updated procD.fit to remove unused levels from factors
Updated all functions using geomorph.data.frame to drop unused factor levels
Updated mshape to be used on lists, arrays, or matrices

Fixed single.factor function to properly maintain factor levels when combining factors
Fixed plotting issues with phylo.integration

CHANGES IN GEOMORPH VERSION 3.0.2 (Patch Release)

Added return of min/max shape matrices to plot.procD.allometry and plot.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 plotTangentSpace when groups are specified
Removed 'verbose' from plotTangentSpace; function now returns PC scores automatically when assigned to object
Updated plotTangentSpace to return min and max shapes for all PC axes in $pc.shapes

Fixed label output issue with bilat.symmetry shape components
Fixed error plotting TPS grids when groups were included in plot.procD.allometry
Fixed error in digit.curves where 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.tps for some tps files

CHANGES IN GEOMORPH VERSION 3.0.1 (Patch Release)

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.allometry to 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 (via plot.pls)
Fixed two small issues with plot.pls, regarding best fit line and matrix reduction.
Fixed three small issues with gpagen source files: indexing errors, arbitrary PC rotations for surface points, maximum iteration disparity.
Fixed digitize2D scaling issue when different scales used in each image
Fixed phylo.integration error when 3+ partitions examined
Fixed typo in modularity.test for CI intervals into matrix input
Updated permutation procedure in phylo.integration so that prob(A,B|phy)~prob(B,A|phy)
Fixed typo in plotAllSpecimens where links were not being plotted

CHANGES IN GEOMORPH VERSION 3.0.0 (Major Release)

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.update of procD.lm objects

Deprecated: compare.modular.partitions, morphol.integr, phylo.pls, and plotAllometry
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.Disp displaying NAs

CHANGES IN GEOMORPH VERSION 2.1.7-1 (Patch Release)

Fixed small change in C-code for gpagen

CHANGES IN GEOMORPH VERSION 2.1.7 (Patch Release)

New function compare.multi.evol.rates for comparing rates of evolution among traits
plotGMPhyloMorphoSpace now plots 3D phylomorphospaces and chronophylomorphospaces
Added ShowPlot option to bilat.symmetry, compare.modular.partitions, globalIntegration, morphol.integr, and phylo.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.nts flexibility with specimen labels; now supports spaces in labels
Generalized read.ply to allow reading meshes with many properties
Generalized input for physignal and compare.evol.rates: univariate data accepted as named vector
Enhanced input for define.links: read and append links to existing links matrix

Corrected error in warpRefMesh where normals were incorrectly assigned to new mesh3d object
Corrected error in readland.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 file
Corrected error in morphol.integr where warpgrids = F did not work for 3D datasets
Corrected issue with globalIntegration for use with 3D data
Corrected bug in plotRefToTarget method = "TPS" where the wrong options from gridPars were being passed

CHANGES IN GEOMORPH VERSION 2.1.6 (Patch Release)

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.rates generalized to use a single evolutionary rate matrix
pairwiseD.test and pairwise.slope.test now defunct
define.sliders.2d and define.sliders.3d now defunct
read.morphologika can read files with missing data
Ability to not show plot added to physignal and compare.evol.rates

Corrected error in defining starting point in digit.curves

CHANGES IN GEOMORPH VERSION 2.1.5 (Patch Release)

ability to include pre-digitized landmarks added to build.template and digitsurface
new gridPar is a new function to customize plots of plotRefToTarget
new digit.curves is a new function to calculate equidistant semilandmarks along 2D and 3D curves
define.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 curve

pairwiseD.test and pairwise.slope.test deprecated
'read' functions now allow both tab and space delimited files
define.sliders.2d and define.sliders.3d deprecated (replaced by define.sliders)

