PatWright / BatSimuPOP

Simulation of population changes over time to assess the use of temporal sampling
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Fail to load fstat file. #1

Closed BoPeng closed 6 years ago

BoPeng commented 6 years ago

simuPOP failed to load the fstat file with genotype lines

1 0305 0505 0204 1113 0304 0611 0511 0913 0808 0305 0710 0916 1016 0913 2 0 1  
1 0910 0505 0203 1518 0406 0610 0710 0512 0410 0202 0707 1618 1012 0709 2 0 1  
1 0509 0606 0204 1011 0407 0615 0109 1212 0813 0304 0708 1318 1114 0715 2 0 1  

The problem is with the last three columns, which should be coded as xxyy unless the genotype is missing (0).

My understanding is that you are using these columns for age, agecat and sex. Is there standard practice (so that I should update simuPOP) or is it something you invented?

BoPeng commented 6 years ago

Also, age information for pop2 is missing:

1 0709 0505 0406 0711 0305 0910 0912 1212 1016 0405 0707 1316 1014 0102 5 2 1  
1 0708 0208 0204 0913 0305 0911 0314 1012 0812 0203 0708 0913 0909 1314 5 2 1  
1 0510 0203 0211 0608 0709 0615 0912 0913 0812 0303 0709 1015 0711 1012 5 2 1  
1 0509 0505 0405 1115 0406 0510 0109 1212 0606 0202 0708 0909 1011 1314 5 2 1  
1 0509 0508 0306 1114 0405 1112 0910 1212 0408 0203 0708 0916 0710 1414 5 2 1  
1 0508 0303 0204 1213 0304 0608 0914 0612 0808 0303 0715 0209 1414 1314 5 2 1  
1 0809 0506 0506 1417 0405 0911 0109 1212 0606 0203 0709 0910 1115 0912 5 2 1  
1 0507 0506 0207 1516 0304 0812 0114 1212 1010 0204 0707 0917 1010 0712 5 2 1  
1 0509 0608 0211 1213 0306 0511 0109 0912 0408 0202 0708 1212 0911 0207 5 2 1  
1 0810 0506 0410 1316 0306 1115 0509 0609 0406 0203 0708 0709 0809 0206 5 2 1  
1 0711 0608 0408 1617 0406 0612 0611 1212 0406 0305 0707 0909 0813 0607 5 2 1  
2 0509 0606 0211 1213 0204 1015 0714 0206 0614 0202 0707 0909 0815 0516  2 1  
2 0710 0505 0205 0919 0410 0910 0609 0606 0608 0404 0708 0516 1212 1212  2 1  
2 0910 0606 0211 1112 0204 1011 0514 0213 0814 0203 0707 0917 1515 0716  2 1  
2 0709 0305 0306 0915 0607 0809 0609 0609 0410 0203 0709 0309 0716 0614  2 1  
2 0505 0306 0404 0916 0404 1011 0111 0612 0608 0304 0810 1317 1012 0205  2 1  
2 0509 0506 0204 1116 0405 0000 0000 1212 0406 0304 0809 1016 1314 0213  2 1  
2 0910 0506 0406 0613 0404 0910 0512 1212 0410 0204 0707 0318 1111 0612  2 1  
PatWright commented 6 years ago

I know that the software Nemo 2.3.46 can add the extra bit of info in the last columns of the fstat file. However, I don't know how they do it. Would it be easier to add that information separately? Unfortunately I don't have the age for pop2 as pop1 is the only one that has been monitored for 18 years.