More IMP Software
Last Addition
New
Releases (After
In order to prevent confusion for researchers working through our textbook on Geometric Morphometrics, called
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 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,
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,
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,
SV3PAC- This is a
version of Simple3D that can load either TPS or IMP format files. Beta 2,
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,
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
SAT6- This is a three dimensional version of the SpaceAngle
program, called SpaceAngleThree6. Beta 2,
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!