R vegdist does not compute distances for all my sites
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Entering edit mode
11 months ago
DNAngel ▴ 210

I'm trying to create some MDS plots for my data. I'm using vegan package's vegdist which does not produce any errors but when I view my resulting matrix there are empty values everywhere in the lower diagonal where only the upper diagonal should be empty.

my code:

data <- read.csv("nematoda.csv",header=TRUE)   # 180 samples with 22 values, 6 of which are env variables
data <- data[apply(data[,-1:-6],1,function(x) !all(x==0)),] # to get rid of sites with no species information

# Transform data into relative abundances
data.total <- decostand(data[,7:length(data)], method="total")

# Distance with Bray-Curtis
data.bray <- vegdist(data.total, method="bray")

data.bray

             1          2          3          5          7          8         10         11         12         13
2   0.00000000                                                                                                   
3   0.00000000 0.00000000                                                                                        
5   0.41421356 0.41421356 0.41421356                                                                             
7   0.00000000 0.00000000 0.00000000 0.41421356                                                                  
8   0.00000000 0.00000000 0.00000000 0.41421356 0.00000000                                                       
10  0.00000000 0.00000000 0.00000000 0.41421356 0.00000000 0.00000000                                            
            14         15         16         17         18         20         21         22         23         24
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            25         27         28         29         30         31         32         33         34         36
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            37         38         40         42         44         45         46         47         48         49
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            50         51         52         53         55         56         57         58         60         61
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            62         63         64         65         66         67         68         69         70         71
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            72         73         75         76         77         78         79         80         81         82
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            83         84         85         86         87         88         89         90         91         93
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
            94         95         96         97         98         99        100        101        102        103
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           104        106        107        108        109        110        111        112        115        117
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           118        119        120        121        122        124        125        126        127        128
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           129        130        131        132        133        134        135        136        137        138
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           139        140        141        142        143        144        145        147        148        149
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           150        151        152        153        154        155        156        157        158        159
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           160        161        162        163        164        165        166        167        168        169
2                                                                                                                
3                                                                                                                
5                                                                                                                
7                                                                                                                
8                                                                                                                
10                                                                                                               
           170        171        172        173        174        175        176        177        179
2                                                                                                     
3                                                                                                     
5                                                                                                     
7                                                                                                     
8                                                                                                     
10                                                                                                    
 [ reached getOption("max.print") -- omitted 153 rows ]

I've tried different transformations, but all the same. When I used sample datasets and even a friend's dataframe from a different project - with the exact same code I see their whole table...not sure why mine is causing an issue. A lot of my species abundance values are 0 though however so would this be causing the incomplete distance matrix?

vegan vegdist R • 222 views
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