Visualisations for Generalized Additive Models

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Documentation for package ‘mgcViz’ version 0.1.11

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ALE	Generic function for Accumulated Local Effect (ALE)
ALE.gam	Create Accumulated Local Effects (ALE) for GAMs
bamV	Fit a GAM model and get a gamViz object
check.gamViz	Some diagnostics for a fitted gam model
check0D	Checking GAM simulated residuals or responses
check1D	Checking GAM residuals or responses along one covariate
check2D	Checking GAM residuals along two covariates
fix.family.cdf	Getting the CDF of a gam family
gamm4V	Fit a GAMM or GAMM4 model and get a gamViz object
gammV	Fit a GAMM or GAMM4 model and get a gamViz object
gamV	Fit a GAM model and get a gamViz object
getGam	Convert gamViz object to gamObject
getViz	Converting gam objects to gamViz objects
gridPrint	Plotting plotSmooth objects on a grid
listLayers	Lists available layers for plotSmooth objects
l_bound	Add boundaries to smooth effect plot
l_ciBar	Adding confidence intervals to barplots
l_ciLine	Adding confidence intervals to effect plot
l_ciPoly	Adding confidence band to effect plots
l_clusterLine	Cluster and plot smooth effects
l_coordContour	Adding coordinate lines
l_dens	Adding density estimate heatmap
l_dens1D	Adding density estimate to a plot
l_dens2D	Adding density estimate heatmap
l_densCheck	Checking residuals conditional density
l_fitBar	Adding barplot to effect plots
l_fitContour	Adding fitted effect contour lines
l_fitDens	Adding density strip of fitted effect
l_fitLine	Add fitted smooth effect curve
l_fitPoints	Adding points representing the fitted effect
l_fitRaster	Adding raster representing the fitted effect
l_glyphs2D	Adding glyphs to 2D plots
l_gridCheck1D	Binning and checking GAM residuals
l_gridCheck2D	Binning and checking GAM residuals
l_gridQCheck1D	Checking sign of residuals along one covariate
l_gridQCheck2D	Binning and checking QGAM residuals
l_hist	Adding histogram to a plot
l_points	Add points to plot
l_poly	Add polygons to effect plots
l_pvContour	Adding contour of p-values
l_pvRaster	Adding raster or heat-map of p-values
l_rug	Adding rug to margins of a plot
l_simLine	Add simulated smooth effect curves
l_vline	Adding vertical line to a plot
mqgamV	Fit multiple QGAM models and get a mgamViz object
plot.ALE1D	Plot 1D Accumulated Local Effects (ALE)
plot.fs.interaction.1D	Plotting one dimensional smooth factor interactions
plot.gamViz	Basic GAM plotting
plot.mgamViz	Plotting multiple quantile GAMs
plot.mgcv.smooth.1D	Plotting one dimensional smooth effects
plot.mgcv.smooth.2D	Plotting two dimensional smooth effects
plot.mgcv.smooth.MD	Plotting slice of higher-dimensional smooth effects
plot.mrf.smooth	Plotting Markov random field smooths
plot.multi.mgcv.smooth.1D	Plotting one dimensional smooth effects
plot.multi.mgcv.smooth.2D	Plotting two dimensional smooth effects
plot.multi.ptermFactor	Plotting factor or logical parametric effects
plot.multi.ptermInteraction	Plotting parametric interactions
plot.multi.ptermLogical	Plotting factor or logical parametric effects
plot.multi.ptermNumeric	Plotting numeric parametric effects
plot.multi.random.effect	Plotting random effects
plot.ptermFactor	Plotting factor or logical parametric effects
plot.ptermInteraction	Plotting parametric interactions
plot.ptermLogical	Plotting factor or logical parametric effects
plot.ptermMatrixNumeric	Plotting numeric parametric effects
plot.ptermNumeric	Plotting numeric parametric effects
plot.random.effect	Plotting random effects
plot.sos.smooth	Plotting smooths on the sphere
plotDiff	Generic plotting of differences
plotDiff.mgcv.smooth.1D	Plotting differences between two 1D smooth effects
plotDiff.mgcv.smooth.2D	Plotting differences between two 2D smooth effects
plotDiff.sos.smooth	Plotting differences between two smooths on the sphere
plotRGL	Generic RGL plotting function
plotRGL.mgcv.smooth.2D	Visualizing 2D smooth effects in 3D
plotRGL.mgcv.smooth.MD	Visualizing a 2D slice of a smooth effects in 3D
plotSlice	Plotting sequence of slices of 2D smooth effect
postSim	Posterior simulation from a GAM object
print.checkGam	Printing the output of check.gamViz
print.plotGam	Printing the output of plot.gamViz
print.plotSmooth	Printing plots of smooth effects
print.qqGam	Printing the output of qq.gamViz
pterm	Extracting parametric effects from a GAM model
qgamV	Fit a QGAM model and get a gamViz object
qq	Generic QQ plots
qq.gamViz	QQ plots for gam model residuals
qqline	Quantile-Quantile Plots
qqnorm	Quantile-Quantile Plots
qqplot	Quantile-Quantile Plots
qqplots	Quantile-Quantile Plots
residuals.gamViz	Generalized Additive Model residuals
shine	Generic shine function
shine.qqGam	Shiny QQ-plots for GAMs
simulate.gam	Simulating responses from a GAM object
sm	Extracting a smooth effect from a GAM model
zoom	Generic zooming function
zoom.qqGam	Efficiently zooming on GAM QQ-plots
zto1	Constructing a decreasing function from (0,1) to (0,1)