OTUtable-package |
OTU table analysis functions |
bog_subset |
Subset OTU table by sampling site |
chao1 |
Chao1 Richness |
clean_mothur_taxonomy |
Clean mothur-format Taxonomy File |
clean_shared |
Reformat a shared file |
clean_TaxAss_taxonomy |
Clean Taxonomy File Output by TaxAss Workflow |
combine_otus |
Combine OTUs based on identical taxonomic assignments |
extract_date |
Extract sampling date from a vector of sample names |
filter_taxa |
Filter Taxa Based on Abundance and Persistence |
grab_group |
Subset OTU table by taxonomic assignment |
make_do_matrix |
Make matrix of dissolved oxygen data |
make_temp_matrix |
Make matrix of temperature data |
metadata |
Lake metadata for OTU table |
obs_richness |
Observed Richness |
OTUtable |
OTU table analysis functions |
otu_table |
OTU table generated from 8 bog lakes over 4 years |
pielou |
Pielou's Evenness |
plot_column |
Plot DO or temperature data from a depth profile over time |
reduce_names |
Shorten taxonomic assignment in table row names |
remove_reps |
Remove the second replicate of each sample, when it exists |
rotate |
Rotate a matrix |
shannon |
Shannon's Biodiversity Index |
taxonomy |
Taxonomic assignments of OTUs |
year_subset |
Subset samples by a specific year |
zscore |
Z-score normalize relative abundance data |