Package: mgcViz 0.1.11

mgcViz: Visualisations for Generalized Additive Models

Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.

Authors:Matteo Fasiolo [aut, cre], Raphael Nedellec [aut], Yannig Goude [ctb], Christian Capezza [ctb], Simon N. Wood [ctb]

mgcViz_0.1.11.tar.gz
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mgcViz.pdf |mgcViz.html✨
mgcViz/json (API)

# Install 'mgcViz' in R:
install.packages('mgcViz', repos = c('https://mfasiolo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mfasiolo/mgcviz/issues

On CRAN:

8.83 score 76 stars 920 scripts 2.4k downloads 95 exports 83 dependencies

Last updated 2 months agofrom:1672b4eba2. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 29 2024
R-4.4-winWARNINGOct 29 2024
R-4.4-macWARNINGOct 29 2024
R-4.3-winWARNINGOct 29 2024
R-4.3-macWARNINGOct 29 2024

Exports:ALEALE.gambamVcheck.gamVizcheck0Dcheck1Dcheck2Dfix.family.cdfgamm4VgammVgamVgetGamgetVizgridPrintl_boundl_ciBarl_ciLinel_ciPolyl_clusterLinel_coordContourl_densl_dens1Dl_dens2Dl_densCheckl_fitBarl_fitContourl_fitDensl_fitLinel_fitPointsl_fitRasterl_glyphs2Dl_gridCheck1Dl_gridCheck2Dl_gridQCheck1Dl_gridQCheck2Dl_histl_pointsl_polyl_pvContourl_pvRasterl_rugl_simLinel_vlinelistLayersmqgamVplot.ALE1Dplot.fs.interaction.1Dplot.gamVizplot.mgamVizplot.mgcv.smooth.1Dplot.mgcv.smooth.2Dplot.mgcv.smooth.MDplot.mrf.smoothplot.multi.mgcv.smooth.1Dplot.multi.mgcv.smooth.2Dplot.multi.ptermFactorplot.multi.ptermLogicalplot.multi.ptermNumericplot.multi.random.effectplot.nested1Dplot.ptermFactorplot.ptermInteractionplot.ptermLogicalplot.ptermMatrixNumericplot.ptermNumericplot.random.effectplot.sos.smoothplotDiffplotDiff.mgcv.smooth.1DplotDiff.mgcv.smooth.2DplotDiff.sos.smoothplotRGLplotRGL.mgcv.smooth.2DplotRGL.mgcv.smooth.MDplotSlicepostSimprint.checkGamprint.plotGamprint.plotSmoothprint.qqGamptermqgamVqqqq.gamVizqqlineqqnormqqplotresiduals.gamVizshineshine.qqGamsimulate.gamsmzoomzoom.qqGamzto1

Dependencies:base64encbootbslibcachemclicodetoolscolorspacecommonmarkcpp11crayondigestdoParalleldplyrfansifarverfastmapfontawesomeforcatsforeachfsgamm4genericsGGallyggplot2ggstatsgluegridExtragtablehmshtmltoolshttpuvisobanditeratorsjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclelme4magrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUIminqamunsellnlmenloptrpatchworkpillarpkgconfigplyrprettyunitsprogresspromisespurrrqgamR6rappdirsRColorBrewerRcppRcppEigenrlangsassscalesshinysourcetoolsstringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithrxtable

An introduction to mgcViz: visual tools for GAMs

Matteo Fasiolo and Raphael Nedellec

Rendered frommgcviz.rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2022-06-13
Started: 2017-10-03

