itsadug: Interpreting Time Series and Autocorrelated Data Using GAMMs

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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
2016-06-13 13:07:04
Maintainer
Jacolien van Rij <vanrij.jacolien@gmail.com>
License
GPL (>= 2)
Version
2.2

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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 post-hoc comparison of the contrasts in a single...

Files in this package

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