Corrected an error in plotAllometry where verbose=T did not return

CHANGES IN GEOMORPH VERSION 2.1.4 (Patch Release)

warpRefMesh generalized - now takes a mesh3d object (i.e. made from read.ply) rather than calling read.ply directly
read.morphologika now reads [groups] option and adds these data to the $labels matrix
plotOutliers now has option groups to plot outliers by levels(groups) using group means
morphol.disparity help 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 gpagen that flipped principal axes
Fixed error in read.morphologika with reading [wireframe] in some morphologika files

CHANGES IN GEOMORPH VERSION 2.1.3 (Patch Release)

new plotOutliers function to identify potential outliers
new define.links function for enhanced plotting of shapes

Additional input options added to pairwiseD.test and pairwise.slope.test
Ability to accommodate singular phylogenetic covariance matrices in: physignal, compare.evol.rates, procD.pgls and phylo.pls
Enhanced digitizing capability in: build.template, define.modules, define.sliders.3d, digit.fixed, digitsurface, and editTemplate )
plotAllometry input can be 2D matrix or 3D array
read.ply reads normals for enhanced downstream digitizing from ply files
readland.tps reads curves from tps files and convert them to landmarks (semilandmarks)
plotTangentSpace has enhanced plotting flexibility with labels and colors

Corrected error printing output of ANOVA table of bilat.symmetry
Removed redundant permutation loop in phylo.pls

CHANGES IN GEOMORPH VERSION 2.1.2 (Patch Release)

New function advanced.procD.lm for 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.pgls pairwiseD.test and pairwise.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.lm when verbose=TRUE
Fixed reflections of aligned coordinate axes when PrinAxes=TRUE in gpagen

CHANGES IN GEOMORPH VERSION 2.1.1 (Patch Release)

Specimens rotated to their principal axes in gpagen with option to disable

Underlying code for ancestral state estimation changed to use fastAnc (phytools)

Fixed concatenated SSCP matrix issue in procD.lm, pairwise.D.test and pairwise.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

CHANGES IN GEOMORPH VERSION 2.1 (Minor Release)

procD.pgls added to assess high-dimensional ANOVA and regression models in a phylogenetic context
pairwise.slope.test added to compare slopes of regression lines
Residual randomization options added to procD.lm and pairwise.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, and phylo.pls
Slight ANOVA table output adjustment in bilat.symmetry
Vector of labels can be added for plotting in plotAllometry and plotTangentSpace
Labels for ancestral states added to plotGMPhyloMorphoSpace

Fixed scale issue in digitize2d

CHANGES IN GEOMORPH VERSION 2.0.1 (Patch Release)

Small change to C-code for gpagen

CHANGES IN GEOMORPH VERSION 2.0 (Major Release)

New function phylo.pls for assessing the multivariate association between two blocks of variables in a phylogenetic context
New function two.b.pls for assessing the multivariate association between two blocks of variables
New function morphol.disparity to 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, and bilat.symmetry
New I/O functions: warpRefMesh 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]
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, and plotGMPhyloMorphoSpace
Ability to input univariate data added to compare.evol.rates and physignal
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 arrayspecs has been removed
Residual shape component (RSC) plot added and scores returned for plotAllometry (method = "CAC")
Procrustes ANOVA added to plotAllometry output
Centering = T/F option added to following 3D digitizing functions: build.Template, digit.fixed, digitsurface, and plotSpec
read.vrml now 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 digitize2D and updated flexibility of the function

CHANGES IN GEOMORPH VERSION 1.1-6 (Patch Release)

Minor I/O enhancements in readmulti.nts
Minor I/O enhancements in define.sliders.3d to 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 in trajectory.analysis only)
Added name.check for groups in compare.evol.rates

CHANGES IN GEOMORPH VERSION 1.1-5 (Patch Release)

New function compare.evol.rates for comparing multivariate evolutionary rates on phylogenies
define.sliders.2d and define.sliders.3d replace curves2d and digit.curves
Option allowing specimens to be colored by group added to plotTangentSpace and PlotAllometry

Simplified options in morphol.integr
curves2d and digit.curves deprecated

Corrected parameter estimates when groups specified for Regression Score option in plotAllometry

