Package index
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fastlmm() - Fast Linear Mixed Model with 1 Random Effect
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fastglmm() - Fit Generalized Linear Mixed Model via PQL
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fastglmm.nb() - Fit Negative Binomial Mixed Model via PQL
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PsychAD - Gene expession of PTPRG in microglia in 60k cells
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anova(<fastlmm>) - ANOVA Tables
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coef(<fastlmm>) - Extract Model Coefficients
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cooks.distance(<fastlmm>) - Cook's Distance Metric
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deviance(<fastlmm>) - Model Deviance
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ddf() - Denominator Degrees of Freedom
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df.residual(<fastlmm>) - Residual Degrees-of-Freedom
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edf() - Effective Degrees-of-Freedom of Model Fit
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extractAIC(<fastlmm>) - Extract AIC from a Fitted Model
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family(<fastlmm>)family(<fastglmm>)family(<glmmPQL>) - Extract Model Family
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fitted(<fastlmm>)fitted(<fastglmm>) - Extract Model Fitted Values
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fixef(<fastlmm>) - Extract Fixed Effects
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hatvalues(<fastlmm>) - Return Diagonals of Hat Matrix
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linearHypothesis() - Test Linear Hypothesis
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logLik(<fastlmm>) - Extract Log-Likelihood
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model.frame(<fastlmm>) - Extracting the Model Frame from a Fit
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nobs(<fastlmm>) - Extract the Number of Observations from a Fit
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plot(<fastlmm>) - Diagnostic Plots for Model Fits
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predict(<fastlmm>)predict(<fastglmm>) - Model Predictions
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ranef(<fastlmm>) - Extract the modes of the random effect
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residuals(<fastlmm>) - Extract Model Residuals
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rstudent(<fastlmm>) - Extract Studentized Residuals
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sigma(<fastlmm>) - Extract Residual Standard Deviation
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simulate(<fastlmm>) - Simulate Responses
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summary(<fastlmm>) - Object Summaries and Hypothesis Testing
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terms(<fastlmm>) - Model Terms
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varpart() - Variance Partitioning Analysis
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vcov(<fastlmm>) - Calculate Variance-Covariance Matrix for a Fitted Model Object
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as.fastlmm() - Convert list to fastlmm class
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getFamilyString() - Convert GLM family to string
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indicator_decomp() - Spectral decomposition of factor indicator matrix
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preprocess_indicator() - Create sparse indicator matrix
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fastlmm.fit() - Fitter Function for Linear Mixed Model
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nb_theta() - Estimate theta of the Negative Binomial
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refitModel() - Refit fastlmm model with new delta
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dispersion() - Overdispersion parameter phi for quasi-likelihood
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varianceTerms() - Array of variance component estimates
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negative.binomial() - Family function for Negative Binomial GLMs
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fastlmm_R() - Fit linear mixed model using SVD of covariance
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fastglmm_R() - Fit generalized linear mixed model via PQL
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fastglmm_R.nb() - Fit negative binomial mixed model via PQL