
PAST
version history
 
Version 1.00:
 Improved ShapiroWilk test (max N increased from 50 to 5000)
 Improved Rayleigh test for directional data (max N increased from 50 to 200)
 Hamming distance for categorical data added to cluster analysis,
PCO and NMDS
 Permutation test added to "compare diversities" module
 Permutation test added to chisquared module
Version 1.01:
Plotting on axes 2+3 in DCA. Eigenvalues 14 reported.
Version 1.02:
RMA now works properly also for negative slopes.
Version 1.03:
 95% confidence interval for autocorrelation
 Black square when copying graphic, bug fixed
 Seriation copy data, bug fixed
 Grid lost when resizing multivariate allometry graphic, bug fixed
 XY graph: added support for row colors and labels
Version 1.04:
RMA: Standard error for the intercept used an incorrect formula
in Davis (1986). Ver. 1.04 follows Miller & Kahn (1962).
Version 1.05
 Click on any graph for setting grid, axes and axis labels
 Convex hull option added to all scatter plots
 Correlations between variables and PCs added to PCA loadings plot
 Data plotted as points or curve in Sinusoidal Fit
 Max number of sinusoids increased from 6 to 8 in Sinusoidal Fit
 Algorithm for Sinusoidal Fit more robust (max iterations in SVD
increased)
Version 1.06
 Bootstrapping of linear regression/RMA
 Onesample t test versus theoretical mean
 Continuity correction in MannWhitney test
 Bug fixed: Crash when quitting PAST for some Windows configurations
Version 1.07
 ANOSIM (Analysis of Similarities) with 12 distance measures
 Stress value in Shepard plot (Nonmetric MDS).
 Taxonomic distinctness: Problem with data not starting in first row fixed.
Version 1.08
 Crosscorrelation with p values
 PCA can now optionally use the SVD algorithm
Version 1.09
 Mahalanobisdistance permutation test for two multivariate groups
 Removed limit of 210 items in cluster analysis
Version 1.10
 Blackandwhite option for all graphics
 Y axis can be scaled in cluster analysis
Version 1.11
 Normal probability (normal QQ) plot with RMA regression
 50% speed increase in Ward's method clustering
 CVA loadings (eigenvectors)
 Affine component (0th partial warp) scores for thinplate
spline deformations.
Version 1.12
 NPMANOVA (NonParametric MANOVA) with 12 distance measures
 'Edit labels' mode in the data entry spreadsheet
 Copy data from the F/t and chi^2 test windows
 Bug fixed: Occasional crash in PCO scatter plot
 Bug fixed: CVA loadings window not staying in front
Version 1.13
 Simple implementation of the CONOP (Constrained Optimization) method for biostratigraphy
 Reporting of residuals from linear regression
Version 1.14:
Added numerical output ("View numbers") to PCO, CA and DCA.
Version 1.15
 User selection of pairs of landmarks to link with lines in
landmark, thinplate spline, partial and relative warp and shape PCA plots.
 Optional row labels in 3D landmark plot
 Warning when quitting PAST without saving changes
 Automatic scaling when reading TPS files (SCALE keyword in file)
 "Dots for blank fields" bug when copying data from PAST to other
programs fixed.
Version 1.16
 Partial warp deformations went opposite way of scores. Fixed.
 Procrustes fitting (2D) occasionally mirrored some configurations.
Fixed.
 When copying graphics with zoomed axes, elements from outside the
window could occasionally be included. Fixed.
 When copying graphics from small windows, curved lines could
become ragged. Partially fixed (by rounding instead of truncation).
Version 1.17
 CONOP: Occasional long pause at startup, bug fixed
 CONOP: Option for using event numbers instead of names in range chart
 RASC: PAST can now read files in the RASC .DATformat
 RASC: Reports the number of cycles
 RASC: Dendrogram truncation at bottom and top, bug fixed
 RASC: Loss of taxa when rerunning RASC without closing window, bug
fixed.
Version 1.18
 "Commatizing" made unnecessary and removed
 View PCA loadings as numbers
 Centering option in PCA scatter plot
 Faster eigenvalue routine
Version 1.19
 Paired Hotelling's T^{2} test
 Twoway cluster analysis (combined Q and R mode)
 Support for missing data added to more functions
 RaupCrick and Horn indices added to MDS and PCO
 Reporting of all eigenvalues in PCA (not only first four)
 Unitary Associations: Added support for marker beds,
substantial speed increase in cycle resolution, status label.
 Histogram: Added ML fit to normal distribution
 Univariate statistics: Added standard error of the estimate of the mean
 Edit labels: Clicking in label cell now makes cell active
 Cancel button in "Evaluate expression" fixed
 Added "Normal" (Gaussian random numbers) to Evaluate expression
Version 1.20
 Fixed two bugs in cladistics: Wrong tree length sometimes given
when changing tree in cladogram display, and wrong character states
sometimes given for terminal taxa when the root state is a question mark.
 Hotelling's T^{2} made more robust using MoorePenrose
generalized matrix inverse.
 Linear regression residuals includes rows with question marks
 Experimental feature: Stratigraphically constrained cluster analysis
Version 1.21
 Raw similarity/distance matrix for all measures
 Cosine similarity measure
 Maximum number of columns for PCA (and rows for PCO) increased from 200
to 512
 Maximum number of characters for cladistics increased from 128 to 200
 Maximum number of taxa for cladistics increased from 255 to 511
 Improved reading of trees from NEXUS files
 Crash when transposing matrices with more columns than rows, bug fixed
Version 1.22
 Minimal spanning trees for PCO and NMDS
 Data set size limit removed for PCA and PCO (but less than
500 columns for PCA and 500 rows for PCO still recommended because
of computation time).
