Description Usage Arguments Value Author(s) References See Also Examples

View source: R/estimating_marked_egg_fraction.R

Estimates the fraction of eggs produced at the source site that are the result of crossing parents, one or both of which have been genotyped. Based on the assumption that probability of breeding between pairs of individuals is completely independent of whether or not one or more of those individuals was genotyped.

1 | ```
dual.mark.transmission(p.female, p.male = p.female)
``` |

`p.female` |
Fraction of all adult females genotyped in the source population |

`p.male` |
Fraction of all adult males genotyped in the source
population. Defaults to be equal to |

A list with the following elements:

- prob.matrix
2x2 matrix with probabilities for producing offspring with male or female known or unknown parents

- p
fraction of all eggs produced at source site that will come from at least one genotyped parent

- p.female.known
Fraction of eggs with a single known female parent among all eggs that have one or more known parents

- p.male.known
Fraction of eggs with a single known male parent among all eggs that have one or more known parents

- p.two.known.parents
Fraction of eggs with two known parents among all eggs that have one or more known parents

David M. Kaplan dmkaplan2000@gmail.com

Kaplan DM, Cuif M, Fauvelot C, Vigliola L, Nguyen-Huu T, Tiavouane J and Lett C (in press) Uncertainty in empirical estimates of marine larval connectivity. ICES Journal of Marine Science. doi:10.1093/icesjms/fsw182.

Other connectivity estimation:
`d.rel.conn.beta.prior()`

,
`d.rel.conn.dists.func()`

,
`d.rel.conn.finite.settlement()`

,
`d.rel.conn.multinomial.unnorm()`

,
`d.rel.conn.multiple()`

,
`d.rel.conn.unif.prior()`

,
`optim.rel.conn.dists()`

,
`r.marked.egg.fraction()`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | ```
library(ConnMatTools)
data(damselfish.lods)
# Histograms of simulated LODs
l <- seq(-1,30,0.5)
h.in <- hist(damselfish.lods$in.group,breaks=l)
h.out <- hist(damselfish.lods$out.group,breaks=l)
# PDFs for marked and unmarked individuals based on simulations
d.marked <- stepfun.hist(h.in)
d.unmarked <- stepfun.hist(h.out)
# Fraction of adults genotyped at source site
p.adults <- 0.25
# prior.shape1=1 # Uniform prior
prior.shape1=0.5 # Jeffreys prior
# Fraction of eggs from one or more genotyped parents
p <- dual.mark.transmission(p.adults)$p
# PDF for relative connectivity
D <- d.rel.conn.dists.func(damselfish.lods$real.children,
d.unmarked,d.marked,p,
prior.shape1=prior.shape1)
# Estimate most probable value for relative connectivity
phi.mx <- optim.rel.conn.dists(damselfish.lods$real.children,
d.unmarked,d.marked,p)$phi
# Estimate 95% confidence interval for relative connectivity
Q <- q.rel.conn.dists.func(damselfish.lods$real.children,
d.unmarked,d.marked,p,
prior.shape1=prior.shape1)
# Plot it up
phi <- seq(0,1,0.001)
plot(phi,D(phi),type="l",
xlim=c(0,0.1),
main="PDF for relative connectivity",
xlab=expression(phi),
ylab="Probability density")
abline(v=phi.mx,col="green",lty="dashed")
abline(v=Q(c(0.025,0.975)),col="red",lty="dashed")
``` |

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