readland.tps "Not all specimens have scale" warning

[rmungui...@gmail.com]

Dear list:


When I import the tps file to R using readland.tps function the following message appears:

postder_comb0 <- readland.tps("postder_201516_orden.TPS", specID = "imageID")
[1] "Not all specimens have scale. Assuming landmarks have been previously scaled."
[1] "Specimen names extracted from line IMAGE="

I have checked all the specimens and all have a scale value. Please see image attached: 


I am also attaching the tps file.

I am worried geomorph is not considering the differences in the scale between individuals when performing the procrustes analysis. 
Could some one provide help/orientation about this issue?

Kind regards,

Roberto Munguía

[Adams, Dean [EEOBS]]

Roberta,

 

The reason is that one of your specimens does not have a scale specified. It is about ½ way down your file:

 

IMAGE=IMG_6543fan.tif

 

Dean

 

Dr. Dean C. Adams

Professor

Department of Ecology, Evolution, and Organismal Biology

       Department of Statistics

Iowa State University

www.public.iastate.edu/~dcadams/

phone: 515-294-3834

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[rmungui...@gmail.com]

Thank you very much Dean, sorry for the

inconvenience.

.
Roberto

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[Emma Sherratt]

Dear Roberta,

I have updated the readland.tps function on the geomorph github repository (see here for details of how to install the latest version from github, which is not yet on CRAN).

Now it should be more intuitive when you have these kind of issues with your TPS file.

e.g.

postder_comb0 <- readland.tps("postder_201516_orden.TPS", specID = "imageID")

Not all specimens have scale. File contains: 183 SCALE lines, 184 Specimens. Assuming landmarks have been previously scaled. 

Specimen names extracted from line 'IMAGE=' 

Emma

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[Anderson Feijo]

Hi everyone,

I am also having a small issue about the scale when try to read my tps file (attached here). I got the following message: "Not all specimens have scale. File contains: 32 SCALE lines, 16 Specimens. Assuming landmarks have been previously scaled." My tps file has 16 specimens, and all of them have scale value. I couldn´t figure out the reason of this "32 SCALE lines". Any ideas?

Thank you very much. 

Anderson

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[Mike Collyer]

Hi Anderson,

I have some good news and some better news.  First, the reason for this error.  Your image names have the word “scale” embedded within then.  That throws off the readland.tps function when it searches for the scale.  It is a programming glitch because we did not anticipate “scale” in other locations than the scale line.  I have added code to catch something like this and the update is now available on Github.  As a reminder, how to update geomorph from Github:

devtools::install_github(“geomorphR/geomorph”, ref = “Stable”)

That was the good news.  You can immediately update geomorph and you should have no issue now.  If your problem persists though, let us know.

We are also currently getting geomorph ready for an update to CRAN, which we expect to happen maybe in a few weeks (after we have some time to test our updates).  As it turns out, readland.tps is one of the functions we are updating.  The better news is that your TPS file did not trigger any issues with our new update.  

Thank you for the indirectly provided opportunity to test our updated function!  

Cheers!

Mike

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<d_question.TPS>

[Anderson Feijo]

Hi Mike,

Thank you very much for your quick reply and the constant effort in keep updating the geomorph.

Best,

Anderson

Mike

Hi everyone,

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