[MORPHMET] GM with live amphibians

[Michael Holmes]

I was wondering if anyone has used GM to study morphological differences
between groups of live amphibians, specifically frogs.  I only have
experience with crania and postcranial elements, which tend to have many
potential landmarks.

Is GM possible with live specimens such as frogs? The literature seems to
be most cranial. If anyone can recommend papers that have good methods for
taking images and placing landmarks, I would much appreciate it.  Thanks in
advance.

—

Michael Holmes, Ph.D.

Assistant Professor

Department of Biology

231 Kenneth E. Swain Hall

Coastal Carolina University

(843) 349-2254

https://scholar.google.com/citations?user=hVEidC8J=en

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[MORPHMET] CVA Goodall's and Procrustes ANOVA discrepancies

[Michael Holmes]

Hello Morphemeticians,
I am getting mixed results when I run a CVA using TwoGroup (Goodall's test)
and a Procrustes ANOVA. I tested several different pairings and got mixed
results with the Procrustess ANOVA but consistent significant differences
in shapes of paired groups when using a CVA.  Are there sensitivity
differences between the two tests? Is the Procrustes ANOVA generally more
conservative? Thanks for any help.

-

Michael W. Holmes, Ph.D.
Assistant Professor
Department of Biology
Coastal Carolina University

https://scholar.google.com/citations?user=hVEidC8J=en

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[MORPHMET] Microscribe on rodents

[Michael Holmes]

Hi Everyone,
Has anyone collected 3D data using a Microscribe on anything smaller than a
squirrel? How accurate are the points? Are there any precautions to using a
Microscribe on small specimens?  Thanks.

-

Michael W. Holmes, Ph.D.
Assistant Professor
Department of Biology
Coastal Carolina University

https://scholar.google.com/citations?user=hVEidC8Jhl=en

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[MORPHMET] p-values for Mahalanobs distances

[Michael Holmes]

Hi All,
When computing Mahalanobis distances, is there a way to get p-values on
these in MorphoJ? Thanks.




Michael W. Holmes

Ph.D. Candidate
University of California, Berkeley
Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

Museum of Vertebrate Zoology
3101 Valley Life Sciences Building
University of California
Berkeley, CA   94720  USA

http://ib.berkeley.edu/labs/lacey/holmes2.html

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[MORPHMET] Warped Grids in MorphoJ

[Michael Holmes]

Hi All,
I am running MorphoJ on Mac OSX. I am looking at morhological variation
between two datasets. In each dataset, each specimen has four replicates. I
combined the datasets, made classifier files and ran the Procrustes fit and
generated the covariance matrix.  How then do I make a vector diagram/warp
grid that visualizes shape change between the average shape of the two
datasets? Thanks in advance for your help.

Mike


Michael W. Holmes

Ph.D. Candidate
University of California, Berkeley
Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

Museum of Vertebrate Zoology
3101 Valley Life Sciences Building
University of California
Berkeley, CA   94720  USA

http://ib.berkeley.edu/labs/lacey/holmes2.html

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[MORPHMET] Centroid Size Units

[Michael Holmes]

Hello,
I am using 2D GM to examine skull shape and size in rodents.  I used Sage
to calculate centroid size based on a millimeter ruler in my photos.  What
are the units of centroid size? mm^2? Thanks.


Michael W. Holmes

Ph.D. Candidate
University of California, Berkeley
Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

Museum of Vertebrate Zoology
3101 Valley Life Sciences Building
University of California
Berkeley, CA   94720  USA

http://ib.berkeley.edu/labs/lacey/holmes2.html

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Re: [MORPHMET] arrayspecs in geomorph giving error message

[Michael Holmes]

I realize I left off a column of my matrix but am still getting the same
error when I try to convert the 2D data to 3D using arrayspecs.

Michael Holmes

Ph.D. Candidate
University of California, Berkeley
Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey



On Mon, Dec 29, 2014 at 1:54 PM, fossilbear fossilb...@gmail.com wrote:


 I have a dataset with 2D landmark data and various independent variables.
 I have defined the shape as the 26 coordinates and used the following code
 coords=as.matrix(file.dat[,-(1-25)])# this works successfully

 shape=arrayspecs(coords, 13,2,byLand=FALSE) #this gives the error message:

 Error in arrayspecs(coords, 15, 2, byLand = FALSE) :
   unused argument (byLand = FALSE)

 It used to work in an older code that I used a few months ago.  Now it is
 giving me the business.  Any idea?

