#' @importFrom stats runif rbinom
#' @importFrom methods new
generate.eqspace.zigzags <- function(design, strata.id, samplers, line.length, spacing, by.spacing, calc.cov.area = TRUE, clip.to.strata = TRUE, quiet = FALSE){
#Generates equal spaced zigzags, optionally with a complementary set of zigzags
region <- design@region
sf.column <- attr(region@region, "sf_column")
#Get the current strata and spacing
strata <- region@region[[sf.column]][[strata.id]]
#Spin round so design angle lies along x axis
rot.angle.rad <- design@design.angle[strata.id]+90
rot.angle.rad <- rot.angle.rad/180*pi
theta <- ifelse(rot.angle.rad == 0, 0, 2*pi-rot.angle.rad)
rot.mat <- matrix(c(cos(theta), sin(theta), -sin(theta), cos(theta)), ncol = 2, byrow = FALSE)
rot.strata <- mat.mult(strata, rot.mat)
#Buffer strata for plus sampling?
if(design@edge.protocol[strata.id] == "plus"){
rot.strata <- sf::st_buffer(rot.strata, design@truncation)
}
#Find the minimum and maximum x and y values
bbox <- sf::st_bbox(rot.strata)
if(!by.spacing && is.na(samplers)){
#Calculate from line.length
width <- bbox$xmax - bbox$xmin
names(width) <- NULL
ave.line.height <- sf::st_area(rot.strata)/width
if(design@design[strata.id] == "eszigzag"){
if(line.length < width){
if(!quiet){
warning("Line length in strata ", strata.id, " is not sufficient to carry out an equal spaced zigzag design. No samplers generated for this strata.", immediate. = TRUE, call. = FALSE)
}
return(NULL)
}
spacing = (width * ave.line.height) / sqrt(line.length^2 - width^2)
}else{
if(line.length/2 < width){
if(!quiet){
warning("Line length in strata ", strata.id, " is not sufficient to carry out a complementary equal spaced zigzag design. No samplers generated for this strata.", immediate. = TRUE, call. = FALSE)
}
return(NULL)
}
spacing = (width * ave.line.height) / sqrt((line.length/2)^2 - width^2)
}
by.spacing = TRUE
}
if(!by.spacing){
spacing <- (bbox[["xmax"]]-bbox[["xmin"]])/(samplers)
if(design@design[strata.id] == "eszigzagcom"){
spacing <- spacing * 2
}
}
if(spacing > (bbox[["xmax"]]-bbox[["xmin"]])){
if(!quiet){
warning(paste("Spacing larger than x-range cannot generate samplers in strata ", strata.id, sep = ""), immediate. = T, call. = F)
}
return(NULL)
}
start.x <- bbox[["xmin"]] + runif(1, 0, spacing) - spacing
x.vals <- seq(start.x, (bbox[["xmax"]] + spacing), by = spacing)
start.y <- rep(bbox[["ymin"]], length(x.vals))
end.y <- rep(bbox[["ymax"]], length(x.vals))
if(design@bounding.shape[strata.id] == "convex.hull"){
clipped.vals <- get.intersection.points(rot.strata, x.vals, start.y, end.y)
start.y <- clipped.vals$start.y
end.y <- clipped.vals$end.y
}
#Randomise zig or zag at start
random.start <- rbinom(1, 1, 0.5)
#Create the lines
lines <- list()
#counter <- 1
zz.set <- "A"
if(design@design[strata.id] == "eszigzagcom"){
for(i in 1:(length(x.vals)-1)){
#Do zig
lines[[paste("set", zz.set, ".tr", i, sep = "")]] <- sf::st_linestring(matrix(c(x.vals[i], x.vals[i+1], start.y[i], end.y[i+1]), ncol = 2))
#counter <- counter + 1
zz.set <- ifelse(zz.set == "A", "B", "A")
#and complementing zag
lines[[paste("set", zz.set, ".tr", i, sep = "")]] <- sf::st_linestring(matrix(c(x.vals[i], x.vals[i+1], end.y[i], start.y[i+1]), ncol = 2))
#counter <- counter + 1
}
}else{
zig <- ifelse(random.start == 1, TRUE, FALSE)
for(i in 1:(length(x.vals)-1)){
#Do zig
if(zig){
lines[[i]] <- sf::st_linestring(matrix(c(x.vals[i], x.vals[i+1], start.y[i], end.y[i+1]), ncol = 2))
}else{
#zag
lines[[i]] <- sf::st_linestring(matrix(c(x.vals[i], x.vals[i+1], end.y[i], start.y[i+1]), ncol = 2))
}
#reverse for next time
zig <- ifelse(zig, FALSE, TRUE)
}
}
#keep everything within the polygon strata
to.keep <- lapply(lines, sf::st_intersection, y = rot.strata)
#Only keep lines (discard points - fragments of line so small they have become points)
test.line <- function(x){ifelse(inherits(x, "LINESTRING") || inherits(x, "MULTILINESTRING"), TRUE, FALSE)}
is.line <- which(unlist(lapply(to.keep, FUN = test.line)))
to.keep <- to.keep[is.line]
#Calculate covered region - do it here as easier before unrotating!