CHANGES IN GEOMORPH VERSION 1.1-4 (Patch Release)

Enhanced plotting of ply files in read.ply
digitsurface, buildtemplate, plotspec, digitfixed, and digitcurves now support ply file input

Minor changes to plot window options in plotting functions
Change to magnification factor usage in plotRefToTartget

CHANGES IN GEOMORPH VERSION 1.1-3 (Patch Release)

Improved NAMESPACE file and package usage
Generalized read.vrml code for additional file formats

CHANGES IN GEOMORPH VERSION 1.1-2 (Patch Release)

pairwiseD.test function added
bilat.symmetry output includes symmetric and asymmetric shape components

Adjusted plotting routines in morphol.integr to be compatible with new CRAN guidelines
Adjusted plotting routines in bilat.symmetry to 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.tps to 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 physignal and PlotGMPhyloMorphoSpace

CHANGES IN GEOMORPH VERSION 1.1-1 (Patch Release)

Removed dependency in physignal on getAncStates from geiger, which is no longer supported
Removed dependency in plotGMPhyloMorphoSpace on getAncStates from geiger, which is no longer supported

CHANGES IN GEOMORPH VERSION 1.1-0 (Patch Release)

bilat.symmetry function added
writeland.tps function added
fixed.angle function added
compare.modular.partitions generalized to allow 2 or more partitions
morphol.integr generalized to allow 2 or more partitions
trajectory.analysis re-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.morphologika accepts greater variety of input file formats

buildtemplate 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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geomorph documentation built on June 24, 2024, 5:07 p.m.

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geomorph Geometric Morphometric Analyses of 2D and 3D Landmark Data

NEWS.md In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

CHANGES IN GEOMORPH VERSION 4.0.8

NEW FEATURES

OTHER CHANGES

Bug fixes

CHANGES IN GEOMORPH VERSION 4.0.7

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Bug fixes

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CHANGES IN GEOMORPH VERSION 4.0.6

Bug fixes

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CHANGES IN GEOMORPH VERSION 4.0.5

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CHANGES IN GEOMORPH VERSION 4.0.4

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CHANGES IN GEOMORPH VERSION 4.0.3

OTHER CHANGES

CHANGES IN GEOMORPH VERSION 4.0.2

BUG FIXES

CHANGES IN GEOMORPH VERSION 4.0.1

BUG FIXES

CHANGES IN GEOMORPH VERSION 4.0.1

NEW FEATURES

BUG FIXES

CHANGES IN GEOMORPH VERSION 4.0.0

NEW FEATURES

BUG FIXES

CHANGES IN GEOMORPH VERSION 3.3.2 (Minor Release)

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BUG FIXES

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CHANGES IN GEOMORPH VERSION 3.3.1 (Patch Release)

BUG FIXES

CHANGES IN GEOMORPH VERSION 3.3.0 (Minor Release)

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CHANGES IN GEOMORPH VERSION 3.2.1.0900 (Minor Release)

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CHANGES IN GEOMORPH VERSION 3.2.1

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CHANGES IN GEOMORPH VERSION 3.2.0 (Minor Release)

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CHANGES IN GEOMORPH VERSION 3.1.3 (Patch Release)

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CHANGES IN GEOMORPH VERSION 3.1.2 (Patch Release)

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CHANGES IN GEOMORPH VERSION 3.1.1 (Patch Release)

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CHANGES IN GEOMORPH VERSION 3.1.0 (Minor Release)

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CHANGES IN GEOMORPH VERSION 3.0.7 (Patch Release)

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BUG FIXED

CHANGES IN GEOMORPH VERSION 3.0.6 (Patch Release)

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CHANGES IN GEOMORPH VERSION 3.0.5 (Patch Release)

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BUG FIXES

CHANGES IN GEOMORPH VERSION 3.0.4

geomorph
Geometric Morphometric Analyses of 2D and 3D Landmark Data

NEWS.md
In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data