BD_shift                Assessing the magnitude of BD shifts with 16S
                        rRNA community data by calculating the beta
                        diversity between unlabeled control and labeled
                        treatment gradient fraction communities.
DESeq2_l2fc             Calculating log2 fold change for HTS-SIP data.
HRSIP                   (MW-)HR-SIP analysis
HTSSIP                  HTSSIP: analyzing high throughput sequence data
                        from nucleotide stable isotope probing
                        experiments
HTSSIP_sim              Simulate a HTS-SIP dataset
OTU_qPCR_trans          Transform OTU counts based on qPCR data
SIP_betaDiv_ord         Calculating & plotting beta diversity for a
                        list of phyloseq objects
as.Num                  conversion to numeric
calc_Gi                 Calculate G+C from unlabeled buoyant density
calc_Mheavymax          Calculate the theoretical maximum molecular
                        weight of fully-labeled DNA
calc_atom_excess        Calculate atom fraction excess
data-physeq_S2D1        (Data) A subset of full HTS-SIP dataset
                        (Substrates=2, Days=1)
data-physeq_S2D1_l      (Data) A subset of full HTS-SIP dataset
                        (Substrates=2, Days=1)
data-physeq_S2D2        (Data) A subset of full HTS-SIP dataset
                        (Substrates=2, Days=2)
data-physeq_S2D2_l      (Data) A subset of full HTS-SIP dataset
                        (Substrates=2, Days=2)
data-physeq_rep3        (Data) A simulated HTS-SIP dataset
data-physeq_rep3_qPCR   (Data) qPCR data associated with the
                        physeq_rep3 HTS-SIP dataset
delta_BD                delta_BD calculation
evaluate_matches        Evaluate String Interpolation Matches
expr_param_extract      Extract all quoted values in the expression
                        used for phyloseq subsetting.
extract_expressions     Extract Expression Objects from String
                        Interpolation Matches
extract_formats         Extract String Interpolation Formats from
                        Matched Placeholders
filter_l2fc             Filter l2fc table
format_metadata         Format phyloseq metadata for calculating BD
                        range overlaps.
fraction_overlap        Calculate the BD range overlap of gradient
                        fractions
get_treatment_params    Get parameters for subsetting the phyloseq
                        dataset
gradient_sim            Simulate HTS-SIP communities for 1 density
                        gradient
match_brace             Utility Function for Matching a Closing Brace
match_placeholders      Match Expression Placeholders for String
                        Interpolation
max_BD_range            Adjusting BD range size if negative.
overlap_wmean_dist      Calculating weighted mean beta-diversities of
                        overlapping gradient fractions.
parse_dist              Filtering out non-relevant distances in
                        distance matrix
perc_overlap            Calculate the percent overlap between two
                        ranges (x & y).
phyloseq2df             phyloseq data object conversion to data.frame
phyloseq2table          Phyloseq conversion to a ggplot-formatted table
phyloseq_list_ord_dfs   Converting ordination objects to data.frames
phyloseq_ord_plot       Plotting beta diversity ordination
phyloseq_subset         Make a list of phyloseq object subsets
physeq_format           Checking format of phyloseq object for HTSSIP
                        compatibility
physeq_list_betaDiv     calculating beta diversity for a list of
                        phyloseq objects
physeq_list_ord         calculating ordinations from a list of distance
                        matrices
qPCR_sim                Simulate qPCR values
qSIP_atom_excess        Calculate atom fraction excess using q-SIP
                        method
qSIP_atom_excess_format
                        Reformat a phyloseq object of qSIP_atom_excess
                        analysis
qSIP_bootstrap          Calculate bootstrap CI for atom fraction excess
                        using q-SIP method
stringterpolate         String Interpolation
tss                     Total sum scaling
