Error in SeqParSib : 'AgePriors' matrix should have size nAgeClasses * 8

[jblamyatifremer]

Dear Jisca,

I am trying to reconstruct pedigree (at least parents-offsprings relationship) in a lab population under experimental infection during 4 generation. I only know the age of individual... In some cases (limited) I know the sex of individual. The good thing is that the design is not with overlapping generation.

My intuition is telling me, that is a format error... but I am not more idea.

Error in SeqParSib("par", Specs, GenoM, LifeHistData, AgePriors, Parents = NULL, : 'AgePriors' matrix should have size nAgeClasses * 8 In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf

I added to files to reproduce the error (I am on window 7 64 bit, using sequoia 0.9.3).

geno2_debug.txt lfh2_debug.txt

Cheers, JB

[JiscaH]

Hello JB,

You closed the issue - does this mean you resolved your problem? Thank you for including the files, it looks indeed like a formatting error. When reading in the genotype data as follows, sequoia runs without problem:

GM <- read.table("geno2_debug.txt", header=T, row.names=2)
GM <- as.matrix(GM[,-1])

I'd like to let you know that I'm working on an update of sequoia, with some added features which could be useful to you. It should hopefully be available on CRAN by the end of next week. After some tweaking it has a better assignment rate for datasets with many individuals of unknown age and sex. It also finds parent-parent-offspring trios among the list of likely relatives where both parents are of unknown sex.

Kind regards, Jisca

[jblamyatifremer]

Hi Jisca,

I found the error myself... i was a bit shameful to open a github issue just for that (rfm error)

Good to know that you are working in another version of sequoia that will manage unknow sex (because in marine species (mollusc and fish) is usually the case).

Thanks for being so quick !

Cheers,

JB

On 2018-03-21 20:45, JiscaH wrote:

Hello JB,

You closed the issue - does this mean you resolved your problem? Thank you for including the files, it looks indeed like a formatting error. When reading in the genotype data as follows, sequoia runs without problem:

GM <- read.table("geno2_debug.txt", header=T, row.names=2) GM <- as.matrix(GM[,-1])

I'd like to let you know that I'm working on an update of sequoia, with some added features which could be useful to you. It should hopefully be available on CRAN by the end of next week. After some tweaking it has a better assignment rate for datasets with many individuals of unknown age and sex. It also finds parent-parent-offspring trios among the list of likely relatives where both parents are of unknown sex.

Kind regards, Jisca

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