 here is my matrix:
X2X3  X4X5  X6X7
X8X9   X10X11   X12   X13X14
 1  0.03997963 0.3367198 -0.03365625 0.3014825 -0.07325888 0.1675589
 -0.00201582 0.1198153 0.1103637 0.08943977 0.1048558 0.1349480 0.09306566
 2  0.03487885 0.3360288 -0.04191770 0.3019065 -0.07568615 0.1773127
  0.00488312 0.1209543 0.1103113 0.08795262 0.1073037 0.1282006 0.10025810
 3  0.03122694 0.3335739 -0.03586701 0.2990588 -0.06906252 0.1835084
 -0.00104611 0.1203527 0.1091257 0.08869470 0.1068174 0.1274445 0.09270893
 4  0.03083083 0.3326056 -0.03908910 0.3004318 -0.07108287 0.1792337
 -0.00165225 0.1319318 0.1058574 0.09170375 0.1092670 0.1310557 0.09552525
 5  0.01549123 0.3443843 -0.03050719 0.3125263 -0.06838448 0.1700543
  0.00161769 0.1176949 0.1166828 0.08556727 0.1156704 0.1246849 0.10702841
 6  0.03307164 0.3389991 -0.03296144 0.3013813 -0.07404540 0.1761324
 -0.00111903 0.1171637 0.1067639 0.08408184 0.1057422 0.1282180 0.08931452
 7  0.03350312 0.3455607 -0.03805888 0.3055496 -0.07362491 0.1634284
 -0.00363214 0.1194372 0.1135201 0.08189299 0.1086072 0.1212518 0.10258651
 8  0.03673053 0.3438029 -0.03566788 0.3090075 -0.06750164 0.1667050
  0.00040803 0.1195644 0.1068360 0.09126465 0.1011679 0.1309072 0.09048932
 9  0.04514989 0.3445413 -0.03499111 0.3068777 -0.07115699 0.1667978
 -0.00709849 0.1197529 0.1062217 0.08585121 0.1042393 0.1203195 0.09658300
 10 0.03941113 0.3368754 -0.03614875 0.3014612 -0.07685012 0.1739622
 -0.00373047 0.1255605 0.1052433 0.09168792 0.1046592 0.1267143 0.09835272
 11 0.04435505 0.3418018 -0.03636860 0.3020457 -0.06808821 0.1652769
 -0.00498531 0.1202878 0.1071845 0.08753606 0.1033531 0.1308717 0.09305898
 12 0.03382660 0.3410164 -0.02758452 0.3042652 -0.06818370 0.1603699
  0.00172079 0.1198990 0.1080929 0.08772879 0.1060758 0.1288913 0.09363879
 13 0.04255165 0.3449338 -0.02981377 0.3073790 -0.07146521 0.1705471
  0.00037987 0.1213191 0.1065837 0.08106710 0.1042081 0.1237737 0.09461133
 14 0.03073561 0.3469995 -0.03886375 0.3069022 -0.07383648 0.1655636
  0.00320057 0.1142681 0.1153341 0.08523485 0.1096984 0.1300842 0.09972374
 15 0.03833599 0.3468734 -0.02902469 0.3117373 -0.07285814 0.1693639
 -0.00069631 0.1096915 0.1085963 0.08663837 0.1030768 0.1299194 0.08930121
 16 0.03216115 0.3437012 -0.03285981 0.3067420 -0.07148509 0.1634199
  0.00288162 0.1189920 0.1071332 0.09068717 0.1053644 0.1296370 0.09244684
 17 0.03847241 0.3440789 -0.03818560 0.3063814 -0.07395364 0.1627708
  0.00468873 0.1135445 0.1142731 0.08248338 0.1067443 0.1249139 0.10083024
 18 0.02843652 0.3421909 -0.03310299 0.3057486 -0.07435036 0.1660656
  0.00813877 0.1155870 0.1126716 0.09130366 0.1097459 0.1262602 0.09857246
 19 0.03655065 0.3401477 -0.04381970 0.3032213 -0.07541966 0.1673756
  0.00183286 0.1177150 0.1120358 0.08981567 0.1061729 0.1334020 0.09264442
 20 0.03737752 0.3456541 -0.02603089 0.3021693 -0.06887650 0.1696384
 -0.00264276 0.1219772 0.1055129 0.08822826 0.1006278 0.1261045 0.09194974
 21 0.04189542 0.3451091 -0.02394418 0.3116268 -0.06460292 0.1606836
  0.00411035 0.1129572 0.1143172 0.07634388 0.1041113 0.1264328 0.10177871
 22 0.04060854 0.3397505 -0.02108206 0.3040336 -0.06508092 0.1728905
  0.01063115 0.1132407 0.1100533 0.08138505 0.1043609 0.1259463 0.09475078
 23 0.04626172 0.3415264 -0.01779378 0.3047242 -0.06208483 0.1691875
  0.00503913 0.1180950 0.1088386 0.08107183 0.1050709 0.1182668 0.09969513
 24 0.04233714 0.3412122 -0.02353006 0.3051835 -0.06472309 0.1640181
  0.00618488 0.1134105 0.1139769 0.08293953 0.1061782 0.1230331 0.10109200
 25 0.04271343 0.3389914 -0.02348183 0.3040175 -0.06045990 0.1728931
  0.00982319 0.1142752 0.1102982 0.08126082 0.1001390 0.1252385 0.09596056
 26 0.04436916 0.3389492 -0.02609471 0.3011717 -0.06847199 0.1740515
  0.01126975 0.1163778 0.1134961 0.08265127 0.1056537 0.1271954 0.10044545
 27 0.05455984 0.3485089 -0.02565360 0.3101353 -0.06505627 0.1602461
  0.00500854 0.1096231 0.1134036 0.08553745 0.1073083 0.1239045 0.09357168
 28 0.05165666 0.3425469 -0.02352171 0.3048061 -0.06014191 0.1640241
  0.00604971 0.1148992 0.1114002 0.07946789 0.1022844