A trait table for the 24 MAGs in gut_counts, mixing continuous, categorical
and binary traits. Convert it to a functional distance with traits2dist()
for the functional-diversity paths.
Format
A data frame with 24 rows (MAGs) and 4 columns:
- genome_size
Approximate genome size in Mbp (numeric).
- gc_content
GC content as a proportion (numeric).
- oxygen
Oxygen tolerance: aerobe, anaerobe or facultative (factor).
- motility
Motility indicator, 0/1 (integer).
Examples
d <- traits2dist(gut_traits)
hilldiv(gut_counts, q = c(0, 1), dist = d)
#> Computing "neutral" and "functional" Hill numbers of "q0" and "q1".
#> ℹ 24 taxa across 12 samples.
#> <hilldiv3 result: neutral, functional>
#> 48 rows x 4 cols
#>
#> q sample type value
#> 1 0 ctrl01 neutral 24.000000
#> 2 1 ctrl01 neutral 12.329592
#> 3 0 ctrl02 neutral 24.000000
#> 4 1 ctrl02 neutral 14.784342
#> 5 0 ctrl03 neutral 24.000000
#> 6 1 ctrl03 neutral 11.832847
#> 7 0 ctrl04 neutral 23.000000
#> 8 1 ctrl04 neutral 11.266414
#> 9 0 ctrl05 neutral 24.000000
#> 10 1 ctrl05 neutral 10.035886
#> 11 0 ctrl06 neutral 24.000000
#> 12 1 ctrl06 neutral 13.277945
#> 13 0 trt01 neutral 24.000000
#> 14 1 trt01 neutral 11.888942
#> 15 0 trt02 neutral 24.000000
#> 16 1 trt02 neutral 8.350790
#> 17 0 trt03 neutral 24.000000
#> 18 1 trt03 neutral 15.681517
#> 19 0 trt04 neutral 23.000000
#> 20 1 trt04 neutral 11.671685
#> 21 0 trt05 neutral 23.000000
#> 22 1 trt05 neutral 9.043005
#> 23 0 trt06 neutral 23.000000
#> 24 1 trt06 neutral 10.901319
#> 25 0 ctrl01 functional 1.903890
#> 26 1 ctrl01 functional 1.864119
#> 27 0 ctrl02 functional 2.011087
#> 28 1 ctrl02 functional 1.997614
#> 29 0 ctrl03 functional 1.962929
#> 30 1 ctrl03 functional 1.928385
#> 31 0 ctrl04 functional 1.947593
#> 32 1 ctrl04 functional 1.913489
#> 33 0 ctrl05 functional 1.864104
#> 34 1 ctrl05 functional 1.816147
#> 35 0 ctrl06 functional 1.914662
#> 36 1 ctrl06 functional 1.874010
#> 37 0 trt01 functional 1.974545
#> 38 1 trt01 functional 1.954243
#> 39 0 trt02 functional 1.841115
#> 40 1 trt02 functional 1.796213
#> 41 0 trt03 functional 1.954853
#> 42 1 trt03 functional 1.941623
#> 43 0 trt04 functional 1.874825
#> 44 1 trt04 functional 1.854832
#> 45 0 trt05 functional 1.763973
#> 46 1 trt05 functional 1.722022
#> 47 0 trt06 functional 1.831259
#> 48 1 trt06 functional 1.802398