help with estimate.missing

[christy...@unimelb.edu.au]

Hi all,

I'm trying to run the estimate.missing function without success, I hope someone can help me troubleshoot why. I'm admittedly rusty with geomorph;)

I have a 3D landmarked dataset of 16 skulls, and 12 of them have missing landmarks (9 specimens missing 1; 2 specimens missing 2; 1 specimen missing 5). I changed the headers of the complete ones to be correct, for example

1 1 180 0 Dim=3

while the missing ones look like 

1 1 180 1 9999 Dim=3

It all seems to read fine into geomorph, but when I run the code the resulting array still has the same missing landmarks for the same specimens, yet the rest of the landmark coordinates are changed.  I paste the code below if anyone has ideas of what I'm doing wrong, or I'm happy to send the dataset directly.

I'm running the latest version of R4.1.1 and installed geomorph from github.

Thanks for any help!

Christy

filelist <- list.files(pattern = ".nts") 

mydata<-readmulti.nts(filelist)

dim(mydata) #60  3 16 

any(is.na(mydata)) #TRUE

mydatareg <- estimate.missing(mydata, method = c("Reg"))

any(is.na(mydatareg)) #TRUE

[Adams, Dean [EEOB]]

Christy,

 

Have you installed geomorph from github? Recently there was a bug-fix in readmulti.nts. Perhaps that is the issue. Please install as:

 

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

 

If that does not resolve things, please contact me offline with your data and script and I’ll go through and see what the issue is.

Dean

 

Dr. Dean C. Adams

Distinguished Professor of Evolutionary Biology

Director of Graduate Education, EEB Program

Department of Ecology, Evolution, and Organismal Biology

Iowa State University

https://faculty.sites.iastate.edu/dcadams/

phone: 515-294-3834

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[Christy Hipsley]

Hi Dean,

 

Yes I did install from GitHub,

 

install.packages("devtools")

library(devtools)

devtools::install_github('geomorphR/geomorph',ref="Stable")

library(geomorph)

 

I will send you the data now , thanks for offering to help. I’ve run that code before with no problems, so I don’t know what I’m doing wrong.

 

Christy

 

Dr Christy Anna Hipsley | Assistant Professor

Department of Biology, University of Copenhagen

Universitetsparken 15, Building 3 Room 513

DK-2100 København, Denmark

 

Mobile: +45 52617701 Email: christy...@bio.ku.dk 

http://blogs.unimelb.edu.au/hipsleylab/ 

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