GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).
Author  Jacolien van Rij [aut, cre], Martijn Wieling [aut], R. Harald Baayen [aut], Hedderik van Rijn [ctb] 
Date of publication  20160613 13:07:04 
Maintainer  Jacolien van Rij <vanrij.jacolien@gmail.com> 
License  GPL (>= 2) 
Version  2.2 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:



All man pages Function index File listing
Man pages  

acf_n_plots: Generate N ACF plots of individual or aggregated time series.  
acf_plot: Generate an ACF plot of an aggregated time series.  
acf_resid: Generate an ACF plot of model residuals. Works for lm, lmer,...  
check_resid: Inspect residuals of regression models.  
compareML: Function for comparing two GAMM models.  
convertNonAlphanumeric: Prepare string for regular expressions (backslash for all...  
derive_timeseries: Derive the time series used in the AR1 model.  
diagnostics: Visualization of the model fit for time series data.  
diff_terms: Compare the formulas of two models and return the...  
eeg: Raw EEG data, single trial, 50Hz.  
fadeRug: Fade out the areas in a surface without data.  
find_difference: Return the regions in which the smooth is significantly...  
fvisgam: Visualization of nonlinear interactions, summed effects.  
gamtabs: Convert model summary into Latex/HTML table for knitr/R...  
get_coefs: Get coefficients for the parametric terms (intercepts and...  
get_difference: Get model predictions for differences between conditions.  
get_fitted: Get model all fitted values.  
get_modelterm: Get estimated for selected model terms.  
get_pca_predictions: Return PCA predictions.  
get_predictions: Get model predictions for specific conditions.  
get_random: Get coefficients for the random intercepts and random slopes.  
info: Information on how to cite this package  
infoMessages: Turn on or off information messages.  
inspect_random: Inspection and interpretation of random factor smooths.  
itsadug: Interpreting Time Series, Autocorrelated Data Using GAMMs...  
missing_est: Return indices of data that were not fitted by the model.  
plot_data: Visualization of the model fit for time series data.  
plot_diff: Plot difference curve based on model predictions.  
plot_diff2: Plot difference surface based on model predictions.  
plot_modelfit: Visualization of the model fit for time series data.  
plot_parametric: Visualization of group estimates.  
plot_pca_surface: Visualization of the effect predictors in nonlinear...  
plot_smooth: Visualization of smooths.  
plot_topo: Visualization of EEG topo maps.  
print_summary: Print a named list of strings, output from 'summary_data'.  
pvisgam: Visualization of partial nonlinear interactions.  
report_stats: Returns a description of the statistics of the smooth terms...  
resid_gam: Extract model residuals and remove the autocorrelation...  
rug_model: Add rug to plot, based on model.  
simdat: Simulated time series data.  
start_event: Determine the starting point for each time series.  
start_value_rho: Extract the Lag 1 value from the ACF of the residuals of a...  
summary_data: Print a descriptive summary of a data frame.  
timeBins: Label timestamps as timebins of a given binsize.  
wald_gam: Function for posthoc comparison of the contrasts in a single... 
Functions  

acf_n_plots  Man page Source code 
acf_plot  Man page Source code 
acf_resid  Man page Source code 
check_resid  Man page Source code 
compareML  Man page Source code 
convertNonAlphanumeric  Man page Source code 
derive_timeseries  Man page Source code 
diagnostics  Man page Source code 
diff_terms  Man page Source code 
eeg  Man page 
fadeRug  Man page Source code 
find_difference  Man page Source code 
fvisgam  Man page Source code 
gamtabs  Man page Source code 
get_coefs  Man page Source code 
get_difference  Man page Source code 
get_fitted  Man page Source code 
get_modelterm  Man page Source code 
get_pca_predictions  Man page Source code 
get_predictions  Man page Source code 
get_random  Man page Source code 
info  Man page Source code 
infoMessages  Man page Source code 
inspect_random  Man page Source code 
itsadug  Man page 
itsadugpackage  Man page 
missing_est  Man page Source code 
onAttach  Source code 
plotDiff  Man page 
plotDiff2D  Man page 
plot_data  Man page Source code 
plot_diff  Man page Source code 
plot_diff2  Man page Source code 
plot_modelfit  Man page Source code 
plot_parametric  Man page Source code 
plot_pca_surface  Man page Source code 
plot_smooth  Man page Source code 
plot_topo  Man page Source code 
print_summary  Man page Source code 
pvisgam  Man page Source code 
report_stats  Man page Source code 
resid.gam  Man page 
resid_gam  Man page Source code 
rug_model  Man page Source code 
simdat  Man page 
start_event  Man page Source code 
start_value_rho  Man page Source code 
summary_data  Man page Source code 
timeBins  Man page Source code 
wald_gam  Man page Source code 
Files  

inst
 
inst/CITATION
 
inst/NEWS
 
inst/doc
 
inst/doc/inspect.Rmd  
inst/doc/inspect.R  
inst/doc/test.html
 
inst/doc/inspect.html
 
inst/doc/acf.R  
inst/doc/acf.html
 
inst/doc/test.R  
inst/doc/test.Rmd  
inst/doc/acf.Rmd  
NAMESPACE
 
data
 
data/eeg.rda
 
data/simdat.rda
 
R
 
R/pca.R  
R/inspect.R  
R/eval.R  
R/plot.R  
R/predict.R  
R/acf.R  
R/itsadug.R  
R/data.R  
R/test.R  
R/util.R  
vignettes
 
vignettes/inspect.Rmd  
vignettes/bibliography.bib
 
vignettes/test.Rmd  
vignettes/acf.Rmd  
MD5
 
build
 
build/vignette.rds
 
DESCRIPTION
 
man
 
man/plot_diff2.Rd  
man/acf_resid.Rd  
man/infoMessages.Rd  
man/start_value_rho.Rd  
man/compareML.Rd  
man/acf_plot.Rd  
man/pvisgam.Rd  
man/acf_n_plots.Rd  
man/summary_data.Rd  
man/derive_timeseries.Rd  
man/plot_topo.Rd  
man/get_fitted.Rd  
man/inspect_random.Rd  
man/convertNonAlphanumeric.Rd  
man/resid_gam.Rd  
man/plot_data.Rd  
man/get_modelterm.Rd  
man/find_difference.Rd  
man/fvisgam.Rd  
man/get_pca_predictions.Rd  
man/get_coefs.Rd  
man/print_summary.Rd  
man/eeg.Rd  
man/get_predictions.Rd  
man/get_random.Rd  
man/plot_diff.Rd  
man/fadeRug.Rd  
man/diagnostics.Rd  
man/plot_modelfit.Rd  
man/wald_gam.Rd  
man/info.Rd  
man/simdat.Rd  
man/timeBins.Rd  
man/plot_pca_surface.Rd  
man/missing_est.Rd  
man/report_stats.Rd  
man/plot_smooth.Rd  
man/gamtabs.Rd  
man/start_event.Rd  
man/get_difference.Rd  
man/plot_parametric.Rd  
man/rug_model.Rd  
man/diff_terms.Rd  
man/check_resid.Rd  
man/itsadug.Rd 
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