cover.polys <- list()
if(calc.cov.area){
trunctn <- design@truncation
xend1 <- xend2 <- numeric(0)
for(tr in seq(along = to.keep)){
if(inherits(to.keep[[tr]], "LINESTRING")){
#Find end points
lx <- to.keep[[tr]][,1]
ly <- to.keep[[tr]][,2]
#Find gradients
lm <- (ly[2]-ly[1])/(lx[2]-lx[1])
if(lm == 0){
x.vals <- lx[c(1,1,2,2,1)]
y.vals <- c(ly[1]-trunctn, rep(ly[1]+trunctn,2), rep(ly[1]-trunctn, 2))
}else if(lm == Inf){
x.vals <- c(rep(lx[1]-trunctn,2), rep(lx[1]+trunctn,2), lx[1]-trunctn)
y.vals <- ly[c(1,2,2,1,1)]
}else{
pm <- -1*(1/lm)
#Calculate x coordinates
xend1[1] <- lx[1] - trunctn/sqrt(1+pm^2)
xend1[2] <- lx[1] + trunctn/sqrt(1+pm^2)
xend2[1] <- lx[2] - trunctn/sqrt(1+pm^2)
xend2[2] <- lx[2] + trunctn/sqrt(1+pm^2)
x.vals <- c(xend1[1], xend2, xend1[2:1])
x0 <- c(lx[1], lx[2], lx[2], lx[1], lx[1])
y0 <- c(ly[1], ly[2], ly[2], ly[1], ly[1])
y.vals = pm*(x.vals-x0)+y0
}
cover.polys[[tr]] <- sf::st_polygon(list(matrix(c(x.vals, y.vals), ncol = 2)))
}else if(inherits(to.keep[[tr]], "MULTILINESTRING")){
#Need to iterate along the list
temp <- list()
for(part in seq(along = to.keep[[tr]])){
#Find end points
lx <- to.keep[[tr]][[part]][,1]
ly <- to.keep[[tr]][[part]][,2]
#Find gradients
lm <- (ly[2]-ly[1])/(lx[2]-lx[1])
if(lm == 0){
x.vals <- lx[c(1,1,2,2,1)]
y.vals <- c(ly[1]-trunctn, rep(ly[1]+trunctn,2), rep(ly[1]-trunctn, 2))
}else if(lm == Inf){
x.vals <- c(rep(lx[1]-trunctn,2), rep(lx[1]+trunctn,2), lx[1]-trunctn)
y.vals <- ly[c(1,2,2,1,1)]
}else{
pm <- -1*(1/lm)
#Calculate x coordinates
xend1[1] <- lx[1] - trunctn/sqrt(1+pm^2)
xend1[2] <- lx[1] + trunctn/sqrt(1+pm^2)
xend2[1] <- lx[2] - trunctn/sqrt(1+pm^2)
xend2[2] <- lx[2] + trunctn/sqrt(1+pm^2)
x.vals <- c(xend1[1], xend2, xend1[2:1])
x0 <- c(lx[1], lx[2], lx[2], lx[1], lx[1])
y0 <- c(ly[1], ly[2], ly[2], ly[1], ly[1])
y.vals = pm*(x.vals-x0)+y0
}
temp[[part]] <- list(matrix(c(x.vals, y.vals), ncol = 2))
}
cover.polys[[tr]] <- sf::st_multipolygon(temp)
}
}
}
#Check if any polygons are invalid - sometimes tiny pieces of line are generated on the boundaries which lead to overlapping multi polygons
invalid <- which(!unlist(lapply(cover.polys, sf::st_is_valid)))
for(i in seq(along = invalid)){
tmp <- cover.polys[[invalid[i]]]
polys.tmp <- list()
mat.tmp <- list()
for(poly in seq(along = tmp)){
polys.tmp[[poly]] <- sf::st_polygon(tmp[[poly]])
mat.tmp[[poly]] <- tmp[[poly]]
}
to.rem <- numeric(0)
for(poly in seq(along = polys.tmp)){
intsec <- which(unlist(lapply(polys.tmp, sf::st_intersects, polys.tmp[poly][[1]], sparse = FALSE)))[-poly]
if(length(intsec) > 0){
intsec <- sort(c(intsec, poly))
areas <- unlist(lapply(polys.tmp[intsec], sf::st_area))
to.rem <- c(to.rem, intsec[which(areas == min(areas))])
#if(min(areas) > sf::st_area(rot.strata)/50000){
# warning("Removing covered area greater than 50,000th of the strata area.", immediate. = TRUE, call. = FALSE)
#}
}
}
to.rem <- unique(to.rem)
new.polys <- mat.tmp[-to.rem]
if(length(new.polys) == 1){
cover.polys[[invalid[i]]] <- sf::st_polygon(new.polys[[1]])
}else{
cover.polys[[invalid[i]]] <- sf::st_multipolygon(new.polys)
}
#Also remove strange corresponding transect part
tmp <- to.keep[[invalid[i]]]
if(length(tmp[-to.rem]) == 1){
to.keep[[invalid[i]]] <- sf::st_linestring(tmp[-to.rem][[1]])
}else{
to.keep[[invalid[i]]] <- sf::st_multilinestring(tmp[-to.rem])
}
}
#Clip to strata
if(clip.to.strata){
cover.polys <- lapply(cover.polys, sf::st_intersection, y = rot.strata)
}
#Rotate back again
reverse.theta <- rot.angle.rad
rot.mat.rev <- matrix(c(cos(reverse.theta), sin(reverse.theta), -sin(reverse.theta), cos(reverse.theta)), ncol = 2, byrow = FALSE)
lines.unrotated <- lapply(to.keep, mat.mult, y=rot.mat.rev)
transects <- lines.unrotated
#Also rotate covered region
if(calc.cov.area){
cover.polys.unrot <- lapply(cover.polys, mat.mult, y = rot.mat.rev)
return(list(transects = transects, cover.polys = cover.polys.unrot, spacing = spacing))
}
return(list(transects = transects, cover.polys = list(), spacing = spacing))
}
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