 Faster Open of very large data files
 Faster Transpose of very large data sets
 "Insert more columns" occasional freeze: Bug fixed
 Diversity indices  bad behaviour for allzero columns: Bug fixed
 Occasional missing lines in multipage dendrograms: Bug fixed
 Occasional incorrect results in polar Fourier shape analysis
(not Elliptic Fourier): Bug fixed
Version 1.23 (bug fixes)
 Convex hulls: Crash when points had identical positions  bug fixed
 PCA: Eigenvalues not always in descending order when using SVD  bug
fixed
 Graph: Drawing area blocked out with color for some graph setting
combinations  bug fixed
 Diversity curve: Crash when viewing numerical output  bug fixed
 Cladistics: Improper handling of characters with identical character
state for all taxa  bug fixed
 DCA: Crash if a column had all zeros  bug fixed
 Ternary plot: Added option for row labels
Version 1.24
 Procrustes fitting (2D): Option for rotation to major axis
 New function for rotating and flipping landmark configurations (2D)
 Directions/rose plot: New "orientations" (0180 degrees) option
 Cladistics: bug fixes for large data sets (now limits of 200 taxa and
400 characters)
Version 1.25
 Added offset value to discriminant function output
 PCO: Added plotting of axes 2+3
 NMDS: Factor 10 speedup
 Unitary Associations: Factor 10 speedup for some data sets
Version 1.26
Important change in PCA:
When using PCA with the correlation matrix, the PCA scores
(scatterplot) was previously computed with respect to original (raw)
variables. From version 1.26, the scores are computed with respect
to standardized variables.
Version 1.27
 Buzas & Gibson's evenness e^H/S added to 'diversity indices' and
'compare diversity indices'.
 Cluster analysis: Option to save dendrogram in NEXUS format (can
be viewed with e.g. TreeView)
 Font name and size added to graphic preferences
 Improved algorithm for automatic selection of plotting axis ranges
 Very rare crash in the 'Univariate statistics' module, bug fixed.
Version 1.28
 Fixed bug introduced in ver. 1.27: Crash in some graphic windows
 PCA scattergram/biplot: Plotting on axes 1+2, 1+3 and 2+3
Version 1.29
 Added Manhattan distance to distance measures, cluster
analysis, PCO, MDS, ANOSIM and NPMANOVA
 Fixed minor problem with placement of some windows under RASC
 Added variable "stdev" (standard deviation) to "Evaluate
expression"
Version 1.30
 "Capturerecapture" species richness estimators: Chao2, first and
secondorder jackknife, bootstrap.
 Size removal of multivariate morphometric data by Burnaby's method
 Bootstrapped confidence intervals in logistic fit
 Option to standardize rotation and starting point in Elliptic Fourier
Analysis
 Increase from 9 to 12 different symbols/colors
Version 1.31
 95% WorkingHotelling confidence bands for linear regression line
 All negative values used to be interpreted as missing data for
computation of similarity indices (in cluster analysis, PCO, MDS,
ANOVA, NPMANOVA etc.). Now only the value 1 (or '?') is accepted as
coding for missing data.
 Improved printing, especially for nonpostscript printers
 Bug fix: New symbols/colors in ver. 1.30 were not included in
clustering labels, confidence ellipses and convex hulls.
 Logistic bootstrap: Better error reporting
Version 1.32
 Gridding (spatial interpolation): Kriging with semivariogram modelling,
thinplate spline, moving average.
 Matrix plot (grayscale)
 Spindle diagram (fossil abundance through stratigraphy)
Version 1.33
 Gaussian mixture analysis with EM algorithm
 Bug fix in Correspondence Analysis (Detrended Correspondence
Analysis not affected): Occasional flip of Q mode axes relative to R mode
 Automatic linear trend surface removal in gridding module
 "Massage" menu changed name to "Transform"
Version 1.34
 Userspecified number of dependent variables (constraints) for
Hotelling's T^{2} and MANOVA
 Contouring in gridding and matrix plotting (slightly buggy on boundaries)
 Option to set symbol size in all plots
 "Sample variance" and "Sample standard deviation" in Univariate statistics
caused confusion  removed.
 Bug fixes in loading of Nexus tree files
Version 1.35
 Twoway ANOVA
 Mardia's multivariate normality tests (multivariate skewness & kurtosis)
 Option to change tick mark density in all plots
 Crossevaluation (leaveoneout) in discriminant analysis
 Choice of allometric or isometric size removal in Burnaby module
 Box's M: Better error reporting
Version 1.36
 Canonical correspondence analysis (CCA)
 Bookstein landmark registration
 Distance/similarity measures: Full symmetric matrix given, not only upper
triangle
 Minor bug fix in kriging: Crash for some datasets
Version 1.37
 Minimal spanning tree added to XY plot
 Usersupplied symmetric distance or similarity matrix option
in cluster analysis, PCO, NMDS, ANOSIM and NPMANOVA
 Option to set number of permutations in permutation t test,
multivariate permutation test, ANOSIM and NPMANOVA
 "Sort ascending" and "Sort descending" now sort all rows
based on the first column (previous versions sorted columns
independently)
 PCO scores automatically scaled using square roots of eigenvalues
 Bug fix in Unitary Associations: Rare failure to detect residual
virtual edges
Version 1.38
 All eigenvalues reported in PCO (not just first four)
 Bug fix in DCA: Crash for zero eigenvalues
 Added "Slope" and "intercept" captions to linear regression
 Bug fix: "Oval" and "Star" row symbols not properly loaded from datafile
 Bug fix in PCO: Numerical output crashed for zero eigenvalues
 Default XY plot mode changed from lines to points
 Point distribuion statistics: Small correction in expected distance
calculation. Added option for edge effect adjustments, and option for
rectangle rather than convex hull for area.
Version 1.39
 Appearance Event Ordination (biostratigraphic method)
 Univariate statistics now works for several columns
 Point distribution statistics: Output of minimal spanning tree segment
directions (for testing linear arrangement)
 Directions module: Bug in chisquared test (introduced in ver. 1.24) fixed.
