Section 1: kin-finding | A quick look at the dataset | Finding and classifying kin pairs | Find 'strong' kin pairs and split out POPs | Find definite FSPs | Examine covariates of kin-pairs data | Alternative POP statistic | Section 2: cleaning the bluefin dataset | Population allele frequencies | Checking for badly-behaved loci | Finding and removing duplicate samples | Samples from another population or species | Cross-contaminated and degraded samples | How has removing bad fish impacted our apparent locus quality? | Kinfer the bluefin dataset | Section Three: do we really need to do all that cleaning? | Duplicates | Contaminated or degraded samples
Package: kinference 1.2.47
Shane Baylis
kinference: Pairwise kin-finding from genotypes
Kin-finding and QC tools for Close-Kin Mark-Recapture
Authors:
kinference_1.2.47.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
kinference/json (API)
| # Install 'kinference' in R: |
| install.packages('kinference', repos = c('https://closekin.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/closekin/kinference/issues
Last updated from:5ffa03bf2a. Checks:11 NOTE, 2 OK. Indexed: yes.
The latest version of this package failed to build. Look at thebuild logs for more information.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | NOTE | 268 | ||
| linux-devel-x86_64 | NOTE | 304 | ||
| source / vignettes | OK | 206 | ||
| linux-release-arm64 | NOTE | 280 | ||
| linux-release-x86_64 | NOTE | 309 | ||
| macos-release-arm64 | NOTE | 229 | ||
| macos-release-x86_64 | NOTE | 491 | ||
| macos-oldrel-arm64 | NOTE | 275 | ||
| macos-oldrel-x86_64 | NOTE | 544 | ||
| windows-devel | NOTE | 267 | ||
| windows-release | NOTE | 306 | ||
| windows-oldrel | NOTE | 343 | ||
| wasm-release | OK | 146 |
Exports:autopick_thresholdchain_pairwisecheck6and4drop_dups_pairwise_equivest_ALF_6wayest_ALF_ABCOest_ALF_ABO_quickest_ALF_nonullsfind_duplicatesfind_dups_with_missingfind_HSPsfind_POPsfind_POPs_lglkget_chainhetzminoo_fancyhistoPLODilglk_genokin_powerkinPaletteprepare_PLOD_SPAre_est_ALFsplit_FSPs_from_HSPssplit_FSPs_from_POPssplit_HSPs_from_HTPsupairidvar_PLOD_kin
Dependencies:ateasegbasicsmvbutilsRcppRcppArmadillotensorAvecless
