# Estimating Absolute Abundance from Microbial Spike-in Controls

## Documentation for package ‘DspikeIn’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

AcceptableRange | Acceptable Range Data
adjusted_prevalence | Adjust Prevalence in a Microbiome Object
adjust_abundance_by_factor | Adjust Abundance by a Custom Factor
adjust_abundance_one_third | Adjust Abundance by a Custom Factor
alluvial_plot | Generate an Alluvial Plot for Microbiome Data
calculate_list_average_scaling_factors | Calculate Sample-specific Average Scaling Factors for Multiple Spike-in Groups
calculate_spikeIn_factors | Calculate Scaling Factors for Spiked Species in Phyloseq or TSE Object
calculate_spike_percentage | Calculate Spike Percentage for Specified Taxa in a Phyloseq or TSE Object
calculate_spike_percentage_list | Calculate Spike-in Percentage for Specified Taxa
calculate_summary_stats_table | Calculate Summary Statistics Table
color_palette | Original, Extended, and Nature-Inspired Color Palette Sequence
conclusion | Compute Summary Statistics for Spiked Species
convert_categorical_to_factors | Convert Categorical Columns to Factors in Sample Data
convert_phyloseq_to_tse | Convert a 'phyloseq' Object to a 'TreeSummarizedExperiment'
convert_to_absolute_counts | Convert Relative ASV/OTU Counts to Absolute Counts
convert_tse_to_phyloseq | Convert a 'TreeSummarizedExperiment' to a 'phyloseq' Object
create_directory | Create a Directory and Optionally Set as Working Directory
create_list | Create a List from a Phyloseq or TSE Object
degree_network | Analyze and Visualize a Microbial Network
detect_common_asvs_taxa | Detect Common ASVs and Taxa from Multiple Phyloseq or TSE Objects
extract_neighbors | Extract First and Second Neighbors of a Target Node
filter_and_split_abundance | Filter and Split Abundance Data by Threshold
get_long_format_data | Convert a Phyloseq or TSE Object into a Long-Format Data Frame
get_otu_table | Extract OTU Tax Metadata from Object
get_phy_tree | Extract Phylogenetic Tree
get_reference_seq | Extract Reference Sequences
get_sample_data | Extract Sample Data
get_sample_sums | Extract Sample Sums from Object
get_tax_table | Extract Taxonomy Table
gm_mean | Calculate Geometric Mean
imbalance_calculate_list_average_scaling_factors | Calculate Per-Sample Scaling Factors for Multiple Spike-in Groups
label | Label Taxonomic Ranks by Hashcode
load_graphml | Load GraphML Without 'id' Conflicts
metadata_full | Metadata for Microbiome Samples
MG_shapes | Predefined Shape Vector for Plot Styling
my_custom_theme | Custom ggplot2 Theme with Consistent Aesthetics
node_level_metrics | Compute and Visualize Node-Level Network Metrics
norm.clr | CLR Normalization (Centered Log-Ratio Transformation)
norm.css | CSS Normalization (Cumulative Sum Scaling)
norm.DESeq | DESeq Normalization with Pseudocount and Integer Conversion
norm.med | Median Normalization
norm.Poisson | Poisson Normalization and Differential Abundance Function
norm.QN | Quantile Normalization (QN) for phyloseq object
norm.rar | Rarefying
norm.rle | RLE Normalization (Relative Log Expression)
norm.TC | TC Normalization (Total Count Scaling)
norm.TMM | TMM Normalization (Trimmed Mean of M component)
norm.tss | TSS Normalization (Total Sum Scaling)
norm.UQ | UQ Normalization (Upper Quartile)
normalization_set | Apply the Selected Normalization Method to the Phyloseq and TSE Objects
perform_and_visualize_DA | Perform and Visualize Differential Abundance Analysis with edgeR or DESeq2
physeq | Example Phyloseq Object with Tree and Reference Sequences
physeq_16SOTU | Example Phyloseq Object for 16S OTUs
physeq_ITSOTU | Example Phyloseq Object for ITS OTUs
plotbar_abundance | Taxa Bar Plot Without Aggregation (Relative or Absolute Abundance)
plot_core_microbiome_custom | Plot Core Microbiome Prevalence Heatmap (Phyloseq & TSE Compatible)
plot_spikein_tree_diagnostic | Spike-in Tree Diagnostic Plot
Pre_processing_hashcodes | Pre-process phyloseq or TSE object based on hashcodes
Pre_processing_species | Pre-process taxa in a phyloseq or TSE object by merging ASVs/OTUs
Pre_processing_species_list | Preprocess and Merge Spike-in Species in a Phyloseq or TSE Object
proportion_adj | Proportionally Adjust Abundance
quadrant_plot | Generate Custom Quadrant Plots for Node Metrics
RandomForest_selected | Select Important ASVs/OTUs Using Random Forest
randomsubsample_Trimmed_evenDepth | Subsampling to an Equal Sequencing Depth
random_subsample_WithReductionFactor | Random Subsampling with Reduction Factor
regression_plot | Create a Regression Plot with Faceting by Range
relativized_filtered_taxa | Filter Taxa from a Phyloseq or TSE Object Based on Custom Thresholds
remove_zero_negative_count_samples | Remove Samples with Zero, Negative Counts, or NA Values and Add Pseudocount
ridge_plot_it | Generate Ridge Plots for Taxonomic Abundance Distribution
set_nf | Set Normalization Factors in the Sample Data of the Phyloseq Object
simulate_network_robustness | Simulate Network Robustness under Node Removal
summ_ASV_OTUID | Summarize ASV Data Based on ASV_ID
summ_count_phyloseq | Summary Statistics of a Phyloseq or TSE Object
summ_phyloseq_sampleID | Generate Summary Statistics for Each Sample
taxa_barplot | Generate a Taxa Barplot with Relative or Absolute Abundance
tidy_phyloseq_tse | Tidy a Phyloseq or TreeSummarizedExperiment Object
tse | Example TreeSummarizedExperiment (TSE) Object with Tree and Reference Sequences
validate_spikein_clade | Validate Spike-In Clade Consistency with NJ Tree and Bootstrap
weight_Network | Analyze and Visualize a Microbial Network