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error with dbFD function in FD library

2 messages · alessia ciraolo, Bert Gunter

alessia ciraolo
# 
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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Bert Gunter
# 
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
downloaded from CRAN, try contacting the package maintainer first. You
can also use find("functionname") and
packageDescription("packagename") to find this information. Only send
such questions to R-help or R-devel if you get no reply or need
further assistance. This applies to both requests for help and to bug
reports."

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: