SimilarityPair Error in colSums(data) : 'x' must be an array of at least two dimensions

[mcrillo]

SimilarityPair is sometimes giving the error:
"Error in colSums(data) : 'x' must be an array of at least two dimensions"
apparently when calculated for assemblages with one very dominant species, and when similarity (abundance) indexes are very close to one.

By "sometimes" I mean that the first time you run the function for the data, it gives the error, but then the second/third time you re-run the same command for the exact same data the error is gone (see code below). This is problematic within a for loop, because the loop keeps crashing due to the error. And every time I run the for loop, the error happens for different data.frames (i.e., different 'i' values) - but the data.frames all share the characteristic of having one very dominant species in at least one of the two assemblages. I of course did not run the function SimilarityPair for assemblages with solely one species, all assemblages have actually at least 3 species (see example below).
Hope I explained the problem clearly and thank you for the attention.

Code:

sessionInfo()

R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] ggplot2_2.2.1 SpadeR_0.1.1 geosphere_1.5-7 reshape_0.8.7

class(sim_null_data)

[1] "data.frame"

colSums(sim_null_data)

holocene lgm
100 100

sim_null_data

holocene lgm
1 0.0 0.0
2 0.0 0.0
3 0.0 0.0
4 0.0 0.0
5 0.0 0.0
6 0.0 0.0
7 0.0 0.0
8 0.0 0.0
9 0.0 0.0
10 0.0 0.0
11 1.0 2.1
12 97.6 97.6
13 0.0 0.0
14 0.0 0.0
15 0.0 0.0
16 0.0 0.0
17 0.0 0.0
18 0.0 0.0
19 0.0 0.0
20 0.0 0.0
21 0.0 0.0
22 0.0 0.0
23 0.0 0.0
24 0.0 0.0
25 0.0 0.0
26 0.0 0.0
27 0.0 0.0
28 1.4 0.0
29 0.0 0.0
30 0.0 0.0
31 0.0 0.0
32 0.0 0.0
33 0.0 0.3
34 0.0 0.0
35 0.0 0.0

sim_null_i <- SimilarityPair(sim_null_data, datatype = c("abundance"), nboot = 10)

Error in colSums(data) : 'x' must be an array of at least two dimensions

sim_null_i <- SimilarityPair(sim_null_data, datatype = c("abundance"), nboot = 10)

class(sim_null_i)

[1] "spadeTwo"

sim_null_i

(1) BASIC DATA INFORMATION:

The loaded set includes abundance/incidence data from 2 communities
and a total of 4 species.

Samples size in Community 1                            n1  = 100 
Samples size in Community 2                            n2  = 100 
Number of observed species in Community 1              D1  = 3 
Number of observed species in Community 2              D2  = 3 
Number of observed shared species in two communities   D12 = 2 
Number of bootstrap replications for s.e. estimate           10 

Some statistics:
      f[11]= 0 ; f[1+]= 1 ; f[+1]= 0 ; f[2+]= 0 ; f[+2]= 0 ; f[22]= 0 

(2) EMPIRICAL SIMILARITY INDICES:

                                   Estimate       s.e.       95%Lower     95%Upper
(a) Classic richness-based similarity

    C02 (q=0, Sorensen)             0.6667       0.1858       0.3025       1.0309 
    U02 (q=0, Jaccard)              0.5000       0.2250       0.0590       0.9410 

(b) Measures for comparing species relative abundances

    C12=U12 (q=1, Horn)             0.9901       0.0066       0.9771       1.0000 

    C22 (q=2, Morisita-Horn)        0.9998       0.0007       0.9985       1.0000 
    U22 (q=2, Regional overlap)     0.9999       0.0004       0.9992       1.0000 

    ChaoJaccard-abundance           0.9831       0.0230       0.9380       1.0282 
    ChaoSorensen-abundance          0.9915       0.0119       0.9682       1.0148 

(c) Measures for comparing size-weighted species relative abundances

    Horn size-weighted (q=1)        0.9901       0.0067       0.9770       1.0000 

(d) Measures for comparing species absolute abundances

    C12=U12 (q=1)                   0.9901       0.0067       0.9770       1.0000 

    C22 (Morisita-Horn)             0.9998       0.0004       0.9990       1.0000 
    U22 (Regional overlap)          0.9999       0.0002       0.9995       1.0000 

    Bray-Curtis                     0.9860       0.0155       0.9556       1.0000 

(3) ESTIMATED SIMILARITY INDICES:

                                   Estimate       s.e.       95%Lower     95%Upper
(a) Classic richness-based similarity:

    C02 (q=0, Sorensen)             0.6667       0.1909       0.2925       1.0409 
    U02 (q=0, Jaccard)              0.5000       0.2295       0.0502       0.9498 

(b) Measures for comparing species relative abundances

    C12=U12 (q=1, Horn)             0.9916       0.0068       0.9781       1.0000 

    C22 (q=2, Morisita-Horn)        1.0000       0.0005       0.9989       1.0000 
    U22 (q=2, Regional overlap)     1.0000       0.0003       0.9995       1.0000 

    ChaoJaccard-abundance           0.9860       0.0228       0.9413       1.0307 
    ChaoSorensen-abundance          0.9930       0.0118       0.9699       1.0161 

(c) Measures for comparing size-weighted species relative abundances

    Horn size-weighted (q=1)        0.9916       0.0049       0.9819       1.0000 

(d) Measures for comparing species absolute abundances

    C12=U12 (q=1)                   0.9916       0.0049       0.9819       1.0000 

    C22 (q=2, Morisita-Horn)        1.0000       0.0004       0.9992       1.0000 
    U22 (q=2, Regional overlap)     1.0000       0.0002       0.9996       1.0000 

    Bray-Curtis                     0.9868       0.0139       0.9595       1.0000 

    NOTE: If an estimate is greater than 1, it is replaced by 1.