phenology (version 10.1)

plot.Remigration: Plot the remigration intervals.

Description

Plot the remigration intervals.

Usage

# S3 method for Remigration
plot(x, legend = TRUE, ...)

Value

An invisible dataframe with values used for plotting.

Arguments

x

Object obtained from Bayesian.remigration()

legend

TRUE or FALSE or c(x, y)

...

Parameters transmitted to plot

Author

Marc Girondot

Details

plot.Remigration plots the remigration intervals.

See Also

Other Model of Remigration Interval: Bayesian.remigration(), LnRI_norm(), RI()

Examples

if (FALSE) {
library(phenology)
# Example

# Each year a fraction of 0.9 is surviving
s <- c(s=0.9)
# Probability of tag retention; 0.8
t <- c(t=0.8)
# Time-conditional return probability - This is the true remigration rate
r <- c(r1=0.1, r2=0.8, r3=0.7, r4=0.7, r5=1)
# Capture probability
p <- c(p1=0.6, p2=0.6, p3=0.6, p4=0.6, p5=0.6)
# Number of observations for 400 tagged females after 1, 2, 3, 4, and 5 years
OBS <- c(400, 10, 120, 40, 20, 10)

kl_s <- length(s)
kl_t <- length(t)
kl_r <- length(r)
kl_p <- length(p)

pMCMC <- data.frame(Density=c("newdbeta", "newdbeta", rep("dunif", kl_r), 
                              rep("newdbeta", kl_p), "dunif"), 
                    Prior1=c(s, t, rep(0, kl_r), rep(0.2, kl_p), 0), 
                    Prior2=c(0.02, 0.02, rep(1, kl_r), rep(0.08, kl_p), 10), 
                    SDProp=c(0.05, 0.05, rep(0.05, kl_r), rep(0.05, kl_p), 0.05), 
                 Min=c(0, 0, rep(0, kl_r), rep(0, kl_p), 0),  
                 Max=c(1, 1, rep(1, kl_r), rep(1, kl_p), 10),  
                 Init=c(s, t, r, p, 1), stringsAsFactors = FALSE, 
                 row.names=c("s", 
                                "t", 
                                names(r), 
                                names(p), "sd")
)
rMCMC <- Bayesian.remigration(parameters = pMCMC, 
n.iter = 1000000, 
n.adapt = 300000,
trace=10000, 
data=OBS)

plot(rMCMC)

}