Rayleigh's test now handles orientations
 Detrended Correspondence Analysis: User control on number of detrending
segments
 Crash when reading large TPS files, fixed
Version 1.40
 Bootstrapping in cluster analysis
 Improved user interface for the "Evaluate expression" function
Version 1.41
 Faster 3D procrustes fitting
Version 1.42
 XY plot with error bars
 Labels in linear regression plot
 Number of bins for chisquared in directional analysis can now be set by user
 Point distribution statistics now outputs all distances and orientations between
nearest neighbours (change from v. 1.39).
 Bug fixed: RaupCrick similarity index caused occasional crash in several
modules
 Bug fixed: Sorting parts of matrix did not work
Version 1.43
 Posthoc analysis for MANOVA, by simple Bonferronicorrected pairwise
Hotelling's T^{2}
 Mantel correlogram and Mantel periodogram for multivariate time series
 Function for regular spacing of irregular time series by interpolation
 Bug fixed: KolmogorovSmirnov always reported p=1 for very large sample sizes
 Bug fixed: MannWhitney crashed for very large sample sizes
Version 1.44
 Posthoc analysis for KruskalWallis (nonparametric ANOVA)
 Welch's ANOVA for groups with unequal variances
 Bug fixed: Incorrect Bonferroni correction for MANOVA posthoc
Version 1.45
(Major internal revision of the code)
 Speed increase in many modules
 Large cluster analysis output no longer split into pages
 Bug fixed: Incorrect KruskalWallis posthoc when data not starting
in first column
 Bug fixed: Crash in MANOVA posthoc for small sample sizes
 Bug fixed: Losing graph settings when a plot is updated
 A number of small improvements in the user interface
 Additional (experimental) corrections in diversity curve module
Version 1.46
 Fixed bugs in Transform menu functions introduced in version 1.45
Version 1.47
 Scripting language (early version!)
 DCA: Popup labels when moving mouse over points
 Undo levels increased to 10
Version 1.48
 Almost 30 new functions available in the scripting language
 Bug fixed: Confidence ellipses and convex hulls incorrectly
drawn for datasets with same color used in several groups
 NMDS scatter plot automatically rotated to major axis
Version 1.49
 Nucleotide codes (A, T, U, C, G) accepted for all analyses
 Interleaved Nexus files accepted
 Genetic distance indices in PCO, NMDS, clustering, ANOSIM, NPMANOVA:
JukesCantor and Kimura
 NMDS automatically runs 10 times with random starting values,
and the best solution is selected
 NMDS scatter plot axes automatically flipped according to input order
 PCO made robust to variates with zero variance
Version 1.50
 Neighbour joining clustering
 Minor bug fixes
Version 1.51
 Redo function (undo an undo operation)
 "Optimal" histogram bin size suggested automatically
 New functions and constructs in the scripting language
Version 1.52
 Mantel test
 Option for showing outliers in box plot
 Minor bug fixes
Version 1.53
 Tests for paired data: t test, sign test (exact) and
Wilcoxon signed rank test (normal approximation and Monte Carlo).
Version 1.54
 New similarity measures: Kulczynski and Ochiai
 Confidence ellipses drawn with Bezier curves (graphical quality improvement)
 "Invisible rectangles" in copied graphics removed
 Files can be opened by dragging from desktop
 Cladistics: Bug fix in character reconstruction with Wagner optimisation (tree
topology was OK)
 Option for showing branch lengths on parsimony trees
 Correspondence analysis: Allzero rows and columns placed on the origin
in the plot (previously an error message was given)
 Some similarity measures (Dice, Jaccard etc.) were undefined
for allzeros data. This caused problems when bootstrapping sparse data
sets in clustering and neighbour joining. Similarity is now set to zero
in such cases.
Version 1.55
 Bug fix: Monte Carlo Wilxocon paired test gave too high p values (bug introduced
in 1.53)
 Bug fix: Rare crash when plotting confidence ellipses and convex hulls
 Bug fix: Plots not scaled correctly to confidence ellipses (bug introduced in
1.54).
Version 1.56
 Option for outgroup rooting in neighbour joining cluster analysis
 Levene's test by medians in ANOVA (previously only Levene's test
by means was available)
 Minor bug fix concerning colors of confidence ellipses
Version 1.56b
Fix of bug in 1.56 causing crash in several modules.
Version 1.57
 Ripley's K statistics for point patterns
 Bubble plot for 3D data
 Linear fit: Permutation test on R^{2}
 Permutation test for Spearman/Kendall nonparametric correlation
 Correlation matrix: Spearman/Kendall option added
 Sort on color
 CA, DCA and PCO: Scatter plot on axes 1+3
 All scatter plots have mouseover labels
 Mixture analysis: Akaike information criterion added (for selecting
number of groups)
 New algorithm for setting tick marks in plots
Version 1.58
 Sinusoidal fitting can now also optimize frequencies
 Chisquared and Akaike statistics in sinusoidal fitting
 Counter window for microfossil counting
 Linear fitting: Fix of bug in bootstrapping, introduced in v. 1.57
 Area used for Ripley's K can now be set manually
 New options for input format in Appearance Event Ordination
Version 1.59 (bug fixes)
 Linear fit: Incorrect permutation test when values were logtransformed
(bug introduced in 1.57)
 Linear fit: Incorrect residuals (introduced in 1.57)
 Plotting of lines (many modules): Distortions when line clipped against
lower edge (introduced in 1.54)
 Rectangles in histograms etc. not always clipped against lower edge
 Improved error messages in Mixture analysis
Version 1.60
Time series analysis: Maximumlikelihood ARMA modelling, and BoxJenkins
intervention analysis.
