# Visualisations for Generalized Additive Models

## Documentation for package ‘mgcViz’ version 0.2.0

- 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.nested1D | Plotting one dimensional nested 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)