Package: discent 0.5.0
Nick Brazeau
discent: Estimation of Deme Inbreeding Spatial Coefficients with Gradient Descent
In the early 1970s, Malécot described the relationship between genetic relatedness and physical distance, forming the framework of isolation by distance, or -- put simply -- pairs that are far apart are less likely to mate. Capitalizing on this framework by using measures of Identity by Descent, we produce a deme inbreeding spatial coefficient (DISC) using "vanilla" gradient descent. For the mathematical formulation of the of DISC, see: <TODO>. Briefly, we assume that the relatedness between two locations (demes) in space is given by the average pairwise IBD between the two locations conditional on the distance that seperates them. Further, we assume that geographic distance is scaled by a migration rate, which is a global parameter among all spatial locations.
Authors:
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discent.pdf |discent.html✨
discent/json (API)
NEWS
| # Install discent in R: |
| install.packages('discent', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nickbrazeau/discent/issues
- IBD_simulation_data - Simulated Identity by Descent from Isolation by Distance
gradient-descentidentity-by-descentspatial
Last updated 7 months agofrom:7f96210377482aa708033dfa4cf474aba38458d0
Exports:%>%deme_inbreeding_spcoefis.DISCresulttidyout
Dependencies:clicpp11crayondplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identify Deme Inbreeding Spatial Coefficients in Continuous Space | deme_inbreeding_spcoef |
| Simulated Identity by Descent from Isolation by Distance | IBD_simulation_data |
| Check if DISCresult S3 Class | is.DISCresult |
| print DISCresult S3 Class | print.DISCresult |
| Summary of DISCresult S3 Class | summary.DISCresult |
| Tidy Out Sim Method | tidyout |
| Tidy Out Sim | tidyout.DISCresult |