# R/coverage.rand.R In BruceKendall/ignorant-conservation: What the package does (short line)

#### Defines functions coverage.rand

```#' Calculate the proportion of a square species range that is covered by a
#' random reserve network
#'
#' @param res.num logical square matrix, with row/column dimension `PR.x`,
#'    indicating which of the planning units within the planning region are
#'    reserves
#' @param range.x length of one side of the species range
#' @param PR.x number of planning units along the side of the planning region
#' @param c1 length-2 vector giving the lower left coordinate of the species
#'    range. Defaults to a random location in the planning region
#' @return fraction of the species range that is included in reserves
#' @details There appears to be no error checking to ensure that the whole
#'    species range is within the planning region. In fact, it seems that the
#'    upper bound on c1 should be `PR.x - range.x`.
coverage.rand <-
function(res.num, range.x, PR.x, c1 = runif(2, 1, PR.x)) {
c2 = c1 + range.x
cf1 = floor(c1)
cf2 = floor(c2)
if (range.x < 1) {
if (cf1[1] == cf2[1]) {
if (cf1[2] == cf2[2]) { # Range entirely w/in one PU
frac = res.num[cf1[1],cf1[2]]
} else { # Range in 2 PUs in direction 2
div = (cf2[2] - c1[2])/range.x
frac = sum(res.num[cf1[1],cf1[2]:cf2[2]] * c(div, 1-div))
}
} else { # spans a PU boundary in direction 1
if (cf1[2] == cf2[2]) { # Range in 2 PUs in direction 1
div = (cf2[1] - c1[1])/range.x
frac = sum(res.num[cf1[1]:cf2[1],cf1[2]] * c(div, 1-div))
} else { # Range in 4 PUs
div1 = (cf2[1] - c1[1])/range.x
div2 = (cf2[2] - c1[2])/range.x
frac = sum(res.num[cf1[1]:cf2[1],cf1[2]:cf2[2]] *
matrix(c(div1*div2, (1-div1)*div2, div1*(1-div2), (1-div1)*(1-div2)),2,2))
}
}
} else if (range.x == 1) { # Range in 4 PUs
div1 = (cf2[1] - c1[1])/range.x
div2 = (cf2[2] - c1[2])/range.x
frac = sum(res.num[cf1[1]:cf2[1],cf1[2]:cf2[2]] *
matrix(c(div1*div2, (1-div1)*div2, div1*(1-div2), (1-div1)*(1-div2)),2,2))
} else {
if (cf2[1]-cf1[1] == 1 & cf2[2]-cf1[2] == 1 ) { # Range in 4 PUs
div1 = (cf2[1] - c1[1])/range.x
div2 = (cf2[2] - c1[2])/range.x
frac = sum(res.num[cf1[1]:cf2[1],cf1[2]:cf2[2]] *
matrix(c(div1*div2, (1-div1)*div2, div1*(1-div2), (1-div1)*(1-div2)),2,2))
} else {  # General purpose calculation
# First do corners
d11 = cf1[1] + 1 - c1[1]
d12 = cf1[2] + 1 - c1[2]
d21 = c2[1] - cf2[1]
d22 = c2[2] - cf2[2]
Ares = res.num[cf1[1],cf1[2]] * d11*d12 +
res.num[cf2[1],cf1[2]] * d21*d12 +
res.num[cf2[1],cf2[2]] * d21*d22 +
res.num[cf1[1],cf2[2]] * d11*d22

# Now do sides as needed
if (cf2[1] - cf1[1] > 1) {
for (ii in (cf1[1]+1):(cf2[1]-1)) {
Ares = Ares + res.num[ii,cf1[2]] * d12 + res.num[ii,cf2[2]] * d22
}
}
if (cf2[2] - cf1[2] > 1) {
for (ii in (cf1[2]+1):(cf2[2]-1)) {
Ares = Ares + res.num[cf1[1],ii] * d11 + res.num[cf1[2],ii] * d12
}
}
# Now do interior PUs as needed
if (cf2[1] - cf1[1] > 1 & cf2[2] - cf1[2] > 1) {
Ares = Ares + sum(res.num[(cf1[1]+1):(cf2[1]-1), (cf1[2]+1):(cf2[2]-1)])
}
frac = Ares/range.x^2
}
}
return(frac)
}
```
BruceKendall/ignorant-conservation documentation built on May 6, 2019, 8:48 a.m.