More IMP Software

Last Addition January 23, 2006

 

New Releases (After July 1, 2004):

 

In order to prevent confusion for researchers working through our textbook on Geometric Morphometrics, called

 

Geometric Morphometrics for Biologists: A Primer

Miriam L. Zeldith, Donald L. Swiderski, H. David Sheets and William L. Fink

 

which was recently published by Academic Press/Elsevier,  and should soon be available, I have started a second page of morphometric software.  The original software is still free for downloading, and will continue to be free at morphsoft.html

 

  I have started a webpage for new releases in the IMP series.  The earlier page will be “frozen” so that the software discussed in the book remains available in the form discussed in the book.  The new releases will be on this page.  I also expect to shift over to Matlab version 7 shortly (ie. Fall 2004), so IMP software version 7 will be appearing here.

 

Mac Users-I have a compiler for the Mac, so I can produce IMP programs that will run under the Mac X11 system in OS 10.  If you are a hard-core MAC user, familiar with X11 and are interested in IMP for MAC and are willing to help debug the installation procedure and manuals for MAC installation, drop me a note.

 

So here are the new and/or updated items:

 

                                 Updates of Existing IMP Software for 2D Landmark Data

         

              Updates to add specific functions, not documented in the textbook, most include users manuals.

 

CVAGen6L-This is an update of CVAGen6 with a jackknife procedure for assessing how well the discriminant function and assignment test work for a given data set.  There is a newer version of CVAGen available below, listed as PCA_CVA

 

PLSMaker6g-This is a version of PLSMaker with a trace correlation calculation available.  The trace correlation may be calculated between the two blocks, and the use of a generalized inverse calculation is available within this calculation.

 

BigFlip6a-This is an updated version of the Big Flip program which can use pairs of off-axis landmarks to estimate the location of the symmetry axis when carrying out reflection and averaging of data. 

REGPAC6P-> This is an update of Regress6k called Regress6K+, it is a Beta version that checks the correlation of the linear tangent space distances with the Procrustes distance in curved space.  Includes a Word file called “Correlation of Euclidean and Procrustes” that explains how it works.

PCAGen6p-> This version has a summed variance calculation in it (the summed squared partial procrustes distance about the mean form divided by (n-1), where n is the sample size). It also has a better window resizing function. On 7/25/06 I updated the write to eps files option. More error trapping added 2/16/07

TMorphGen6c-> This expanded version of Tmorphgen computes angles on organismal structures based on landmark coordinates, as well as lengths along structures based on landmarks. Users specify the angles to be measured using a protocol and angles are output in degrees and radians.

CoordGen6h-> This version will compute a matrix of all pairwise Partial Procrustes Distances between specimens in the input file.  The option is available on the file menu to run this calculation. Also has the ability to display individual specimens one by one, and a zoom function has been added

 

New Two-D Software

PairDisparity (PAIRDPAC.EXE)-This is a program for testing whether the disparity of one group of organisms/species (ie. a clade, local population, ecologically related group) is statistically significantly larger or smaller than that of another group using a permutation test.  This compliments DisparityBox6.

 

Vis_Proto- This is a tool for visually editing a number of different “protocols” used in other pieces of software.  It is currently under   development, so I would like to restrict it’s use to direct collaborators only please.

 

TMCorr-Traditional Morphometrics Correlation Structure Tool.  Currently under   development, so I would like to restrict it’s use to direct collaborators only please.

 

ChainMan-This is the ChainMan tool for outline data. It can carry out a PCA of outline-based data, and can extract evenly spaced semi-landmarks from chain-codes or curves into semi-landmarks. This is currently under development, so direct collaborators only please. ChainMan runs under Matlab version 6.5 so it needs the mglinstaller version 6.5 drivers, mg_linstaller6_5.exe. If you are downloading mglinstaller6_5.exe, download it and install it in a new director, not, repeat, not, the same directory as the mglinstaller for version 6, which you presumably already have installed.

 

ChainMan3D-This is a 3D version of the ChainMan tool. It runs under the Matlab 6.0 drivers, and now includes the ability to handle 2D data also. 10/30/06. Still in Beta, let me know about problems!

 

PCA_CVA- This is a version of CVAGen (CVAGen6o) which is capable of performing a PCA on the data first, and then carrying out the CVA on a subset of the PC scores to reduce the dimensionality of the data. This program is currently in Beta Form. As of 3/30/2005, there is also a Jackknife test of the assignment of specimens to groups, as well as the more complex assignment test. The 7/25/06 update fixed some problems with the save eps format file and other issues.

