Package: LMMstar 1.2.0

LMMstar: Repeated Measurement Models for Discrete Times

Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers" taught by the section of Biostatistics of the University of Copenhagen. It implements linear mixed models where the model for the variance-covariance of the residuals is specified via patterns (compound symmetry, toeplitz, unstructured, ...). Statistical inference for mean, variance, and correlation parameters is performed based on the observed information and a Satterthwaite approximation of the degrees of freedom. Normalized residuals are provided to assess model misspecification. Statistical inference can be performed for arbitrary linear or non-linear combination(s) of model coefficients. Predictions can be computed conditional to covariates only or also to outcome values.

Authors:Brice Ozenne [aut, cre], Julie Forman [aut]

LMMstar_1.2.0.tar.gz
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LMMstar_1.2.0.tgz(r-4.4-any)LMMstar_1.2.0.tgz(r-4.3-any)
LMMstar_1.2.0.tar.gz(r-4.5-noble)LMMstar_1.2.0.tar.gz(r-4.4-noble)
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LMMstar.pdf |LMMstar.html
LMMstar/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/bozenne/lmmstar/issues

Datasets:

On CRAN:

6.19 score 4 stars 85 scripts 523 downloads 25 exports 55 dependencies

Last updated 17 days agofrom:fa91789685. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 20 2024
R-4.5-winERROROct 20 2024
R-4.5-linuxERROROct 20 2024
R-4.4-winERROROct 20 2024
R-4.4-macERROROct 20 2024
R-4.3-winERROROct 20 2024
R-4.3-macERROROct 20 2024

Exports:addapproxAUCbaselineAdjustmentcorrelateCSCUSTOMIDINDlmmlmmCCLMMstar.optionsmlmmmt.testpartialCorREremrepetitionresamplerestaureNAsampleRemscatterplotsummarizesummarizeNATOEPLITZUN

Dependencies:ADGofTestclicodetoolscolorspacecopuladigestdoSNOWfansifarverforeachfuturefuture.applyggplot2globalsgluegslgtableisobanditeratorslabelinglatticelavalifecyclelistenvmagrittrMASSMatrixmgcvmultcompmunsellmvtnormnlmenumDerivparallellypcaPPpillarpkgconfigprogressrpsplineR6RColorBrewerrlangsandwichscalessnowSQUAREMstabledistsurvivalTH.datatibbleutf8vctrsviridisLitewithrzoo

LMMstar: overview

Rendered fromoverview.pdf.asisusingR.rsp::asison Oct 20 2024.

Last update: 2024-05-14
Started: 2021-06-09

LMMstar: partial residuals

Rendered frompartial-residuals.pdf.asisusingR.rsp::asison Oct 20 2024.

