Sample ID codes:
Format: x08F.#Cxx, where x represents host and treatment letter codes, # indicates plot number, "08" represents the year roots were collected (2008), "F" stands for "fungal sequences," and "C" indicates which long-term treatment plots out of several these samples belong.
The first x will either be D or G, for Deschampsia cespitosa or Geum rossii.  Plot # can be 1 through 7. The second x will be either X or D, for no D. cespitosa removal, or D. cespitosa removal.  The last x will be either X or N, for no N or N addition.
Example: D08F.1CXN represents roots from D. cespitosa in plot 1, under N enrichment.
G08F.5CDN represents roots from G. rossii in plot 5, under D. cespitosa removal and N enrichment
G08F.3CXX represents roots from G. rossii in plot 3, control

Raw data files received from Research and Testing Laboratories:

raw sequences: NiwotDG08F.fna, sequence file, fasta format

quality file: NiwotDG08F.qual, quality score file

OTU tables and other R input files

OTU and sequence counts: stats.csv, file containing sequence and OTU counts for each sample

Unrarefied OTU table Lx: reduced_nosingletons_sorted_host_Lx.csv, Unrarefied taxa x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

rarefied OTU table Lx: reduced_nosingles_rarefied_557_99_Lx.csv, Rarefied taxa x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

NiwotDGF map: NiwotDGF_map3.csv, Environmental mapping file

Observed_species_Lx: Observed_species_Lx.csv, Taxa richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

Simpson_e_Lx: Simpson_evenness_Lx.csv, Taxa evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

Simpson_Lx: Simpson_diversity_Lx.csv, Taxa Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

R code:

alpha diversity code: alpha.R, code to test for correlations between alpha diversity and treatment (collated alpha diversity files are produced in Qiime from taxa x SampleID tables)

NMDS code: NMDS.R, NMDS ordination and permutation test (input is unrarefied taxa x sampleID table and mapping file)

ANOVA code, N effects per host: otu_anova_N_isolated_host.R, code to use ANOVA to test individual taxa for correlation with N in each host 

ANOVA code, Nxhost: otu_anova_Nxhost.R, code to use ANOVA to test individual taxa for correlation with N or host, or interactions between the two 

ANOVA code, remxN: otu_anova_remxN.R, code to use ANOVA to test individual taxa for correlation with treatment or treatment interactions in single host

rarefaction plot code: rarefaction.R, alpha rarefaction code (collated alpha rarefaction table produced in Qiime from taxa x SampleID tables)

RDA code: RDA.R, RDA ordination and permutation test 

SE of OTU and seq counts: SE otus seqs.R Code to calculate standard error of sequence and OTU counts for each host.