Package: mgcViz 0.2.2

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_0.2.2.tar.gz
mgcViz_0.2.2.zip(r-4.7)mgcViz_0.2.2.zip(r-4.6)mgcViz_0.2.2.zip(r-4.5)
mgcViz_0.2.2.tgz(r-4.6-any)mgcViz_0.2.2.tgz(r-4.5-any)
mgcViz_0.2.2.tar.gz(r-4.7-any)mgcViz_0.2.2.tar.gz(r-4.6-any)
mgcViz_0.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mgcViz/json (API)

# Install 'mgcViz' in R:

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

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

On CRAN:

10.50 score 82 stars 1 packages 976 scripts 5.5k downloads 6 mentions 95 exports 62 dependencies

Last updated from:1655df6e57. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	277
source / vignettes	OK	237
linux-release-x86_64	OK	255
macos-release-arm64	OK	228
macos-oldrel-arm64	OK	186
windows-devel	OK	240
windows-release	OK	244
windows-oldrel	OK	247
wasm-release	OK	144

Exports:ALE ALE.gam bamV check.gamViz check0D check1D check2D fix.family.cdf gamm4V gammV gamV getGam getViz gridPrint l_bound l_ciBar l_ciLine l_ciPoly l_clusterLine l_coordContour l_dens l_dens1D l_dens2D l_densCheck l_fitBar l_fitContour l_fitDens l_fitLine l_fitPoints l_fitRaster l_glyphs2D l_gridCheck1D l_gridCheck2D l_gridQCheck1D l_gridQCheck2D l_hist l_points l_poly l_pvContour l_pvRaster l_rug l_simLine l_vline listLayers mqgamV plot.ALE1D plot.fs.interaction.1D plot.gamViz plot.mgamViz plot.mgcv.smooth.1D plot.mgcv.smooth.2D plot.mgcv.smooth.MD plot.mrf.smooth plot.multi.mgcv.smooth.1D plot.multi.mgcv.smooth.2D plot.multi.ptermFactor plot.multi.ptermLogical plot.multi.ptermNumeric plot.multi.random.effect plot.nested1D plot.ptermFactor plot.ptermInteraction plot.ptermLogical plot.ptermMatrixNumeric plot.ptermNumeric plot.random.effect plot.sos.smooth plotDiff plotDiff.mgcv.smooth.1D plotDiff.mgcv.smooth.2D plotDiff.sos.smooth plotRGL plotRGL.mgcv.smooth.2D plotRGL.mgcv.smooth.MD plotSlice postSim print.checkGam print.plotGam print.plotSmooth print.qqGam pterm qgamV qq qq.gamViz qqline qqnorm qqplot residuals.gamViz shine shine.qqGam simulate.gam sm zoom zoom.qqGam zto1

Dependencies:boot cli codetools cpp11 crayon doParallel dplyr farver forcats foreach gamm4 generics GGally ggplot2 ggstats glue gridExtra gtable hms isoband iterators KernSmooth labeling lattice lifecycle lme4 magrittr MASS Matrix matrixStats mgcv minqa nlme nloptr patchwork pillar pkgconfig plyr prettyunits progress purrr qgam R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr

