error with dbFD function in FD library
The posting guide, linked below (please read it!), says:
"For questions about functions in standard packages distributed with R
(see the FAQ Add-on packages in R), ask questions on R-help.
If the question relates to a contributed package , e.g., one
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So your query is inappropriate here. I think you should try the
r-sig-ecology list -- or the maintainer -- instead.
However, I will make a totally ignorant guess (so feel free to
ignore): your data have linear dependencies which reduce its effective
dimensionality. If this is (approximately?) correct, your data cannot
support the analyses that you are trying to do.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Wed, Sep 15, 2021 at 11:44 AM alessia ciraolo <alessiacir at hotmail.it> wrote:
Hi everyone,
I have a question about FD package. I?m trying to calculate functional
diversity indices on my marine organisms data. My trait data includes mobility, feeding type and reworking sediment type. I allowed more than one functional trait for a given taxon for each category, and scored from 0 to 1 based on the extent to which they displayed each trait. If two traits were shared by one taxa, I gave it 0.5 and 0.5 per trait.
ex1<-dbFD(fi,abund,calc.FRic = F/T, corr="cailliez",
w.abun = T, CWM.type = "all" )
However, when I set ?calc.Frich=T?, I got the Feve, Fdis, RaoQ and CWM values
for my data, BUT when I set ?calc.Frich=T? I receive the following error:
Error in convhulln(tr.FRic, "FA") :
Received error code 2 from qhull. Qhull error:
qhull precision warning:
The initial hull is narrow (cosine of min. angle is 1.0000000000000000).
Is the input lower dimensional (e.g., on a plane in 3-d)? Qhull may
produce a wide facet. Options 'QbB' (scale to unit box) or 'Qbb' (scale
last coordinate) may remove this warning. Use 'Pp' to skip this warning.
See 'Limitations' in qh-impre.htm.
QH6114 qhull precision error: initial simplex is not convex. Distance=-2.5e-015
While executing: | qhull FA Qt
Options selected for Qhull 2015.2.r 2016/01/18:
run-id 748402268 FArea-total Qtriangulate Qxact_merge _zero-centrum
Q3-no-merge-vertices-dim-high _max-width 5.4 Error-roundoff 2.2e-014
_one-merge 3.7e-013 _near-inside 1.8e-012 Visible-distance 1.3e-013
U-coplanar-distance 1.3e-013 Width-outside 2.6e-013 _wide-facet 7.8e-013
_narrow-hull 0
precision problems (corrected unless 'Q0' or an error)
1 flipped facets
7 nearly singular or axis-parall
Could you please tell me how can I fix this problem and have the FRic value
for my data?
If you can hel me with that, it would be very appreciated.
Regards,
Alessia
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