inst/examples/make_downstream_ex.R

In danStich/anadrofish: Anadromous Fish Population Responses to Habitat Changes

# Example usage
\dontrun{
  
# Example 1. ----  
# Calculate population-level survival during outmigration
# for fixed upstream and downstream dam passage probabilities
s_down <- make_downstream(
  habitat_data = habitat,
  river = 'Susquehanna',
  downstream = 0.95,
  upstream = 0.80
  )
  
# Example 2. ----
# Explore how upstream passage affects catchment-wide survival
# during outmigration for a fixed downstream passage
upstream_p <- seq(from=0, to=1, by=0.01)
s_down <- vector(mode='numeric', length=length(upstream_p))
for(i in 1:length(upstream_p)){
  s_down[i] <- make_downstream(
    habitat_data = habitat,
    river = 'Susquehanna',
    downstream = 0.5,
    upstream = upstream_p[i]
    )  
} 

Zd = 1 - s_down

plot(x=upstream_p, y=Zd, type = 'l',
     xlab='Upstream passage',
     ylab = 'Total downstream mortality',
     main = 'Susquehanna River'
     )

# Example 3. ----
# Explore interactions between upstream and downstream 
# passage probabilities when both vary. This changes
# drastically from one river to another depending on
# habitat above and below dams, and number of dams.
upstream_p <- seq(from=0, to=1, by=0.01)
downstream_p <- seq(from=0, to=1, by=0.01)
s_down <- matrix(data = NA, nrow=length(upstream_p), ncol = length(downstream_p))

for(i in 1:length(upstream_p)){
  for(t in 1:length(downstream_p)){
    s_down[i,t] <- make_downstream(
      habitat_data = habitat,
      river = 'Susquehanna',
      downstream = downstream_p[t],
      upstream = upstream_p[i]
      )  
  }   
}

zd <- 1 - s_down
filled.contour(x=upstream_p, y=downstream_p, z=zd,
               xlab = 'Upstream passage probability',
               ylab = 'Downstream survival per dam',
               main = 'Catchment-wide dam mortality'
               )

}