Setup:

packageVersion("ggplot2")
## [1] '2.1.0'
packageVersion("cowplot")
## [1] '0.6.3'
packageVersion("data.table")
## [1] '1.9.6'
packageVersion("phyloseq")
## [1] '1.16.2'
packageVersion("plyr")
## [1] '1.8.4'
packageVersion("phytools")
## [1] '0.5.64'
packageVersion("vegan")
## [1] '2.4.1'
packageVersion("MASS")
## [1] '7.3.45'

HMP-mock data

Setup:

Figure 3a:

Figure 3b:

Sup Fig 5:

Sup Fig 6:

Setup:

Count number of OTUs > 0-10:

Figure 4a, HMP-mock1:

Figure 4a, HMP-mock2:

Sup Fig 7, n=1:

Sup Fig 8, n=0:

Sup Fig 9:

## quartz_off_screen 
##                 2

Sup Fig 10:

Setup:

Figure 5a:

Sup Fig 11:

Sup Fig 12:

Figure 6, expected values:

## Processing map file...
## Processing otu/tax file...
## Reading file into memory prior to parsing...
## Detecting first header line...
## Header is on line 2  
## Converting input file to a table...
## Defining OTU table... 
## Parsing taxonomy table...

Figure 6a:

## quartz_off_screen 
##                 2

Figure 6b:

Figure 6c:

Figure 6d (perl code here for completeness):

Sup Fig 13a:

Sup Fig 13b:

URTCul-Single data

Setup:

Figure 4b:

Figure 5b: Initialize function from http://stackoverflow.com/questions/13673894/suppress-nas-in-paste

URTCul-combined

Setup:

Figure 4c, URT-combined

Figure 5c, URT-combined

URTCul-unique

Setup:

Figure 4c, URT-unique

Figure 5c, URT-unique