Version 1.61
 Pairwise posthoc comparisons in ANOSIM and NPMANOVA
 Twoway cluster analysis plot improved, and size limit removed
 Rare crash in sinusoidal fit fixed
 New definition of Akaike information criterion in sinusoidal fit
 Correspondence analysis: All eigenvalues reported, not just four
 Rayleigh test for directional data: Limit of N=200 removed
 "p=0" changed to "p<1/number_of_permutations" in permutation tests
 Slight statistical improvement in random number generator
 Operators +, , * and / in script language now accept mixed types
such as array+double
 Default number of permutations in t test, ANOSIM and NPMANOVA increased
to 10,000
Version 1.62
 Faster save
 Improved contour plots (matrix plot and gridding)
 Colour map option in matrix plot and gridding
 Option for thick lines in all plots
 Rose plot: Option for circular "grid"
 Univariate statistics: Sum of values included
 Polar and elliptic Fourier shape analysis: Number of harmonics increased to 20
 PCA: The SVD option is now default
 Script language: Decimal point/comma issue resolved
 Log (transform menu): Constant no longer automatically added for
zero or negative data.
Version 1.63
 Mixed similarity/distance measures in cluster analysis,
PCO, NMDS, ANOSOIM/NPMANOVA etc.
 Fisher's exact test for 2x2 contingency tables
 JarqueBera test for normal distribution (in addition to ShapiroWilk)
 Changed scale factor in PCO from sqrt(2)/2 to 1
 Support for outline and curve data types in TPS files
 A number of minor improvements and speed increases
Version 1.64
 A number of bug fixes (most of them introduced in 1.63)
 Confidence intervals in t tests
 Row colors increased from 12 to 16
 All geometric plots are forced to unit aspect ratio
 Replace function can search for empty cells (use "empty")
 Paired tests: Missing data supported by deletion
Version 1.65
 Procrustes fitting now according to Rohlf & Slice (1990)
 Solar forcing from 100 Ma to Recent (Laskar et al. 2004)
 Kernel Density Estimation in histograms
 3D scatter/landmark plot improved
 Graphic size in pixels can be set by user
 PCA: SVD and eigenalanalysis now report eigenvalues in the
same scale
 Curves made smoother using Bezier splines in a number
of modules
 Width of each column can be set by dragging with mouse
 Bug fix: Imperfect printing of graphics in a number of modules
 All geometric plots are forced to unit aspect ratio
Version 1.66
 Percentile plot
 Eigenvalue and biplot scalings in PCA are now according
to Legendre & Legendre
 Bug fix: Distortion of scatter plot for PCA on the correlation matrix with
large datasets
 Images can be saved as file in the EMF format
 Cluster analysis results can be saved as text lists
 CONOP: Data size limits removed, and bug fix (suboptimal solutions
found in some cases)
 Unitary Associations speedup, and bug fix (residual virtual edges not
properly inserted in very rare cases)
 CCA bug fix (variable labels incorrect in triplot if data not
taken from first column in spreadsheet).
Version 1.67
 Samplebased species accumulation curves ("Mao tau")
 Open and save Excel files
 Shape PCA can be visualized as relative warp grids
 Twoway ANOVA now supports unbalanced designs (unequal sample sizes)
 Box plot now includes column labels
 Geometric mean in Univariate Statistics
 Open files in the CONOP format
 Filter stratigraphic events on type (FAD, LAD etc.)
Version 1.68 (bug fixes)
 Fixed incorrect interaction term in twoway ANOVA with very unequal sample
sizes (introduced in ver. 1.67)
 Scale factor in TPS files now applied to all specimens even if
specified only for first specimen
 Unitary Associations: Fixed crash for degenerate data sets with
only one residual horizon
 Fixed reading of interleaved NEXUS files with nonWindows
line breaks
Version 1.69
 Abundance models: added "broken stick" model, chisquared values,
linearaxis plot.
 Cladistics: added phylogram plot (scaled to branch lengths)
 All scatter plots: added option for centered axes through the origin
 Sample rarefaction: rare crash fixed
 Spline interpolation now supports several points with same x
value
Version 1.70
 Bug fix in Elliptic Fourier Analysis: incorrect rotations
for some data sets when using "Invariant to rotation" option.
 Partial warps: affine component now included also in the
numerical output
Version 1.71
 SIMPER (Similarity Percentage analysis of ecological assemblage dissimilarity)
 PCA: bootstrapped confidence intervals for both eigenvalues and loadings.
Confidence intervals and Broken Stick random model in the scree plot.
 Bug fix: crash in Horn, Ochiai and Kulczynski similarities for allzero rows
Version 1.72
 Polynomial regression
 New in directional statistics: Angular kernel density estimation,
confidence interval on angular mean, plot of mean with CI.
 Bug fix: Incorrect p values in NPMANOVA posthoc tests for Euclidean, Horn
and Manhattan distance (introduced in ver. 1.61)
 R^{2} and p values in sinusoidal fitting
 Bug fix: Minimal spanning tree of only two points crash
 XY plot for several pairs of columns now support unequal N
 Chisquared test for normal distribution removed from menu and added to
Normality module
 Output from twoway ANOVA can now be copied
 Detrending option now ticked by default in DCA
Version 1.73
 3D surface plot
 Color scale bar in matrix and gridding plots
 ANOSIM: R values for the pairwise comparisons, and support for groups with one sample
 Faster copy of large numerical data sets
 Bug fix in chisquared test: Incorrect copying of text
 Bug fix in ternary plot: Column labels lost when copying graph
Version 1.74
 Genetic sequence statistics
 New distance measure: TajimaNei (for sequence data)
 NMDS: Extra trial using PCO as initial condition
 NMDS bug fix: Stress value was not always taken from the best trial
 ANOSIM+NPMANOVA bug fix: Incorrect pairwise (posthoc) results for
userdefined distance/similarity matrix with more than two groups
 CCA: Eigenvalue scaling for triplot removed, and improved convergence
Version 1.75
 One independent, several dependent variates regression with MANOVA
 NMDS now has option for three ordination axes
 Gradient species packing modelling: Gaussian fit with least squares or
weighted average
 Reconstruction of environmental parameters from abundance data and
species packing model, using weighted averages ("calibration")
 Directional statistics: Rao's spacing test
 Multivariate normality: Doornik & Hansen omnibus test
 SIMPER now supports more than two groups
 Improved algorithm for correspondence analysis by eigenanalysis
(DCA module not affected)
 Sinusoidial fitting: Fitted curve can be plotted outside data range
 PCO: Plotting on axes 1+3 (and 2+3)
 Rare crash in histogram module fixed
Version 1.76
 Imbrie & Kipp factor analysis of abundance data, with
optional regression of environmental data.
