Update to terra / add directions argument

[mcgregorian1]

Per #15 and the conversion by @niekkoelewijn, could the ForestGapsR function be updated in the package to be terra-compatible?

Also, can the directions argument in terra::patches() be included as an argument to the main function? Overall this would look like the following:

getForestGaps <- function(chm_layer, threshold = 10, size = c(1, 10^4), directions = 8){
chm_layer[chm_layer > threshold] <- NA
chm_layer[chm_layer <= threshold] <- 1
gaps <- terra::patches(chm_layer, directions, allowGaps = F)
rcl <- terra::freq(gaps)
rcl[, 3] <- rcl[, 3] * terra::res(chm_layer)[1]^2
z <- terra::classify(gaps, rcl = rcl, right = NA)
z[is.na(gaps)] <- NA
gaps[z > size[2]] <- NA
gaps[z < size[1]] <- NA
gaps <- terra::patches(gaps, directions, allowGaps = F)
names(gaps) <- "gaps"
return(gaps)
}

[mcgregorian1]

Similarly, GapSPDF can be changed to the following. Note that this returns only a data frame, but to return the polygons themselves then the function should return gaps_poly directly.

gapsToTable <- function(gap_layer){
    gaps_poly <- terra::as.polygons(x=gap_layer, dissolve=TRUE, na.rm=TRUE,
                                    values=TRUE)
    names(gaps_poly) <- "gap_id"
    gaps_df <- terra::as.data.frame(terra::centroids(gaps_poly), geom="XY")
    return(gaps_df)
  }