Expose possible bug in jnd computation for dichromats and fix it

[Bisaloo]

Bug demo:

library(pavo)

data(flowers)

canis.flowers <- vismodel(flowers, visual = "canis")
cd.flowers <- coldist(canis.flowers, n = c(1, 1))
#> Quantum catch are relative, distances may not be meaningful
#> Calculating noise-weighted Euclidean distances

jnd_x <- jnd2xyz(cd.flowers, rotate = FALSE)

# These two approaches should give the same values
dist_via_jnd <- as.matrix(dist(jnd_x, diag = TRUE, upper = TRUE))
dist_direct <- coldist2mat(cd.flowers)[["dS"]]

all.equal(
  dist_via_jnd,
  dist_direct,
  tolerance = 1e-6
)
#> [1] "Mean relative difference: 0.1121901"

dist_via_jnd[8, ]
#>     Goodenia_heterophylla       Goodenia_geniculata         Goodenia_gracilis 
#>                 4.5170525                 3.9266110                24.8100216 
#>          Xyris_operculata             Eucalyptus_sp        Faradaya_splendida 
#>                 0.6461969                 0.9980937                 4.7972590 
#>        Gaultheria_hispida    Geitonoplesium_cymosum   Euryomyrtus_ramosissima 
#>                 2.2628834                 0.0000000                 1.8853302 
#>         Genista_linifolia     Genista_monspessulana               Geranium_sp 
#>                 2.5420288                 1.0826285                 4.2308624 
#>       Glycine_clandestina  Gompholobium_ecostatum_1  Gompholobium_ecostatum_2 
#>                 1.7986383                 1.8554007                 2.5622591 
#> Gompholobium_grandiflorum     Gompholobium_huegelii     Gompholobium_virgatum 
#>                10.6122520                 1.7876028                 1.9291622 
#>        Gonocarpus_humilis    Gonocarpus_teucrioides     Hibbertia_obtusifolia 
#>                 0.1255897                 0.5628188                 3.0623861 
#>        Zieria_arborescens           Goodenia_lanata            Goodenia_ovata 
#>                 4.4429840                15.6985496                 2.7000931 
#>     Goodenia_rotundifolia       Grevillea_buxifolia   Grevillea_steiglitziana 
#>                 5.8229615                 2.8302123                10.5154479 
#>        Grevillea_oleoides       Gymnostachys_anceps             Hakea_actites 
#>                 1.8528836                19.7127205                 5.1314456 
#>    Hardenbergia_violaceae      Hibbertia_acicularis       Hibbertia_bracteata 
#>                 6.4667959                 0.6395585                 4.8124184 
#>    Hibbertia_empetrifolia      Hibbertia_procumbens        Hibbertia_linearis 
#>                 3.4538905                 0.2026285                 3.8542609
dist_direct[8, ]
#>     Goodenia_heterophylla       Goodenia_geniculata         Goodenia_gracilis 
#>                  4.517052                 12.960716                 33.844127 
#>          Xyris_operculata             Eucalyptus_sp        Faradaya_splendida 
#>                  8.387908                  8.036011                 13.831364 
#>        Gaultheria_hispida    Geitonoplesium_cymosum   Euryomyrtus_ramosissima 
#>                  6.771222                  0.000000                 10.919435 
#>         Genista_linifolia     Genista_monspessulana               Geranium_sp 
#>                 11.576134                 10.116733                  4.803243 
#>       Glycine_clandestina  Gompholobium_ecostatum_1  Gompholobium_ecostatum_2 
#>                 10.832743                  7.178704                 11.596364 
#> Gompholobium_grandiflorum     Gompholobium_huegelii     Gompholobium_virgatum 
#>                 19.646357                  7.246502                  7.104943 
#>        Gonocarpus_humilis    Gonocarpus_teucrioides     Hibbertia_obtusifolia 
#>                  9.159695                  9.596924                 12.096491 
#>        Zieria_arborescens           Goodenia_lanata            Goodenia_ovata 
#>                 13.477089                 24.732655                 11.734198 
#>     Goodenia_rotundifolia       Grevillea_buxifolia   Grevillea_steiglitziana 
#>                  3.211144                  6.203893                 19.549553 
#>        Grevillea_oleoides       Gymnostachys_anceps             Hakea_actites 
#>                 10.886989                 28.746825                  3.902659 
#>    Hardenbergia_violaceae      Hibbertia_acicularis       Hibbertia_bracteata 
#>                 15.500901                  8.394546                  4.221687 
#>    Hibbertia_empetrifolia      Hibbertia_procumbens        Hibbertia_linearis 
#>                 12.487995                  8.831477                 12.888366

^{Created on 2025-02-07 with reprex v2.1.1}