 KruskalWallis test now accepts groups with only one value
 Sinusoidal fitting: the fitted constant term is now reported
 UPGMA clustering five times faster
 Individual rarefaction: more options for step size and maximum N
for very large data sets
Version 1.77
 Bug fix: incorrect UPGMA clustering (introduced in 1.76)
 Reconstruction of environmental parameters with Imbrie & Kipp
transfer functions
 Improvements in semivariogram modelling for kriging
 Reading TPS files: Independent scale tags now supported
 Reading RASC files: Decimal depth format now supported
 Conversion from biostratigraphic FAD/LAD events to occurrence
matrix (RASC to UA)
Version 1.78
 2way ANOVA bug fix: Incorrect p values when p>0.5
 Polynomial fit bug fix: Incorrect p values when p>0.5
 MANOVA posthoc pairwise tests bug fix: did not test for p values larger than 1
Version 1.79
 WatsonWilliams test for equal mean in two directional samples
 DCA now expects samples in rows and species in columns
 Paste function in Rename Columns
 RASC: Speed increase, and increased maximum number of cycles to 3000
 Bug fix: EDMA crashed for large number of landmarks
 Bug fix: Zero plotting range (giving blank plot) in rare cases
Version 1.80
 Unitary Associations: Speedup, and addition of several new
interpretation modules
 CONOP: Numerical output of ranges
 Bug fix: Kulczynski, Ochiai and Simpson indices were
mixed up in the Cluster Analysis module
Version 1.81
 Modern Analog Technique for paleoclimate reconstruction
 Euclidean distances no longer normalized for number of variables
 Individual rarefaction: Multiple samples in one run
 PCA loadings numerical output: All components given
 NMDS now starts without annoying default run
 Wavelet transform: Color option and numerical output
 Bug fix: Crash when reading large Nexus files
 Numerous minor improvements in efficiency, graphics, error
reporting.
Version 1.82
 Save graphics in JPG or BMP format (in addition to EMF)
 No. of tick marks can be set independently for both axes
 Mixture analysis: group assignment probabilities for all points
 Modern Analog Technique: semivariogram
 Bug fix: Paried tests crashed for very large data sets
 Graph preferences: graph is now updated instantly
Version 1.83
 All similarity measures available in all relevant windows
 Improved plot of constrained clustering dendrogram
 Improved plot of twoway clustering dendrogram
 Point+line option in Graph and XY Graph
 Copy text from all windows in the Statistics menu
 Significant posthoc p values marked in pink for ANOVA,
KruskalWallis, MANOVA, ANOSIM, NPMANOVA
 Standard font in graphics changed from Small Fonts 7 pt to Arial 8 pt
 "Illegal value in input data" message now reports position of
offending cell
 CVA scatter plot is now centered on zero, and "nuisance" axes higher
than Ngroups1 not reported
 Rare crash in NMDS for duplicate points fixed
 A number of other minor improvements in user interface
Version 1.84
 Bug fix in multivariate linear regression: Inaccurate overall MANOVA
 New function: Stack colored rows into columns
 Copy text in polynomial fit
 Fixed occasional 'Fail' for MANOVA posthoc, introduced in 1.83
 Fixed apparent doubling of topmost row when flipping 'Edit labels'
 Directional stats: New bootstrapped confidence interval on mean
 Normality: Warning for chi2 test when N<20
 Wavelets: Turned upsidedown, and added "Power" option
 Detrending now accepts one (y) or two (x and y) columns
Version 1.85
 Bug fix: Occasional crash in Spectral Analysis View Numbers
 Bug fix: Numerical instability in calibration from CABFAC (factor analysis was OK)
 Missing values implemented in chisquared and SpearmanKendall (by row deletion)
 Chisquared: Max total for Monte Carlo test increased to 30000. Improved error messages.
 CCA: All eigenvalues reported, not just four
 New (experimental) plotting method for multivariate time series: "Mantel scalogram"
 Elliptic Fourier Analysis: Number of harmonics increased to 30
 Scripting bug fixes: First row not included when copying data from numerical output window.
Function 'fprob' was faulty.
 New scripting functions: abs and anova
Version 1.86
 Skewness and kurtosis now computed as sample values (unbiased estimators)
 Reading Nexus interleaved files: bug fix
 Gridding: Halfcell offset bug fixed
 Bitmap zoomin bug fixed (matrix, gridding, wavelets etc.).
 Scripting: Progress bar procedure
Version 1.87
 Twoway ANOSIM
 FlignerKilleen test for equal coefficients of variation
 Univariate statistics: 25 and 75 percentiles were incorrect
 CCA now uses SVD, improving numerical stability for illconditioned data
 CCA: copy and print buttons were swapped
 "Point symbols" option in graph preferences (all symbols plot as points)
Version 1.88
 Twoblock Partial Least Squares analysis
 Concentration ellipses: Level can be set by user (was fixed at 95%)
 Transform menu: Conversion to rowwise percentages
 Appearence Event Ordination: Numerical output for taxon ranges
 Minor improvements in plotting functions
Version 1.89
 Smoothing spline: New algorithm with weighting, crossvalidation, bootstrapping etc.
