example_qsip | R Documentation |
A data set demonstrating the general organization and data necessary for the calculation of fractional enrichment via qSIP
data(example_qsip)
A data.table with 14387 rows and 18 variables
asv_id. unique identifier for individual microbial taxa (here, amplicon sequence variants or ASVs) as identified by 16S amplicon sequencing
sampleID. unique identifier or code for experimental replicates
fraction. the fraction number of a replicate (1–22)
timepoint. the time of sampling for a replicate in days (0, 7)
isotope. factor of isotopes added to sample (values: NA, 16O, 18O)
iso_trt. factor specifying whether isotopes were added (light, label)
ecosystem. the site where soil samples originate from Northern Arizona (MC = mixed conifer, GL = grassland)
treatment. factor of nutrient amendments added (control, C for glcuose, CN for glucose and ammonium)
rep. numeric replicate from each plot (1–4 for unlabeled samples, 1–3 for labeled samples)
Density.g.ml. the density of individual fractions in grams per milliliter (1.6509988–1.736474)
avg_16S_g_soil. the concentration of bacterial 16S copies of individual fractions expressed per g dry soil (47–803,489)
seq_abund. the number of sequence reads per taxon (1–20,186)
Kingdom. the assigned kingdom of a taxon (Archaea, Bacteria, Unassigned, or Eukaryota)
Phylum. the assigned phylum of a taxon
Class. the assigned class of a taxon
Order. the assigned order of a taxon
Family. the assigned family of a taxon
Genus. the assigned genus of a taxon
<https://github.com/bramstone/density-dependence-qSIP/tree/main/data>
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