itsadug: Interpreting Time Series and Autocorrelated Data Using GAMMs
Version 2.2

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).

AuthorJacolien van Rij [aut, cre], Martijn Wieling [aut], R. Harald Baayen [aut], Hedderik van Rijn [ctb]
Date of publication2016-06-13 13:07:04
MaintainerJacolien van Rij <vanrij.jacolien@gmail.com>
LicenseGPL (>= 2)
Version2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("itsadug")

Getting started

Checking for and handling autocorrelation
Testing for significance
Visual inspection of GAMM models

Popular man pages

acf_resid: Generate an ACF plot of model residuals. Works for lm, lmer,...
compareML: Function for comparing two GAMM models.
gamtabs: Convert model summary into Latex/HTML table for knitr/R...
itsadug: Interpreting Time Series, Autocorrelated Data Using GAMMs...
plot_diff: Plot difference curve based on model predictions.
pvisgam: Visualization of partial nonlinear interactions.
resid_gam: Extract model residuals and remove the autocorrelation...
See all...

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 post-hoc 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
itsadug-package 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
itsadug documentation built on May 19, 2017, 7:11 p.m.

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