Comments (3)
Bisaloo
commented on May 30, 2024
1
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) pCreated 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.
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Rekyt
commented on May 30, 2024
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
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Rekyt
commented on May 30, 2024
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
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Related Issues (20)
- Hex logo
- Managing error from qhull transferred to geometry::convhulln() in fd_chull()
- Error when site contains no species in fd_fdiv() and fd_feve() HOT 2
- Errors when using non-quantitative traits in fd_fric()
- Release fundiversity 0.2.1
- Investigate RCGAL as a replacement of geometry HOT 4
- Simplify CI matrix by using `_R_CHECK_DEPENDS_ONLY_TESTS_` HOT 2
- fd_fdiv() returns `NaN` on datasets without rownames
- FRic returns NA without warnings nor messages HOT 1
- Add tip in error message because of non-continuous traits HOT 1
- Renaming the vignettes to order them logically? HOT 2
- Change title of package in DESCRIPTION as it doesn't only computes "Alpha functional diversity indices"
- fd_fdis() bugs when site-species object is a data.frame() expects a matrix. HOT 2
- Using future and memoise together HOT 2
- Add link to published paper
- Should we write a vignette for non-continuous trait data? HOT 1
- fd_dis gives error if site x species matrix does not have row names HOT 4
- Be more specific in the help with memoization HOT 2
- Have a worked through example with individual level dataset
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