Hello,
I am trying to calculate functional indices from my biological data (happy
to share it, if needed) but I got an error that I am not able to fully
understand and consequently have to fix it. I am here to ask for some help,
please. I will paste my code and the error below.
The *code* I used is:
"library(FD)
library(geometry)
fi<-read.csv("475 funct.csv",row.names = 1)
fi
abund<-read.csv("Abund 475.csv",row.names = 1)
abund
ex1<-dbFD(fi,abund,calc.FRic = T, corr="cailliez",
w.abun = T, CWM.type = "all" )
ex1".
However, when I run "ex1<-dbFD (etc.,)", I get the following *error*:
FEVe: Could not be calculated for communities with <3 functionally singular
species.
FRic: To respect s > t, FRic could not be calculated for communities with
<3 functionally singular species.
FRic: Dimensionality reduction was required. The last 3 PCoA axes (out of
15 in total) were removed.
FRic: Quality of the reduced-space representation = 0.98865
FDiv: Could not be calculated for communities with <3 functionally singular
species.
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=-1.1e-15
While executing: | qhull FA Qt
Options selected for Qhull 2015.2.r 2016/01/18:
run-id 814727584 FArea-total Qtriangulate Qxact_merge _zero-centrum
Q3-no-merge-vertices-dim-high _max-width 7.1 Error-roundoff 3.6e-14
_one-merge 8.9e-13 _near-inside 4.5e-12 Visible-distance 2.1e-13
U-coplanar-distance 2.1e-13 Width-outside 4.3e-13 _wide-facet 1.3e-12
_narrow-hull 0
precision problems (corrected unless 'Q0' or an error)
1 flipped facets
8 nearly singular or axis-parallel hyperp
In addition: Warning messages:
1: In is.euclid(x.dist) : Zero distance(s)
2: In is.euclid(x.dist) : Zero distance(s)
3: In is.euclid(x.dist) : Zero distance(s)
4: In is.euclid(x.dist) : Zero distance(s)
5: In is.euclid(x.dist) : Zero distance(s)
>From my understanding, it is not a FD error, but it might be linked to my
data matrix. However, I am not sure about that....Please, if I can get any
directions on how to solve this issue, I would be more than happy!
Many thanks,
Alessia
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