An introduction to mgcViz: visual tools for GAMs

Rendered frommgcviz.rmdusingknitr::rmarkdown

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

Help page	Topics
Generic function for Accumulated Local Effect (ALE)	ALE
Create Accumulated Local Effects (ALE) for GAMs	ALE.gam
Fit a GAM model and get a gamViz object	bamV gamV
Some diagnostics for a fitted gam model	check.gamViz
Checking GAM simulated residuals or responses	check0D
Checking GAM residuals or responses along one covariate	check1D
Checking GAM residuals along two covariates	check2D
Getting the CDF of a gam family	fix.family.cdf
Fit a GAMM or GAMM4 model and get a gamViz object	gamm4V gammV
Convert gamViz object to gamObject	getGam
Converting gam objects to gamViz objects	getViz
Plotting plotSmooth objects on a grid	gridPrint
Add boundaries to smooth effect plot	l_bound
Adding confidence intervals to barplots	l_ciBar
Adding confidence intervals to effect plot	l_ciLine
Adding confidence band to effect plots	l_ciPoly
Cluster and plot smooth effects	l_clusterLine
Adding coordinate lines	l_coordContour
Adding density estimate to a plot	l_dens1D
Adding density estimate heatmap	l_dens l_dens2D
Checking residuals conditional density	l_densCheck
Adding barplot to effect plots	l_fitBar
Adding fitted effect contour lines	l_fitContour
Adding density strip of fitted effect	l_fitDens
Add fitted smooth effect curve	l_fitLine
Adding points representing the fitted effect	l_fitPoints
Adding raster representing the fitted effect	l_fitRaster
Adding glyphs to 2D plots	l_glyphs2D
Binning and checking GAM residuals	l_gridCheck1D
Binning and checking GAM residuals	l_gridCheck2D
Checking sign of residuals along one covariate	l_gridQCheck1D
Binning and checking QGAM residuals	l_gridQCheck2D
Adding histogram to a plot	l_hist
Add points to plot	l_points
Add polygons to effect plots	l_poly
Adding contour of p-values	l_pvContour
Adding raster or heat-map of p-values	l_pvRaster
Adding rug to margins of a plot	l_rug
Add simulated smooth effect curves	l_simLine
Adding vertical line to a plot	l_vline
Lists available layers for plotSmooth objects	listLayers
Fit multiple QGAM models and get a mgamViz object	mqgamV
Plot 1D Accumulated Local Effects (ALE)	plot.ALE1D
Plotting one dimensional smooth factor interactions	plot.fs.interaction.1D
Basic GAM plotting	plot.gamViz
Plotting multiple quantile GAMs	plot.mgamViz
Plotting one dimensional smooth effects	plot.mgcv.smooth.1D plot.multi.mgcv.smooth.1D
Plotting two dimensional smooth effects	plot.mgcv.smooth.2D plot.multi.mgcv.smooth.2D
Plotting slice of higher-dimensional smooth effects	plot.mgcv.smooth.MD
Plotting Markov random field smooths	plot.mrf.smooth
Plotting factor or logical parametric effects	plot.multi.ptermFactor plot.multi.ptermLogical plot.ptermFactor plot.ptermLogical
Plotting random effects	plot.multi.random.effect plot.random.effect
Plotting one dimensional nested effects	plot.nested1D
Plotting parametric interactions	plot.multi.ptermInteraction plot.ptermInteraction
Plotting numeric parametric effects	plot.multi.ptermNumeric plot.ptermMatrixNumeric plot.ptermNumeric
Plotting smooths on the sphere	plot.sos.smooth
Generic plotting of differences	plotDiff
Plotting differences between two 1D smooth effects	plotDiff.mgcv.smooth.1D
Plotting differences between two 2D smooth effects	plotDiff.mgcv.smooth.2D
Plotting differences between two smooths on the sphere	plotDiff.sos.smooth
Generic RGL plotting function	plotRGL
Visualizing 2D smooth effects in 3D	plotRGL.mgcv.smooth.2D
Visualizing a 2D slice of a smooth effects in 3D	plotRGL.mgcv.smooth.MD
Plotting sequence of slices of 2D smooth effect	plotSlice
Posterior simulation from a GAM object	postSim
Printing the output of check.gamViz	print.checkGam
Printing the output of plot.gamViz	print.plotGam
Printing plots of smooth effects	print.plotSmooth
Printing the output of qq.gamViz	print.qqGam
Extracting parametric effects from a GAM model	pterm
Fit a QGAM model and get a gamViz object	qgamV
Generic QQ plots	qq
QQ plots for gam model residuals	qq.gamViz
Quantile-Quantile Plots	qqline qqnorm qqplot qqplots
Generalized Additive Model residuals	residuals.gamViz
Generic shine function	shine
Shiny QQ-plots for GAMs	shine.qqGam
Simulating responses from a GAM object	simulate.gam
Extracting a smooth effect from a GAM model	sm
Generic zooming function	zoom
Efficiently zooming on GAM QQ-plots	zoom.qqGam
Constructing a decreasing function from (0,1) to (0,1)	zto1

Package: mgcViz 0.2.2

mgcViz: Visualisations for Generalized Additive Models

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