Package: kronos 1.0.0.9000

kronos: Microbiome Oriented Circadian Rhythm Analysis Toolkit

The goal of 'kronos' is to provide an easy-to-use framework to analyse circadian or otherwise rhythmic data using the familiar R linear modelling syntax, while taking care of the trigonometry under the hood.

Authors:Thomaz Bastiaanssen [aut, cre], Sarah-Jane Leigh [aut]

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kronos.pdf |kronos.html✨
kronos/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/thomazbastiaanssen/kronos/issues

Datasets:
  • bigdata - Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups
  • bigmeta - Descriptional metadata for the 'bigdata' object, for the purpose of demonstration.
  • groupdata - Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groups
  • onevariable - Snippet of example data to demonstrate the functionality of 'kronos' in the most simple scenario.
  • twowaydata - Snippet of example data to demonstrate the functionality of 'kronos' in the two-factor design scenario.

On CRAN:

15 exports 7 stars 1.32 score 28 dependencies 18 scripts 157 downloads

Last updated 1 years agofrom:248f762243. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winOKSep 18 2024
R-4.5-linuxOKSep 18 2024
R-4.4-winOKSep 18 2024
R-4.4-macOKSep 18 2024
R-4.3-winOKSep 18 2024
R-4.3-macOKSep 18 2024

Exports:fw_kronosgetKronosgetKronos_fitgetKronos_groupwisegetKronos_inputgetKronos_pairwisegetKronos_pairwise_pgetKronos_paramsgetKronos_tracegg_kronos_acrogramgg_kronos_circlegg_kronos_sinusoidkronoskronosListToTableshow

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groupsbigdata
Descriptional metadata for the 'bigdata' object, for the purpose of demonstration.bigmeta
Update 'kronos' formula in light of sine and cosine componentsbuild_kronos_formula
Get Results from list of KronosOut ObjectsdelistKronos_groupwise
Get Results from list of 'KronosOut' ObjectsdelistKronos_pairwise
Fit cosinor modelfit_cosinor_model
Fit cosinor modelfit_groupwise_model
Fit a cosinor model and extract relevant parameters on a feature table.fw_kronos
Get sine and cosine componentsget_cos_sine
Figure out what variable represents time. Called by main 'kronos' function.get_vars
Get Results from 'KronosOut' ObjectgetKronos
Get Results from 'KronosOut' ObjectgetKronos_fit
Get Results from 'KronosOut' ObjectgetKronos_groupwise
Get Results from 'KronosOut' ObjectgetKronos_input
Get Results from 'KronosOut' ObjectgetKronos_pairwise
Get Results from 'KronosOut' ObjectgetKronos_pairwise_p
Get Results from 'KronosOut' ObjectgetKronos_params
Get Results from 'KronosOut' ObjectgetKronos_trace
A plotting method for acrophase circleplots using 'ggplot2'.gg_kronos_acrogram
A plotting method for circadian plots using 'ggplot2'.gg_kronos_circle
A plotting method for circadian plots using 'ggplot2'.gg_kronos_sinusoid
Snippet of example data to demonstrate the functionality of 'kronos' between and among three different groupsgroupdata
Fit a cosinor model and extract relevant parameterskronos
Extract p-value from full fitkronos_anova
Give tracing information for plotting purposeskronos_predict
Wrangle results from list of 'KronosOut' Objects to publication ready table.kronosListToTable
An S4 class to contain all output parameters and plotting information from the 'kronos' main pipelinekronosOut-class
Snippet of example data to demonstrate the functionality of 'kronos' in the most simple scenario.onevariable
Fit pairwise cosinor models as some sort of TukeyHSD.pairwise_cosinor_model
Show method for 'kronosOut' object.show,kronosOut-method
Snippet of example data to demonstrate the functionality of 'kronos' in the two-factor design scenario.twowaydata