Package: QsRutils 0.2.1.9000

QsRutils: R Functions Useful for Community Ecology

A collection of utility functions for community ecology analyses, with emphasis on workflows using the 'phyloseq' and 'vegan' packages. Includes functions for normalizing OTU tables, computing alpha diversity via rarefaction (using a fast C++ implementation), differential abundance comparisons with compact letter displays, primer checking for amplicon sequencing, plotting QIIME 2/DADA2 generated transition stats and miscellaneous helpers for ordination plots and taxonomic name formatting.

Authors:John Quensen [aut, cre, cph]

QsRutils_0.2.1.9000.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
QsRutils/json (API)
NEWS

# Install 'QsRutils' in R:
install.packages('QsRutils', repos = c('https://jfq3.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jfq3/qsrutils/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • expt - A 16S Experiment Level phyloseq Object
  • its.root - An ITS Experiment Level phyloseq Object
  • plot_df - A Data File in Long Format

On CRAN:

Conda:

cpp

6.08 score 3 stars 40 scripts 536 downloads 43 exports 152 dependencies

Last updated from:db324f1d87. Checks:11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE334
linux-devel-x86_64NOTE399
source / vignettesOK315
linux-release-arm64NOTE335
linux-release-x86_64NOTE402
macos-release-arm64NOTE212
macos-release-x86_64NOTE596
macos-oldrel-arm64NOTE283
macos-oldrel-x86_64NOTE507
windows-develNOTE348
windows-releaseNOTE394
windows-oldrelNOTE346
wasm-releaseOK207

Exports:%wo%arc_sineasterixavg_alphacheck_primer_hitscheck_varcld_dunncld_hsdclear_warningscombcomp_assemblecomp_comparisonscomp_make_f_testscomp_means_sdcomp_prepare_otu_tablecomp_prepare_phyloseqdeg2radformat_taxongenerate_passwordget_groupsget_plot_limitsgoodshash_dna_seqslog_arc_sinemake_comparisonsmake_letter_assignmentsmerge_2_framesord_labelspca_labelspermplot_transition_statsprop_filterrad2degrda_labelsroot_phyloseq_treesesqrt_arc_sinesrs_psubset_by_refseq_lengthssubset_distvegan_standveganotuvegansam

Dependencies:abindade4agricolaeAlgDesignapeaphidaskpassbase64encBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitbit64bitopsbslibcachemcigarilloclicliprclustercodetoolscommonmarkcpp11crayoncrosstalkcurldada2data.tableDelayedArraydeldirdigestdplyrDTevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhwriterigraphinsectinterpIRangesisobanditeratorsjpegjquerylibjsonlitekmerknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemultcompViewmulttestnlmeopensslotelpermutephylogramphyloseqpillarpixmappkgconfigplyrpngprettyunitsprogresspromisespwalignqpdfR6RANNrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadrreshape2RhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorsS7sassscalessegmentedSeqinfoseqinrshinyshinybusyshinycssloadersShortReadsnowsourcetoolsspSparseArraySRSstringistringrSummarizedExperimentsurvivalsystibbletidyselecttinytextzdbutf8vctrsveganviridisLitevroomwithrxfunxml2xtableXVectoryaml

Compare Relative Abundances Among Treatments

John Quensen

Rendered frommake_comparisons.Rmdusingknitr::rmarkdownon Jun 13 2026.

Last update: 2026-05-01
Started: 2017-08-21

Recreate arc sine Conversion Table A-16

John Quensen

Rendered fromtable_a16.Rmdusingknitr::rmarkdownon Jun 13 2026.

Last update: 2025-03-06
Started: 2017-08-21

Readme and manuals

Help Manual

Help pageTopics
Remove elements from a vector%wo%
arc_sinearc_sine
Indicate Significance with Starsasterix
Average Alpha Diversity (faster implementation)avg_alpha
Check Primer Hitscheck_primer_hits
Check Variancecheck_var print.check_var
CLDs from DUNNcld_dunn
Make CLD tibble from Tukey HSD Resultscld_hsd
Clear Warningsclear_warnings
combcomb
Assemble Comparison Partscomp_assemble
Make Comparisonscomp_comparisons
Make F Testscomp_make_f_tests
Calculate Means and Standard Deviationscomp_means_sd
Prepare OTU Tablecomp_prepare_otu_table
Prepare Phyloseqcomp_prepare_phyloseq
deg2raddeg2rad
A 16S Experiment Level phyloseq Objectexpt
Format a taxonformat_taxon
Genererate a Passwordgenerate_password
get_groupsget_groups
Get ggplot Plot Limitsget_plot_limits
Calculate Good's Coveragegoods
Hash DNA sequenceshash_dna_seqs
An ITS Experiment Level phyloseq Objectits.root
log_arc_sinelog_arc_sine
Make Multiple Comparisons on Transformed Datamake_comparisons
Make Letter Assignmentsmake_letter_assignments
Merge Two Data Framesmerge_2_frames
Make Ordination Axis Labelsord_labels
Make PCA Axis Labelspca_labels
Permutationsperm
A Data File in Long Formatplot_df
Plot DADA2 Transition Statsplot_transition_stats
Filter OTUs by Abundanceprop_filter
QsRutils: R Functions Useful for Community EcologyQsRutils
rad2degrad2deg
Make RDA Axis Labelsrda_labels
Root Tree in phyloseq Objectroot_phyloseq_tree
Standard errorse
sqrt_arc_sinesqrt_arc_sine
srs_psrs_p
Subset physeq by refseq lengthssubset_by_refseq_lengths
Subset Distance Matrixsubset_dist
Standardize a Phyloseq OTU Tablevegan_stand
Extract Vegan OTU Tableveganotu
Extract Sample Data Tablevegansam