 Circular correlation
 Chisquared Monte Carlo test now supports sampled vs. expected frequencies
 Standardize to unit row vector length
 Transform abundance to presence/absence
 Improved handling of missing data in several transforms
 Evaluate expression: Power with base 0 bug fix, better handling of missing data, new sum function
 Fixed bug introduced in 1.88: Incorrect default graph zoom when including concentration ellipses
Version 1.90
 Multiple regression
 Oneway ANCOVA
 Measures of beta diversity
 Minor improvements in user interface and error reporting
Version 1.91
 MannWhitney test now includes exact and Monte Carlo significance for small sample sizes
 Concentration ellipse parameters can be viewed as numbers (from the graph preferences window)
 Individual rarefaction: Curves for all samples can be viewed together
 When pasting into spreadsheet: Only tab is interpreted as separator, not any whitespace
 Missing data supported for Graph and XY Graph (Plot menu)
 Bug fix: Incorrect labels in spindle diagram when selection not from first column
 Bug fix: Crash in logseries abundance model for very large data sets
Version 1.92
 Runs test: New Monte Carlo significance value
 Size removal for linear measurements: New method added  removal of allometric
size with respect to a single specified variate.
 Parsimony analysis (cladistics): Removed limit of 400 characters.
Maximum number of stored trees increased to 10,000. Slight speedup.
 CCA bug fix: Results occasionally corrupted when rerunning analysis
on same data
 Linear model, 1 independent, n dependents: Numerical output of
regressed values
 NMDS: Coefficient of determination given for each axis
 Wavelets: Axis values given in numerical output
Version 1.93
 Bug fix: Mixed data distance measure sometimes incorrect
 Bug fix: Occasional crash in permutation test for CCA
 Spindle plot: Option for specifying sample levels
 MannWhitney test: Mean ranks given in output
 Diversity t test: Degrees of freedom given in output
Version 1.94
 Stereo plot for spherical data, with contouring
 Autoassociation, for sequences of nominal data
 Crosscorrelation: Support for missing values
 Walsh transform: More intuitive units on frequency axis
 Spindle diagram: Column labels position bug fixed
 Reading Past files: Faster, and supports Unixtype line breaks
 Elliptic Fourier: Error message for duplicate points
 Taxonomic distinctness: Speedup
 NMDS: Axis labels not updated when switching from 2+3 to 1+2
 Cluster analysis: Gower distance crash for zero variance, fixed
 Cluster analysis: Gower, Euclidean and Manhattan now shown as
positive distances, not negative similarities
Version 1.94b (emergency bug fix)
 Fixed bug introduced in 1.94: Some row colors incorrectly read from Past
files.
 Oneway ANOVA now includes omegasquared effect size statistic
Version 1.95
 Oneway ANOVA: Option for repeated measures (withinsubjects)
 Twoway ANOVA: Option for repeated measures
 Discriminant analysis: Visualization of shape deformations along
the discriminant axis, both for landmark and outline (EFA) data
 Linear model: Option for robust regression (Least Trimmed Squares)
 Sample rarefaction: Fix to compute variance even if s2=0
 Removed superfluous "Shape PCA" button in PCA
 Box plot and histogram: Crash for some degenerate data, fixed
Version 1.96
 SHE diversity analysis
 Kernel density estimation for 2D points
 Monte Carlo version of the JarqueBera normality test
 Spline deformation grid for linear regression of landmark shapes
 Diversity profiles: Support for multiple columns, and numerical output
 Normality tests: Support for multiple columns.
 Box plot: Quartiles now computed as in Percentile plot module, with userselected method
 Added t label for significance of correlation in Linear model
 PCA shape deform: Now allows negative PCA scores, and expansion map
 Landmark linking for 3D: Incorrect labeling of columns, corrected
Version 1.97
 Survival analysis: KaplanMeier curves; logrank, Wilcoxon and
TaroneWare tests
 Incorrect reading of some Past files, fixed (bug introduced in 1.94)
 Crash in MannWhitney if n2>n1, fixed (bug introduced in 1.91)
 Output of residuals for multivariate linear regression
 Numerical output for kernel density estimation
 Visualization of PCA of Elliptic Fourier Analysis shapes
Version 1.98
 Can now open NTSYS files. Trees and multiple tables not supported.
 Risk difference, risk ratio and odds ratio, all with confidence intervals and tests
 LOESS curve smoothing
 Mixture analysis: Now includes exponential and Poisson distributions. Moved to
Model menu
 Spearman's rho correlation: Automatically switches to exact test for N<=10
 Ripley's k: Confidence intervals by Monte Carlo instead of approximate equation
 Sinusoidal fitting: Options for fitting to pure sines or cosines (no phase)
 Convex hulls and concentration ellipses can now be color filled
 PLS: Incorrect labels for second block in plot of loadings, fixed
 Linear n indep 1 dep.: Incorrect labels when first column not selected, fixed
 New distance measure: Greatcircle distance on Earth's surface (WGS84)
 Bivariate linear regression: r^2 reported in addition to r.
 PLS: "Squared covar %" made available also when using correlation matrix
Version 1.99
 Import text file (whitespace, tab and comma separated, label options)
 Numerical inaccuracy in MANOVA/CVA, introduced in 1.83, fixed
 Diversity profiles: Incorrect results for noninteger abundance data, fixed
 Diversity indices: Now accepts noninteger abundance data (bootstrapping still rounds to integers)
 PLS: New equation for "Squared covar %" when used on the covariance matrix (introduced in 1.98)
Version 2.00
 Oneway ANOVA: Analysis of residuals (plots and tests)
 Visualization of Elliptic Fourier linear regression
 Elliptic Fourier Analysis now also reports sizes
 Smoothing of Mantel scalogram
 Copy text from bivariate linear regression window
 Landmarks: New option for projection to tangent space
 PCA axes automatically flipped if sum of loadings is negative
Version 2.01
 REDFIT spectral analysis with rednoise model
 Zero intercept option in linear regression (OLS, RMA and LTS)
 Markov chain analysis for sequences
 Renyi diversity profiles: Now with bootstrapping. Hole removed for alpha=1.
 New algorithm for CVA
 Test for random (Poisson) timing of events
 CABFAC paleoenvironmental reconstruction: Now with kfold cross validation.
