vignettes/a4Development_Plans.Rmd
a4Development_Plans.Rmd
Amanda Vinson wrote this in an e-mail on 20170901:
I’m very interested in hearing about your idea of adding algorithms related to selecting/maintaining specific alleles in a colony. I think your idea could be related to what I need to work on next, which is an algorithm for assessing the long-term impact on colony genetic diversity of removing specific animals/alleles.
This is a need we have here at the ONPRC due to assigning animals to
research, and I have been tasked with implementing the solution.
Remove individuals that can never breed again from genetic analyses. (From page 29 of PMx User Manual, version 1.0). It is generally recommended to remove living individuals that can never breed or will never be bred again (e.g., post reproductive, sterilized, poor health, hybrid) from the genetic mean kinship calculations, as these individuals can no longer pass on their genetic material to the next generation and their inclusion influences the mean kinship values of other individuals in the population. However, these non-reproductive individuals may occupy cage space and need to be managed in other ways. In addition, their demographic information is valuable. Managers therefore often chose to include these individuals in the demographic analysis but to exclude them from genetic analysis.
It would be nice to have multiple “selected populations” that could be set up and easily selected for various analyses and plots.
Talk to Amanda about developing a general way to handle animals without two known parents that are not founders. There are the following lines of code in orderReport.R
# ONPRC-born animals with no parentage
i <- (is.na(rpt\$origin) & (rpt\$totalOffspring == 0) &
(rpt\$id %in% founders))
noParentage <- rpt[i, ]
Find some ways to use genetic marker data in the evaluation of genetic value. This needs to be discussed.
Add breeding productivity measure calculations. For example, (a) number of offspring per year of exposure to male or female. (b) Number of months since last birth. (c) Number of months between births with range and standard deviation.
Consider developing a simulation module to allow users to simulate breeding decisions.