 

CCoder- This is the utility tool for producing customized group codes for use with CVAGen and PCAGen.

 

                                          Revised Three-D Software

 

Revised 1/23/06 to correct a programming error in the Procrustes Superimposition.  Please download the revised versions and check all results obtained using earlier IMP 3D software.  Details of the error

 

ThreeDPCA6- I have added the ability to save the eigenvalues and eigenvectors (PC axis loadings) from the PCA analysis.  The save

options are on the File menu.  Beta 2, 1/23/06

 

V3pac- This is a program called V3Comp6, which is a version of VecCompare meant for use with 3 dimensional data.  Very limited

manual. Beta 2, 1/23/06

 

TDSPAC- This is a three dimensional version of Standard6, for removing variance attributable to an independent variable, using a

regression model.  The program enclosed is ThreeDStand6 (which means Three Dimensional Standardization).  It can load

either IMP or TPS files. Beta 2, 1/23/06

 

SV3PAC- This is a version of Simple3D that can load either TPS or IMP format files. Beta 2, 1/23/06

 

 

WireMan6- Visual editing tool for constructing wireframes, traditional measurements data sets and block structures using 3D landmark

data.   There is a manual for this, but it is in Beta form. Beta 2, 1/23/06

 

PLS3PAC- This is a three dimensional version of the PLSBlock program, called PLS3D, for carrying out Partial Least Squares

analysis of 3D data. It is in beta form, with only the sketchiest of users manuals. Direct collaborators only please. Beta 3, fixed a bug that appeared when using non-shape data 2/23/07

 

SAT6- This is a three dimensional version of the SpaceAngle program, called SpaceAngleThree6. Beta 2, 1/23/06

 

R3PAC-This is the the 3D regression tool ThreeDRegress

 

CVAPAC3-This is an the 3D alpha version of a 3D CVA tool-very rough-collaborators only, thanks! ThreeDCVA

 

Other Software

Below are one or two other items, which are fundamentally univariate tools I need to make available.  When time allows, I’m going to put these on a different page on the website, but for now, here they are:

walkpac.exe -> This is the Walkbox6 tool for testing time series against the null model of a random walks, and contains  some of the tests discussed 

in Sheets, H. D. and Michell C.E., 2001. Why the Null Matters: statistical tests, random walks and evolution. Genetica 112-113 pg 105-125.  There is a pdf manual included that should be reasonable complete.

walkpac65.exe->This is WalkBox65 with multivariate random walk models included. It requires the matlab version 6.5 driver files , mg_linstaller6_5.exe. This is a

program for direct collaborators only, thanks.

                         

agropac.exe-> This is the GrowChoice software tool used in Zelditch, M.L, B.L. Lundrigan, H.D. Sheets and T.Garland, Jr. 2003. Do precocial

                         mammals develop at a faster rate? A comparison of rates of skull development in Sigmodon fulviventer and Mus musculus                       

                        domesticus. Journal of Evolutionary Biology, Volume 16, pgs not known at present.  The manual may be a bit sketchy for this                        

                       program at the moment, let me know how it goes.

DefCat-> This is the DefCat retrodeformation operations test frame software, not currently intended for general distribution, collaborators only, thanks!

FMC-> This is the FMC Finite Mixture Coding Program for phylogenetic coding, test frame software, not currently intended for general distribution, collaborators only, thanks!

CorrExplore6-> This is a tool for exploring matrix correlations.  Collaborators only, thanks.

OmitBox-> This is a tool for selecting taxa to omit in a rarefaction study-very limited, direct collaborators only, thanks

manpac.exe-> This is the Manova/Mancova tool for 2D geometric morphometric data, allowing up to 2 classification variables and 1 covariate. This is currently in a very early beta version, direct collaborators only, thanks!

cardwalkpac.exe-> this is a simulation designed for classroom laboratory use, direct collaborators only at the moment, thanks!

RepManPac-> This is a repeated measures manova tool, using permutations and procrustes distances, direct collaborators only, thanks!

 

Test

 

CoordGen-> Version via ANGEL-password protected

 

IMP7 Page -> Test purposes only, thanks!

 

OModel->Direct collaborators only! Runs under version 6 (Matlab 6.0).