Package: GLMMcosinor 0.2.1.9000

Rex Parsons

GLMMcosinor: Fit a Cosinor Model Using a Generalized Mixed Modeling Framework

Allows users to fit a cosinor model using the 'glmmTMB' framework. This extends on existing cosinor modeling packages, including 'cosinor' and 'circacompare', by including a wide range of available link functions and the capability to fit mixed models. The cosinor model is described by Cornelissen (2014) <doi:10.1186/1742-4682-11-16>.

Authors:Rex Parsons [aut, cre], Oliver Jayasinghe [aut], Nicole White [aut], Oliver Rawashdeh [aut, fnd], Prasad Chunduri [ctb, fnd], Margaret Doyle [ctb], Michael Sachs [rev], Joaquin Cavieres [rev]

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

# Install 'GLMMcosinor' in R:
install.packages('GLMMcosinor', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/glmmcosinor/issues

Pkgdown:https://docs.ropensci.org

Datasets:
  • cosinor_mixed - Cosinor_mixed dataset for cosinor modeling examples.
  • vitamind - Vitamin D dataset for cosinor modeling examples.

On CRAN:

5.82 score 1 stars 22 scripts 548 downloads 11 exports 48 dependencies

Last updated 2 months agofrom:2dd22d42b2 (on main). Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 05 2024
R-4.5-winOKDec 05 2024
R-4.5-linuxOKDec 05 2024
R-4.4-winOKDec 05 2024
R-4.4-macOKDec 05 2024
R-4.3-winOKDec 05 2024
R-4.3-macOKDec 05 2024

Exports:amp_acroautoplotbellcglmmfit_model_and_processpolar_plotsigmasimulate_cosinortest_cosinor_componentstest_cosinor_levelsupdate_formula_and_data

Dependencies:assertthatbootclicolorspacecowplotcpp11fansifarverggforceggplot2glmmTMBgluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixmgcvminqamunsellnlmenloptrnumDerivpillarpkgconfigpolyclipR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangscalessystemfontstibbletidyselectTMBtweenrutf8vctrsviridisLitewithr

Simulating data

Oliver Jayasinghe and Rex Parsons

Rendered fromdata-simulations.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2024-01-11
Started: 2023-02-08

GLMMcosinor

Oliver Jayasinghe and Rex Parsons

Rendered fromGLMMcosinor.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2024-10-31
Started: 2023-02-08

Mixed models

Oliver Jayasinghe and Rex Parsons

Rendered frommixed-models.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2024-01-11
Started: 2023-02-08

Model specification

Oliver Jayasinghe and Rex Parsons

Rendered frommodel-specification.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2024-10-31
Started: 2023-02-08

Visualizing models

Oliver Jayasinghe and Rex Parsons

Rendered frommodel-visualizations.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2024-10-31
Started: 2024-10-31

Multicomponent cosinor modeling

Oliver Jayasinghe and Rex Parsons

Rendered frommultiple-components.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2024-10-31
Started: 2023-02-08

Readme and manuals

Help Manual

Help pageTopics
Used to specify a cosinor component in the model formula.amp_acro
Plot a cosinor modelautoplot.cglmm
Fit cosinor model with '{glmmTMB}'cglmm
cosinor_mixed dataset for cosinor modeling examples.cosinor_mixed
Fit the cosinor GLMM model using the output from 'update_formula_and_data()' and a new formulafit_model_and_process
Generates a polar plot with elliptical confidence intervalspolar_plot
Generates a polar plot with elliptical confidence intervalspolar_plot.cglmm
Predict from a cosinor modelpredict.cglmm
Print a brief summary of the 'cglmm' model.print.cglmm
Print test of modelprint.cglmmSubTest
Print the summary of a cosinor modelprint.cglmmSummary
Print results of test of cosinor modelprint.cglmmTest
Extract residual standard deviation or dispersion parametersigma.cglmm
Simulate data from a cosinor modelsimulate_cosinor
Summarize a cosinor model Given a time variable and optional covariates, generate inference a cosinor fit. Gives estimates, confidence intervals, and tests for the raw parameters, and for the mean, amplitude, and acrophase parameters. If the model includes covariates, the function returns the estimates of the mean, amplitude, and acrophase for the group with covariates equal to 1 and equal to 0. This may not be the desired result for continuous covariates.summary.cglmm
Test for differences in a cosinor model between components.test_cosinor_components
Test for differences in a cosinor model between levels of the grouping variable.test_cosinor_levels
Update data and formula for fitting cglmm modelupdate_formula_and_data
Vitamin D dataset for cosinor modeling examples.vitamind