Last update: 2024-05-14
Started: 2024-05-12

Readme and manuals

Help Manual

Help pageTopics
Data From The Bland Altman Study (Long Format)abetaL
Data From The abeta Study (Wide Format)abetaW
Add Columns to Outputadd
Multivariate Tests For a Linear Mixed Modelanova.lmm
AUC: numerical integral of a functionapproxAUC
Graphical Display For Correlation Matrixautoplot.correlate plot.correlate
Graphical Display For a Linear Mixed Modelautoplot.lmm plot.lmm
Graphical Display of Wald Tests For Multiple Linear Mixed Models.autoplot.mlmm plot.mlmm
Graphical Display For Partial Correlationautoplot.partialCor plot.partialCor
Graphical Display of Profile Likelihoodautoplot.profile_lmm plot.profile_lmm
Graphical Display of the Residualsautoplot.residuals_lmm plot.residuals_lmm
Graphical Display of the Descriptive Statisticsautoplot.summarize plot.summarize
Graphical Display of Missing Data Patternautoplot.summarizeNA plot.summarizeNA
Graphical Display For Wald Tests Applied to a Linear Mixed Modelautoplot.Wald_lmm plot.Wald_lmm
Perform Baseline AdjustmentbaselineAdjustment
Data From The Bland Altman Study (Long Format)blandAltmanL
Data From The Bland Altman Study (Wide Format)blandAltmanW
Data From The Blood Pressure Study (Long Format)bloodpressureL
Data From The Calcium Supplements Study (Long Format)calciumL
Data From The Calcium Supplements Study (Wide Format)calciumW
CKD longckdL
CKD wideckdW
Extract Coefficients From a Linear Mixed Modelcoef.lmm
Extract Coefficients From Multiple Linear Mixed Modelscoef.mlmm
Extract Coefficients From Combined Wald Tests Applied to Linear Mixed Modelscoef.rbindWald_lmm
Extract Coefficients From Wald Tests Applied to a Linear Mixed Modelcoef.Wald_lmm
Confidence Intervals for a Linear Mixed Modelconfint.lmm
Confidence Intervals for Multiple Linear Mixed Modelsconfint.mlmm
Confidence Intervals From Combined Wald Tests Applied to Linear Mixed Modelsconfint.rbindWald_lmm
Resampling Confidence Intervals for Linear Mixed Modelconfint.resample
Confidence Intervals From Wald Tests Applied to a Linear Mixed Modelconfint.Wald_lmm
Compute correlation matrixcorrelate
Compound Symmetry StructureCS
Custom StructureCUSTOM
Residual Degrees-of-Freedom From a Linear Mixed Model.df.residual.lmm
Residuals Degrees-of-Freedom From From Multiple Linear Mixed Model.df.residual.mlmm
Extract Mean Coefficients in Original Coding From a Linear Mixed Modeldummy.coef.lmm
Effects Derived For a Linear Mixed Modeleffects.lmm
Extract the Score Function for Multcompestfun.lmm
Delta Method for a Linear Mixed Modelestimate.lmm
Delta Method for Multiple Linear Mixed Modelsestimate.mlmm
Fitted Outcome Value by a Linear Mixed Model.fitted.lmm
Fitted Outcome Value by Multiple Linear Mixed Models.fitted.mlmm
Data From The Gastric Bypass Study (Long Format)gastricbypassL
Data From The Gastric Bypass Study (Wide Format)gastricbypassW
identity StructureID
Extract the Influence Function From a Linear Mixed Modeliid.lmm
Extract the Influence Function From Multiple Linear Mixed Modelsiid.mlmm
Extract the Influence Function From Wald Tests Applied to a Linear Mixed Modeliid.Wald_lmm
Independence StructureIND
Extract The Information From a Linear Mixed Modelinformation.lmm
Contrasts and Reference Level in a Linear Mixed Modellevels.lmm
Fit Linear Mixed Modellmm
Fit Linear Mixed Model on Complete Case datalmmCC lmmCC.formula lmmCC.lm
Global options for LMMstar packageLMMstar.options
Log-Likelihood From a Linear Mixed ModellogLik.lmm
Log-Likelihood From Multiple Linear Mixed ModelslogLik.mlmm
Fit Multiple Linear Mixed Modelmlmm
Extracting the Model Frame from a Linear Mixed Modelmodel.frame.lmm
Design Matrix for a Linear Mixed Modelmodel.matrix.lmm
Statistical Inference and parametrization of a Linear Mixed Modelmodel.tables.lmm
Statistical Inference and parametrization of Multiple Linear Mixed Modelmodel.tables.mlmm
Statistical Inference From Combined Wald Tests Applied to Linear Mixed Modelsmodel.tables.rbindWald_lmm
Statistical Inference for Wald tests Applied to a Linear Mixed Modelmodel.tables.Wald_lmm
Multiple Student's t-Testmt.test
Data From National Cooperative Gallstone Study (Long Format)ncgsL
Data From National Cooperative Gallstone Study (Wide Format)ncgsW
Number of Observations from a Linear Mixed Modelnobs.lmm
Number of Observations from Multiple Linear Mixed Modelsnobs.mlmm
Data From The toenail onycholysis Study (Long Format)onycholysisL
Data From The toenail onycholysis Study (Wide Format)onycholysisW
Partial CorrelationpartialCor partialCor.formula partialCor.list partialCor.lmm
Data From The Potassium Intake Study (Long Format with intermediate measurements)potassiumRepeatedL
Data From The Potassium Intake Study (Long Format)potassiumSingleL
Data From The Potassium Intake Study (Wide Format)potassiumSingleW
Predicted Outcome Value by a Linear Mixed Model.predict.lmm
Predicted Outcome Value by Muliple Linear Mixed Model.predict.mlmm
Log-Likelihood Contour For a Linear Mixed Modelprofile.lmm
Estimate Random Effect From a Linear Mixed Modelranef.lmm
Combine Wald Tests From Linear Mixed Modelsrbind.Wald_lmm
Random Effect StructureRE
Remove Columns from Outputrem
Number of Repetitions Within Clusterrepetition
Inference via Resampling for a Linear Mixed Modelresample resample.lmm resample.mlmm
Extract The Residuals From a Linear Mixed Modelresiduals residuals.clmm residuals.lmm residuals.mlmm
Sample Longuitudinal DatasampleRem
Scatterplot for Continuous Variablesscatterplot
Simulated Data with 3-level struture (Long Format)schoolL
Extract The Score From a Linear Mixed Modelscore.lmm
Extract The Score From Multiple Linear Mixed Modelsscore.mlmm
Extract The Residuals Variance-Covariance Matrix From a Linear Mixed Modelsigma.lmm
Summary Statisticssummarize
Summarize missing data patternssummarizeNA
Summary Output for a Linear Mixed Modelsummary.lmm
Summary of Multiple Linear Mixed Modelssummary.mlmm
Summary for partial correlationsummary.partialCor
Summary of Testing for a Linear Mixed Modelssummary.Wald_lmm
Data From The SWABS Study (Long Format)swabsL
Data From The SWABS Study (Wide Format)swabsW
Model Terms For Linear Mixed Modelsterms.lmm
Toeplitz StructureTOEPLITZ
Unstructured StructureUN
Variables Involved in a Linear Mixed Modelvariable.names.lmm
Variables Involved in Multiple Linear Mixed Modelsvariable.names.mlmm
Data From The VAS Study (Long Format)vasscoresL
Data From The VAS Study (Wide Format)vasscoresW
Extract The Variance-Covariance Matrix From a Linear Mixed Modelvcov.lmm
Extract The Variance-Covariance Matrix From Multiple Linear Mixed Modelsvcov.mlmm
Extract the Variance-Covariance From Wald Tests For Linear Mixed Modelsvcov.rbindWald_lmm
Extract the Variance-Covariance Matrix From Wald Tests For Linear Mixed Modelvcov.Wald_lmm
Data From The Vitamin Study (Long Format)vitaminL
Data From The Vitamin Study (Wide Format)vitaminW
Extract Weights Used to Pool Estimatesweights.rbindWald_lmm