Re: independent variable files and regression

[morphmet_moderator]

----- Forwarded message from "K. James Soda" <k.jamess...@gmail.com> -----

Date: Fri, 5 Apr 2013 05:01:35 -0400
From: "K. James Soda" <k.jamess...@gmail.com>
Reply-To: "K. James Soda" <k.jamess...@gmail.com>
Subject: Re: independent variable files and regression
To: morphmet@morphometrics.org

Hi Bernd,

I think the easiest way to create an independent variable file is through tpsUtil.  Here are the steps:

1)  Launch tpsDig2, and open the tps file in which you digitized your images.

2)  For each image, go to Options -> Specimen Info...

3)  In the Variable field of the resulting window, enter the variable values relevant to that image in the following format: variableName1=variableValue1,variableName2=variableValue2 (and so forth)

If your independent variable is categorical, you may need to code it.  For example, if you have two groups give one group the value -1 and the other the value 1.  It is a bit more complicated if you have more than two groups; see Help -> Contents -> Analysis of more complex designs in tpsRegr for more information.  As an example, I could enter:

sex=-1,height=23.4

4)  Once you have provided variable values for every image, save the tps file.

5)  Launch tpsUtil.

6)  In the drop down menu, select "Build Variable Matrix"

7)  Click the Input file button, and select the tps file containing your digitized images and variable values.

8)  Click the Output file button, and create a name for your variable matrix in the desired directory (aka folder).

9)  Click Setup.

The program should make a ding noise, and you are finished.  You now have a variable matrix to upload to tpsRegr.  I think that should all work.  It has been a while since I have had to use tpsRegr in my own work.

Best wishes,

James

On Thu, Apr 4, 2013 at 12:17 AM, <morphmet_modera...@morphometrics.org> wrote:

----- Forwarded message from "bfrankemoe...@t-online.de" <bfrankemoe...@t-online.de> -----

Date: Wed, 3 Apr 2013 10:54:30 -0400
From: "bfrankemoe...@t-online.de" <bfrankemoe...@t-online.de>
Reply-To: "bfrankemoe...@t-online.de" <bfrankemoe...@t-online.de>
Subject: independent variable files and regression
To: morphmet@morphometrics.org

Hello guys,

I would like to do a "Regression" in tpsRegr and I don´t know how to do that. I´m following the instructions of an online workbook called "A Practical Companion to Geometric Morphometrics for Biologists: Running analyses in freely-available software" by Miriam Leah Zelditch, Donald L. Swiderski, and H. David Sheets.

The following text passage is from that online workbook. Here they tell me how to do a regression in tpsRegr, however, I have no Idea what an "independent variable file" could be and how to construct one.

"Regression in tpsRegr
To run tpsRegr, you need a shape data file and an independent variable file. The shape data file can be in either *.tps or *.NTS format, the independent variable must be in *.NTS format. The first line of the independent variable file thus contains the control line giving the matrix type (1), number of rows (which is your sample size), number of columns (the number of variables in the file), and the missing data option (0). If you labeled the independent variable, add an L to the third (column) number, e.g. 1L. The remainder of the file consists of the column(s) of values for your independent variable. For studies of allometry, you can produce your independent variable file within tpsRegr if you used the scale factor in tpsDig. Go to the File menu, select Save and then select centroid size. That produces a file of centroid sizes in *.NTS format. If you want to do the analysis using log-centroid size instead, open your *.NTS file in a spreadsheet and add a second column, this one of log-transformed values. Just remember to change the control line to a 2 for the number of columns and whenever you have two or more variables in the file, it is useful to include their labels, so make sure that the control line has 2L for the number of columns. Below that control line, add a line with the two labels in it, e.g. CS LCS (no punctuation goes in this line). Save that as a text file with an *.NTS extension (you may have to change the name of the file if your spreadsheet automatically adds *.txt to all files that are saved as text files)."

Is there anyone among you who could help me out with this?

Thank you very much,

Bernd

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