R Functions Useful for Community Ecology

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Documentation for package ‘QsRutils’ version 0.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

%wo%	Remove elements from a vector
arc_sine	arc_sine
asterix	Indicate Significance with Stars
avg_alpha	Average Alpha Diversity (faster implementation)
check_primer_hits	Check Primer Hits
check_var	Check Variance
cld_dunn	CLDs from DUNN
cld_hsd	Make CLD tibble from Tukey HSD Results
clear_warnings	Clear Warnings
comb	comb
comp_assemble	Assemble Comparison Parts
comp_comparisons	Make Comparisons
comp_make_f_tests	Make F Tests
comp_means_sd	Calculate Means and Standard Deviations
comp_prepare_otu_table	Prepare OTU Table
comp_prepare_phyloseq	Prepare Phyloseq
deg2rad	deg2rad
expt	A 16S Experiment Level phyloseq Object
format_taxon	Format a taxon
generate_password	Genererate a Password
get_groups	get_groups
get_plot_limits	Get ggplot Plot Limits
goods	Calculate Good's Coverage
hash_dna_seqs	Hash DNA sequences
its.root	An ITS Experiment Level phyloseq Object
log_arc_sine	log_arc_sine
make_comparisons	Make Multiple Comparisons on Transformed Data
make_letter_assignments	Make Letter Assignments
merge_2_frames	Merge Two Data Frames
ord_labels	Make Ordination Axis Labels
pca_labels	Make PCA Axis Labels
perm	Permutations
plot_df	A Data File in Long Format
plot_transition_stats	Plot DADA2 Transition Stats
print.check_var	Check Variance
prop_filter	Filter OTUs by Abundance
QsRutils	QsRutils: R Functions Useful for Community Ecology
rad2deg	rad2deg
rda_labels	Make RDA Axis Labels
root_phyloseq_tree	Root Tree in phyloseq Object
se	Standard error
sqrt_arc_sine	sqrt_arc_sine
srs_p	srs_p
subset_by_refseq_lengths	Subset physeq by refseq lengths
subset_dist	Subset Distance Matrix
veganotu	Extract Vegan OTU Table
vegansam	Extract Sample Data Table
vegan_stand	Standardize a Phyloseq OTU Table