Specific error obtained with Qhull

[Rekyt]

Here is an issue that aims to be a list of specific errors due to Qhull to better manage #38 in the future.

I obtained the following error in Qhull:

Error: Received error code 5 from qhull. Qhull error:
QH6271 qhull precision error (qh_check_dupridge): wide merge (1122660224434 times wider) due to duplicate ridge with nearly coincident points (0.027) between f102531 and f102515, merge dist 0.093, while processing p2261

• Ignore error with option 'Q12'
• To be fixed in a later version of Qhull
• Vertex distance 0.027 is greater than 100 times maximum distance 8.3e-14
  Please report to [email protected] with steps to reproduce and all output
  ERRONEOUS FACET:
• f102531
  • flags: top new seen mergehorizon dupridge mergeridge2
  • normal: 0.05806 0.1744 -0.5788 0.7752 -0.174
  • offset: 0.1009689
  • vertices: p2261(v1312) p2266(v1046) p2272(v799) p2262(v289) p2265(v160)
  • neighboring facets: f12145 f12159 f102533 f102515 f102532
  • ridges:
  • r74938 tested
    vertices: p2266(v1046) p2272(v799) p2262(v289) p2265(v160)
    between f102531 and f12145
  • r97773
    vertices: p2261(v13

When running the inst/new_benchmark.R script with the following parameter: 50 sites, 5 traits, 200 species, code at c9d85d8 commit.

[Bisaloo]

Somewhat smaller reprexes:

Trimmed down inst/new_benchmark.R

pkgload::load_all()  # Need last version of fundiversity
source(here::here("inst", "benchmark_fcts", "make_data.R"))

n_sites   = c(5e1)

n_traits  = c(5)

n_species = c(2e2)

set.seed(20210906)
given_data = make_data(n_species, n_traits, n_sites)

fd_fric_intersect(given_data[["traits"]], given_data[["site_sp"]])

Actual reprex

given_data <- dget("https://gist.githubusercontent.com/Bisaloo/f3a8042be8a55a887e1f9a2bbcce9a8d/raw/dea950268d971229cd1b91bda47c45f31d418acb/fundiversity_qhull_error.txt")

library(fundiversity)
fd_fric_intersect(given_data[["traits"]], given_data[["site_sp"]])
#> Error in convhulln(ps, "n FA"): Received error code 5 from qhull. Qhull error:
#> QH6271 qhull precision error (qh_check_dupridge): wide merge (798797635164 times wider) due to duplicate ridge with nearly coincident points (0.0055) between f159315 and f159297, merge dist 0.028, while processing p3702
#> - Ignore error with option 'Q12'
#> - To be fixed in a later version of Qhull
#> - Vertex distance 0.0055 is greater than 100 times maximum distance 3.5e-14
#>   Please report to [email protected] with steps to reproduce and all output
#> ERRONEOUS FACET:
#> - f159315
#>     - flags: top new seen mergehorizon dupridge mergeridge2
#>     - normal:   0.04571 -0.002063  -0.0352 -0.08176    0.995
#>     - offset: -0.8682543
#>     - vertices: p3702(v2235) p6412(v1056) p2282(v632) p3731(v13) p4214(v3)
#>     - neighboring facets: f35106 f159297 f159316 f159325
#>     - ridges:
#>      - r36029 tested
#>            vertices: p6412(v1056) p2282(v632) p3731(v13) p4214(v3)
#>            between f159315 and f35106
#>      - r113711
#>            vertices: p3702(v2235) p2282(v632) p

^{Created on 2021-10-26 by the reprex package (v2.0.1.9000)}

I feel like this can be trimmed down even more but it's a good start.

[Rekyt]

Not actually a reprex but:

> fd_benchmark_multicore(fd_fric_intersect)
Running with:
  n_sites n_traits n_species
1     100        4       200
 Error: Received error code 5 from qhull. Qhull error:
QH6271 qhull precision error (qh_check_dupridge): wide merge (10000524017918 times wider) due to duplicate ridge with nearly coincident points (0.002) between f2144 and f2123, merge dist 0.59, while processing p118
- Ignore error with option 'Q12'
- To be fixed in a later version of Qhull
- Vertex distance 0.002 is greater than 100 times maximum distance 5.9e-14
Please report to [email protected] with steps to reproduce and all output
ERRONEOUS FACET:
- f2144
- flags: top new seen mergehorizon dupridge mergeridge2
- normal: 0.1284 -0.5988 0.3437 0.7119
- offset: 0.1695765
- vertices: p118(v130) p128(v108) p347(v52) p125(v0)
- neighboring facets: f1022 f2123 f2145
- ridges:
- r778
vertices: p128(v108) p347(v52) p125(v0)
between f2144 and f1022
- r1071
vertices: p118(v130) p128(v108) p347(v52)
between f1022 and f2144
- r1069
vertices

[Rekyt]

Another case with fd_fric_intersect()

fd_fric_intersect 
Running with:
  n_sites n_traits n_species
1      50        4       500
Error: Received error code 5 from qhull. Qhull error:
QH6271 qhull precision error (qh_check_dupridge): wide merge (6453987413504 times wider) due to duplicate ridge with nearly coincident points (0.0038) between f3040 and f3036, merge dist 0.35, while processing p539
- Ignore error with option 'Q12'
- To be fixed in a later version of Qhull
- Vertex distance 0.0038 is greater than 100 times maximum distance 5.5e-14
  Please report to [email protected] with steps to reproduce and all output
ERRONEOUS FACET:
- f3040
    - flags: top new seen mergehorizon dupridge mergeridge2
    - normal:   -0.7599   0.2833   0.4993   0.3051
    - offset: -0.4838983
    - vertices: p539(v191) p540(v146) p543(v137) p132(v74)
    - neighboring facets: f2198 f3041 f3036
    - ridges:
     - r1112
           vertices: p540(v146) p543(v137) p132(v74)
           between f3040 and f2198
     - r1614
           vertices: p539(v191) p543(v137) p132(v74)
           between f2198 and f3040
     - r1616
           ve