Readme and manuals

Help Manual

Help pageTopics
Generic function for Accumulated Local Effect (ALE)ALE
Create Accumulated Local Effects (ALE) for GAMsALE.gam
Fit a GAM model and get a gamViz objectbamV gamV
Some diagnostics for a fitted gam modelcheck.gamViz
Checking GAM simulated residuals or responsescheck0D
Checking GAM residuals or responses along one covariatecheck1D
Checking GAM residuals along two covariatescheck2D
Getting the CDF of a gam familyfix.family.cdf
Fit a GAMM or GAMM4 model and get a gamViz objectgamm4V gammV
Convert gamViz object to gamObjectgetGam
Converting gam objects to gamViz objectsgetViz
Plotting plotSmooth objects on a gridgridPrint
Add boundaries to smooth effect plotl_bound
Adding confidence intervals to barplotsl_ciBar
Adding confidence intervals to effect plotl_ciLine
Adding confidence band to effect plotsl_ciPoly
Cluster and plot smooth effectsl_clusterLine
Adding coordinate linesl_coordContour
Adding density estimate to a plotl_dens1D
Adding density estimate heatmapl_dens l_dens2D
Checking residuals conditional densityl_densCheck
Adding barplot to effect plotsl_fitBar
Adding fitted effect contour linesl_fitContour
Adding density strip of fitted effectl_fitDens
Add fitted smooth effect curvel_fitLine
Adding points representing the fitted effectl_fitPoints
Adding raster representing the fitted effectl_fitRaster
Adding glyphs to 2D plotsl_glyphs2D
Binning and checking GAM residualsl_gridCheck1D
Binning and checking GAM residualsl_gridCheck2D
Checking sign of residuals along one covariatel_gridQCheck1D
Binning and checking QGAM residualsl_gridQCheck2D
Adding histogram to a plotl_hist
Add points to plotl_points
Add polygons to effect plotsl_poly
Adding contour of p-valuesl_pvContour
Adding raster or heat-map of p-valuesl_pvRaster
Adding rug to margins of a plotl_rug
Add simulated smooth effect curvesl_simLine
Adding vertical line to a plotl_vline
Lists available layers for plotSmooth objectslistLayers
Fit multiple QGAM models and get a mgamViz objectmqgamV
Plot 1D Accumulated Local Effects (ALE)plot.ALE1D
Plotting one dimensional smooth factor interactionsplot.fs.interaction.1D
Basic GAM plottingplot.gamViz
Plotting multiple quantile GAMsplot.mgamViz
Plotting one dimensional smooth effectsplot.mgcv.smooth.1D plot.multi.mgcv.smooth.1D
Plotting two dimensional smooth effectsplot.mgcv.smooth.2D plot.multi.mgcv.smooth.2D
Plotting slice of higher-dimensional smooth effectsplot.mgcv.smooth.MD
Plotting Markov random field smoothsplot.mrf.smooth
Plotting factor or logical parametric effectsplot.multi.ptermFactor plot.multi.ptermLogical plot.ptermFactor plot.ptermLogical
Plotting random effectsplot.multi.random.effect plot.random.effect
Plotting one dimensional nested effectsplot.nested1D
Plotting parametric interactionsplot.multi.ptermInteraction plot.ptermInteraction
Plotting numeric parametric effectsplot.multi.ptermNumeric plot.ptermMatrixNumeric plot.ptermNumeric
Plotting smooths on the sphereplot.sos.smooth
Generic plotting of differencesplotDiff
Plotting differences between two 1D smooth effectsplotDiff.mgcv.smooth.1D
Plotting differences between two 2D smooth effectsplotDiff.mgcv.smooth.2D
Plotting differences between two smooths on the sphereplotDiff.sos.smooth
Generic RGL plotting functionplotRGL
Visualizing 2D smooth effects in 3DplotRGL.mgcv.smooth.2D
Visualizing a 2D slice of a smooth effects in 3DplotRGL.mgcv.smooth.MD
Plotting sequence of slices of 2D smooth effectplotSlice
Posterior simulation from a GAM objectpostSim
Printing the output of check.gamVizprint.checkGam
Printing the output of plot.gamVizprint.plotGam
Printing plots of smooth effectsprint.plotSmooth
Printing the output of qq.gamVizprint.qqGam
Extracting parametric effects from a GAM modelpterm
Fit a QGAM model and get a gamViz objectqgamV
Generic QQ plotsqq
QQ plots for gam model residualsqq.gamViz
Quantile-Quantile Plotsqqline qqnorm qqplot qqplots
Generalized Additive Model residualsresiduals.gamViz
Generic shine functionshine
Shiny QQ-plots for GAMsshine.qqGam
Simulating responses from a GAM objectsimulate.gam
Extracting a smooth effect from a GAM modelsm
Generic zooming functionzoom
Efficiently zooming on GAM QQ-plotszoom.qqGam
Constructing a decreasing function from (0,1) to (0,1)zto1