## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 754 taxa and 70 samples ]
## sample_data() Sample Data:       [ 70 samples by 69 sample variables ]
## tax_table()   Taxonomy Table:    [ 754 taxa by 8 taxonomic ranks ]
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 754 taxa and 70 samples ]
## sample_data() Sample Data:       [ 70 samples by 69 sample variables ]
## tax_table()   Taxonomy Table:    [ 754 taxa by 8 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 754 tips and 752 internal nodes ]

It’s time to make a tree. Check out a helpful stack exchange page: http://unix.stackexchange.com/questions/253499/extracting-subset-from-fasta-file

Faiths PD

Taxa.Labels

## 
##  Wilcoxon rank sum test
## 
## data:  mpd.obs.z by fraction
## W = 55, p-value = 0.3474
## alternative hypothesis: true location shift is not equal to 0
## 
##  Wilcoxon rank sum test
## 
## data:  mpd.obs.z by fraction
## W = 143, p-value = 1.479e-06
## alternative hypothesis: true location shift is not equal to 0
## # A tibble: 2 × 3
##    fraction `mean(mpd.obs.z)` `median(mpd.obs.z)`
##      <fctr>             <dbl>               <dbl>
## 1 WholePart         0.7346088           0.8119896
## 2 WholeFree        -1.8572351          -2.0238057
## 
##  Wilcoxon rank sum test
## 
## data:  mntd.obs.z by fraction
## W = 93, p-value = 0.2415
## alternative hypothesis: true location shift is not equal to 0
## 
##  Wilcoxon rank sum test
## 
## data:  mntd.obs.z by fraction
## W = 126, p-value = 0.001115
## alternative hypothesis: true location shift is not equal to 0
## Error in eval(expr, envir, enclos): object 'mpd.obs.z' not found

Richness

Frequency

Sample Pool

Phylogeny Pool

Independent Swap

Trial Swap