Comments (5)
JiscaH
commented on June 2, 2024
1
Thanks! That does sound like a bug that should be fairly easy to fix.
The alternative is to edit the age prior matrix 'by hand' in the same way that MinAgeParent does (should do) in the new version, see https://jiscah.github.io/articles/vignette_age/book/sec-customAP.html#other-tweaks
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JiscaH
commented on June 2, 2024
1
Hi,
Turned out to be just a matter of a forgotten na.rm=TRUE . For now: if you replace all NA's in the Sex column of life.history.table by a 3 , it should work fine.
Cheers, Jisca
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JiscaH
commented on June 2, 2024
Hi Alex,
Actually, I've added this feature just a few weeks back, and it's in the version you can find here on GitHub! Please let me know if/how it works for you; since it's brand new it's not been extensively tested yet.
I'm still tripple checking for bugs, but plan to submit the new version to CRAN this/next week
edit: new parameter is called 'MinAgeParent', see ?MakeAgePrior
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alexkrohn
commented on June 2, 2024
What a wonderful coincidence! Thank you. I'll give it a shot.
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alexkrohn
commented on June 2, 2024
I encountered an error that I don't quite understand.
sibship <- sequoia(GenoM = geno.low.missing.inds, LifeHistData = life.history.table, Err = 0.05, Module="ped", quiet = FALSE, Plot = TRUE, args.AP = list(MinAgeParent = 10))
Warning: There are 1058 monomorphic (fixed) SNPs, these will be excluded
After exclusion, There are 87 individuals and 725 SNPs.
Ageprior: Flat 0/1, overlapping generations, MaxAgeParent = 62,62
Error in if ((Herm != "no" | any(LifeHistData$Sex == 4)) & length(DummyPrefix) == :
missing value where TRUE/FALSE needed
While the regular call to sequoia used to work, it also gives that same error. Any advice?
sibship <- sequoia(GenoM = geno.low.missing.inds, LifeHistData = life.history.table, Err = 0.05, Module="ped", quiet = FALSE, Plot = TRUE)
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] googlesheets4_1.0.0 forcats_0.5.1 stringr_1.5.0 dplyr_1.1.0 purrr_1.0.0 readr_2.1.1
[7] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.4.1 tidyverse_1.3.2 sequoia_2.5.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 lubridate_1.8.0 prettyunits_1.1.1 ps_1.6.0 assertthat_0.2.1 rprojroot_2.0.2
[7] utf8_1.2.3 R6_2.5.1 cellranger_1.1.0 plyr_1.8.8 backports_1.4.1 reprex_2.0.1
[13] httr_1.4.2 pillar_1.8.1 rlang_1.0.6 readxl_1.3.1 curl_4.3.2 rstudioapi_0.13
[19] callr_3.7.0 desc_1.4.0 devtools_2.4.3 googledrive_2.0.0 munsell_0.5.0 broom_0.7.11
[25] compiler_4.1.2 modelr_0.1.8 askpass_1.1 pkgconfig_2.0.3 pkgbuild_1.3.1 openssl_2.0.0
[31] tidyselect_1.2.0 fansi_1.0.4 tzdb_0.2.0 crayon_1.5.2 dbplyr_2.1.1 withr_2.5.0
[37] rappdirs_0.3.3 grid_4.1.2 jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3
[43] magrittr_2.0.3 scales_1.2.1 stringi_1.7.12 cli_3.6.0 cachem_1.0.6 fs_1.6.1
[49] remotes_2.4.2 testthat_3.1.1 xml2_1.3.3 ellipsis_0.3.2 generics_0.1.3 vctrs_0.5.2
[55] tools_4.1.2 glue_1.6.2 hms_1.1.1 processx_3.5.2 pkgload_1.2.4 fastmap_1.1.0
[61] colorspace_2.1-0 gargle_1.2.0 sessioninfo_1.2.2 rvest_1.0.2 memoise_2.0.1 haven_2.4.3
[67] usethis_2.1.5
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