d.rel.conn.finite.settlement {ConnMatTools} | R Documentation |
These functions calculate the probability mass function
(d.rel.conn.finite.settlement
), the cumulative distribution function
(p.rel.conn.finite.settlement
) and the quantile function
(q.rel.conn.finite.settlement
) for the true number of settlers at a
site that originated in a particular site given a known fraction of marked
eggs among the eggs originating at the source site, a sample of settlers at
the destination site, a known fraction of which are marked, and a finite
settler pool of known size.
d.rel.conn.finite.settlement( n.origin, p, k, n.obs, n.settlers, prior.n.origin = 1 ) p.rel.conn.finite.settlement( n.origin, p, k, n.obs, n.settlers, prior.n.origin = 1 ) q.rel.conn.finite.settlement(q, p, k, n.obs, n.settlers, prior.n.origin = 1)
n.origin |
Vector of integers of possible numbers of settlers in the
cohort that originated at the site of marking. All values should be
integers |
p |
Fraction of individuals (i.e., eggs) marked in the source population |
k |
Number of marked settlers in sample |
n.obs |
Total number of settlers collected |
n.settlers |
Total number of settlers at the destination site from which
the |
prior.n.origin |
A prior probability mass function for the number of
settlers in the cohort originating at the site of marking. Must be a scalar
or a vector of length |
q |
Vector of quantiles |
The relative connectivity between the source and destination sites is
calculated as n.origin/n.settlers
.
A vector of probabilities or quantiles.
d.rel.conn.finite.settlement
: Returns the probability mass
function for the numbers of settlers in the cohort that originated at the
source site (i.e., site of marking).
p.rel.conn.finite.settlement
: Returns the cumulative distribution
function for the numbers of settlers in the cohort that originated at the
source site (i.e., site of marking).
q.rel.conn.finite.settlement
: Returns quantiles of the cumulative
distribution function for the numbers of settlers in the cohort that
originated at the source site (i.e., site of marking).
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.multinomial.unnorm()
,
d.rel.conn.multiple()
,
d.rel.conn.unif.prior()
,
dual.mark.transmission()
,
optim.rel.conn.dists()
,
r.marked.egg.fraction()
library(ConnMatTools) k <- 10 # Number of marked settlers among sample n.obs <- 87 # Number of settlers in sample n.settlers <- 100 # Total size of settler pool p <- 0.4 # Fraction of eggs that was marked phi <- seq(0,1,length.out=101) # Values for relative connectivity # Probability distribution assuming infinite settler pool and uniform prior drc <- d.rel.conn.unif.prior(phi,p,k,n.obs) prc <- p.rel.conn.unif.prior(phi,p,k,n.obs) qrc <- q.rel.conn.unif.prior(c(0.025,0.975),p,k,n.obs) # 95% confidence interval # Test with finite settlement function and large (approx. infinite) settler pool # Can be a bit slow for large settler pools dis <- d.rel.conn.finite.settlement(0:(7*n.obs),p,k,n.obs,7*n.obs) # Quantiles qis <- q.rel.conn.finite.settlement(c(0.025,0.975),p,k,n.obs,7*n.obs) # Finite settler pool dfs <- d.rel.conn.finite.settlement(0:n.settlers,p,k,n.obs,n.settlers) # Quantiles for the finite settler pool qfs <- q.rel.conn.finite.settlement(c(0.025,0.975),p,k,n.obs,n.settlers) # Make a plot of different distributions plot(phi,drc,type="l",main="Probability of relative connectivity values", xlab=expression(phi),ylab="Probability density") lines(phi,prc,col="blue") lines((0:(7*n.obs))/(7*n.obs),dis*(7*n.obs),col="black",lty="dashed") lines((0:n.settlers)/n.settlers,dfs*n.settlers,col="red",lty="dashed") abline(v=qrc,col="black") abline(v=qis/(7*n.obs),col="black",lty="dashed") abline(v=qfs/n.settlers,col="red",lty="dashed")