Custom mesohabitat classifications

library(hydromeso)

Custom schemes are validated rectangular regions. Required columns are class_id, label, depth_min, depth_max, velocity_min, and velocity_max.

rules <- data.frame(
  class_id = c(1L, 2L), label = c("Slow", "Fast"),
  depth_min = c(0, 0), depth_max = c(Inf, Inf),
  velocity_min = c(0, 0.5), velocity_max = c(0.5, Inf)
)
custom <- meso_scheme(rules, name = "Two velocity classes")
validate_meso_scheme(custom)
plot_meso_scheme(custom)

Overlaps are always rejected. Gaps are rejected unless allow_gaps = TRUE; observations in an allowed gap return NA. Validation evaluates exact breakpoints and representatives of every interval, not a random sample.

overlap <- rules
overlap$velocity_min[2] <- 0.4
meso_scheme(overlap)

## Error:
## ! Overlapping classes 1 ('Slow') and 2 ('Fast') near depth 0 and velocity 0.4.

gap <- rules
gap$velocity_max[1] <- 0.4
gap$velocity_min[2] <- 0.6
meso_scheme(gap)

## Error:
## ! Uncovered depth-velocity region near depth 0 and velocity 0.4. Set `allow_gaps = TRUE` only when gaps are intentional.

gap_scheme <- meso_scheme(gap, allow_gaps = TRUE)
classify_mesohabitat_values(1, 0.5, gap_scheme)

##   depth velocity mesohabitat_class mesohabitat
## 1     1      0.5                NA        <NA>

The custom scheme can be supplied to every table, vector, raster, and scenario classifier. Users are responsible for scientifically justifying and reporting custom thresholds and units.

h <- mesohabitat_example_rasters()
custom_raster <- classify_mesohabitat_raster(
  h$depth, h$velocity, scheme = custom
)
plot_mesohabitat(custom_raster, scheme = custom)

Example raster classified with the custom two-class scheme.