 Multiple regression: Added R^2 for each independent variable
 Polynomial regression: Equation displayed on the plot
 NMDS made much faster
Version 2.02
 Linear regression: Major Axis regression included
 Linear regression: Corrected confidence bands for OLS regression with zero intercept
(introduced in 2.01)
 Smoothing spline: Option for enforcing monotone curve
 Fitting to logistic equation: Bootstrapped confidence bands. Enforce a=1.
 Survival analysis: Divisionby zero for some data sets, fixed.
 Wavelet analysis: Plot of one particular scale
 Mixed similarity measure in NPMANOVA and oneway ANOSIM: Problem with repeated
popup windows fixed.
Version 2.03
 Eventsintime analysis (tests for Poisson process and trend)
 Geographical coordinate transformations (WGS84, UTM etc.)
 CVA: Visualization of landmark and EFA deformations along discriminant axes
 PCA: Plot any axis against any other
 Mixture analysis: Max n=300 limitation removed
 CCA: Percentages of eigenvalues reported
 REDFIT: Monte Carlo simulation now optional
 Correlation: Exact test of Spearman's rs for n<10, not n<11 (was too slow)
 Removed option for Gaussian fit algorithm from species packing modelling (weighted averaging better)
Version 2.04
 Directional: Watson's goodnessoffit test for von Mises distribution.
 Directional: MardiaWatsonWheeler test for equal distribution
 ParksMcClellan linearphase filters (lowpass, highpass, bandpass, bandstop).
 Open files: Support for the FASTA (NCBI specification) molecular sequence format
 Eigenshapes: All axes reported. Fixed rare crash for view scores as numbers.
 Runs test: Options for "runs about the mean" and "runs up and down"
 Modern Analoque Technique: Started crashing in some recent version. Fixed.
 PCO: User similarity and distance indices were swapped in the radio box
 PCA: Grid and EFA deformation now use eigenvalue scaling
 Polynomial and sinusoidal regression: AIC now uses the AIC_chisquared definition
with smallsample correction
Version 2.05
 Detection of alignments in point patterns
 Quadrat richness: Chao2 updated to latest biascorrected form. Jackknife1 variance. Bootstrapping.
 Sinusoidal fitting: List of residuals. Occasional phase shift in plot when changing plot type,
fixed.
 PCA shape (landmark) and EFA deformation now have option for eigenvalue scaling
 Expansion plots for grid deformation: Visual quality improved, occasional "leakage" of color fixed.
 View numbers in Ripley's K: bug fix in copy function
 Ripley's K: 2x speedup
 Smoothing spline: Plotting of the given error bars
 Rare crash in ParksMcClellan filter fixed
 Automatic detrending in Spectral analysis
 Autoassociation: P values were not updated when unticking "no repetitions" option.
 PCA: Now reports only rows1 axes if rows1 < columns (the rest are zero).
 Correspondence analysis: Plot any axis against any
Version 2.06
 Shorttime Fourier transform
 Bar chart with error bars
 New distance measure, Mahalanobis, in clustering, PCoA, NMDS, ANOSIM etc.
 CVA now reports classifications and confusion matrix
 Gridding (spatial interpolation) now includes crossvalidation
 Semivariogram modeling: Reports residual sum of squares. Automatic model and parameter
optimization. New model: Cubic
 Contingency table now includes permutation test
 Fitting to MichaelisMenten equation
 Expansion map for thinplate spline deformations: Option for grayscale
 Gridding and 2D kernel density: Option for cropping to convex hull
 KruskalWallis posthoc analysis by MannWhitney now uses the same version of the test
as the MannWhitney module
Version 2.07
 Partial Mantel test
 Cross validation for CVA classifier
 95% confidence band for LOESS smoothing
 Stereoplots now include density maps (colour or grey scale)
 Read molecular sequence files in the Arlequin format
 Bitmaps made smoother in gridding and kernel density modules
 Procrustes fitting: Option to rescale to original centroid sizes
 MANOVA posthoc pairwise comparisons: Now reports sequential Bonferroni corrections and
Mahalanobis distances. Now based on withingroups covar matrix pooled over all groups, not
only the two compared.
 Fitting to growth functions (logistic etc.): Now includes Akaike Information
Criterion. New model Gompertz curve. Bootstrapping made more robust.
 Gridding: New gridding method, multiquadric. Crossvalidation now reports mean squared error.
Kriging made faster.
 Frame around plots.
 Bug fix: Parsimony analysis failed for missing values (bug introduced in 2.06)
 Bug fix: Cluster analysis failed with correlation similarity (bug introduced in 2.06)
 Bug fix: Mahalanobis distance was reported incorrectly in the Twogroup Permutation
Test module (the p value from the test was correct)
 Bug fix: ShapiroWilks normality test gave incorrect results when running several samples
with unequal sample sizes (bug introduced in 1.96)
 Bug fix: PCA landmark deformation: Vector plot did not honour eigenvalue scaling option
 Bug fix: Semivariance model "cubic" was not supported by kriging (introduced in 2.06).
Version 2.08
 Plot quality improved (antialiasing, floating point coordinates,
cardinal splines, alpha blending, etc.)
 Generalized Linear Model, including logistic (logit) regression.
 Partial linear correlation with any number of controlling variables
 Combination of errors (weighted mean, plot of summed probability density)
 Brillouin diversity index
 CCA: option to amplify triplot vectors
 Ternary plot: Show fourth variable with bubble plot or gridding
 New file formats for saving graphic: TIF, GIF, PNG (in addition to JPG, BMP, EMF).
 Wavelets: Plotting of Cone of Influence.
 Linear 1 independent, n dependent regression: Outputs overall MSE and R2.
Table of all coefficients.
 2D kernel density: Choice between four different kernel functions
 KolmogorovSmirnov test: Added permutation test.
 NPMANOVA: Option for sequential Bonferroni correction in pairwise posthoc
 Past file format: Now accepts space character inside cells (doublequoted
in file)
 Minor bug fixes.
Version 2.09
 Fourier shape analysis by the Haines & Crampton method (Hangle)
 PCA now has three alternative methods for missing data, including iterative imputation
 "Jitter plot" in the box plot module
 Option to flip the axes in Graph, XY graph, XY error bar, histogram, box plot.
 Twogroup multivariate permutation test: Added Euclidean distance option
 Bug fix: "Mixed" distance measure in cluster analysis did not handle missing data correctly
 Mixed distance measure: Now robust to failure in one data type due to excessive missing data
 2D kernel density plot: Row labels and convex hulls
 Bug fix: Histogram for several columns used only first column to set start and end values.
 Concentration ellipses plotted for N>=3 (was N>=2)
 Another bug fix in sequential Bonferroni correction for pairwise MANOVA, NPMANOVA, ANOSIM
Version 2.10
 Twoway NPMANOVA
 SIMPER: Added Euclidean, cosine and chord distances
 Beta diversity: Added matrix of pairwise comparisons
 Regular interpolation: New options for point spacing and interpolation method
 Bug fix: Displaced labels in cluster analysis (introduced in 2.09)
 Bug fix: Stratigraphic range confidence intervals: Joint alpha was incorrect for n<=6
 Bug fix: Multiple linear regression: Crash for negative R2 (rare)
 Bug fix: Unitary associations: Crash in biostratigraphic graph
 Bug fix: Concentration ellipses sometimes plotted with very thick lines
Version 2.11
 Polyserial correlation (for continuous vs. ordinal variates)
 Multitaper spectral analysis
 NMDS: Optional biplot showing correlation with environmental variables
 Oneway ANOSIM: Box plot of within and acrossgroup distances
 Univariate statistics: Now with bootstrapped confidence intervals
 Survival analysis: Now accepts one or several columns
 All digits retained for all functions in Transform menu
 Fixes of bugs causing rare crashes in NMDS, EDMA, reading of NTSYS files, and compare diversities.
Version 2.12
 Friedman test with pairwise Wilcoxon posthoc
 Spatial autocorrelation (Moran's I) for point data
 Exact version of the Wilcoxon test for n<26
 Bug fix: Wilcoxon test could be inaccurate if any pair contained identical values
 SIMPER now much faster for large data sets
 Shorttime Fourier analysis now has option for the multitaper method
 Markov chain analysis can now read multiple columns for pooled analysis
Version 2.13
 Multivariate multiple regression (several dependent and independent variables)
 Chisquared: Fisher's exact test now handles more than two rows (n x 2 tables)
 Linear regression: DurbinWatson test for autocorrelation of residuals
 Date/time conversions
 Polynomial fit: Table of residuals, and improved error handling
 Shorttime Fourier: Bug fix for multitaper method (introduced in 2.12)
 SHE analysis: Improved handling of rare divisionbyzero error
 Permutation t test: Speedup, and max permutations increased to one million
 Matrix plot: Y axis now shows first row at top
 PCA: Fixed rare crash in scatter plot, view numbers
 Oneway ANOVA: Copy text now copies whole window
 Contouring: Small improvement in quality
Version 2.14
 Simple smoothing filters: Moving average, Gaussian, median, exponential
 Linear regression: BreuschPagan test for homoskedasticity of residuals
 Fitting points to logarithmic spiral
 Functions to remove allzero, allmissing or singleton rows or columns
 Spherical (stereoplot): Calculation and plot of mean direction
 NMDS: Numerical output of correlations with environmental variables
 Pairwise Hotelling's test: Exact test for N<=16.
 F and t test: Bootstrapped confidence interval for difference in means
 Box's M test: Monte Carlo permutation
 Wavelets: New wavelet bases: DOG(m=0) and DOG(m=1). Color scale bar.
 Correspondence analysis: Speed increase for matrices with many more columns than rows
 Similarity and distance indices: Improved error handling
 DCA: Improved error handling. Limit on size of dataset increased.
Version 2.15
 Withingroup and betweengroup centered PCA
 Wavelets: Significance test against rednoise hypothesis
 KruskalWallis: p value was inaccurate for data with very many ties
 Bar chart: More options for whiskers (1sigma or 95%, stdev or stderr)
 SIMPER: Output format made more similar to the PRIMER software
 Linear 1 indep n dep: Now accepts zero stdev on dependents
 CVA: Bug in biplot when only two groups present, fixed
 Crash when viewing phylogenetic trees loaded from Nexus files: Fixed
 Twogroup multivariate permutation test now has Euclidean as default distance
Version 2.16
 BoxCox transformation with max likelihood estimation of lambda
 AndersonDarling normality test
 Nearest neighbor point analysis: Plotting of distance histogram vs. expected distribution
 Hangle (outline shape analysis) now includes 'Htree' fitting
 Coefficient of variation: Now with bootstrapped confidence intervals
 Similarity indices: Added Mixed (as available in other modules)
 Rarefaction: Labels added for multiplesample plot
 User controllable range of color maps, new color maps
 User controllable number of lines in spline deformation grids
 Bubble plot: Option for 95% confidence ellipses
 Rarefaction: Option to not show standard deviations
 Improvement on number of decimals in graph axes
 Directions: Crash for pathological input, fixed
 Sinusoidal fitting: Crash for pathological input, fixed
Version 2.17
 Twoway ANOVA without replication
 Chao1 species richness estimator (bias corrected)
 Landmark 3D plot: Added animation function
 Coefficient of variation now also available in the Univariate statistics module
 BoxCox: Automatic addition of constant for zero or negative values
 KolmogorovSmirnov: Permutation test was inaccurate, fixed
 Rarefaction: Option to leave out confidence intervals in banana plot
 Cluster analysis: Dendrogram export, displacement of labels bug, fixed
 Wavelet analysis: Color coding changed (again)
 Fourier shape analysis: Number of harmonics increased to 30
 Some other minor improvements
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