Package: bartMan 0.2.1

Alan Inglis

bartMan: Create Visualisations for BART Models

Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.

Authors:Alan Inglis [aut, cre], Andrew Parnell [aut], Catherine Hurley [aut], Claus Wilke [ctb]

bartMan_0.2.1.tar.gz
bartMan_0.2.1.tar.gz(r-4.7-any)bartMan_0.2.1.tar.gz(r-4.6-any)
bartMan_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bartMan/json (API)

# Install 'bartMan' in R:

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

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

Datasets:

input_data - Input_data
tree_data_example - Tree_data_example

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openjdk

2.20 score 16 scripts 315 downloads 41 exports 110 dependencies

Last updated from:4d0a3c46d1. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	209
source / vignettes	OK	211
linux-release-x86_64	OK	217
wasm-release	OK	184

Exports:acceptRate bartClassifDiag bartDiag bartRegrDiag bartReorder bivariate_range bivariate_scale clusterTrees combineDummy extractTreeData getChildren getObservations guide_colorfan guide_colourfan localProcedure mdsBart node_depth pal_vsup permVimp permVint plotProximity plotSingleTree plotTrees proximityMatrix RangeBivariate ScaleBivariate sort_trees_by_depthMax splitDensity terminalFunction train_bivariate tree_dataframe treeBarPlot treeDepth treeList treeNodes vimpBart vimpPlot vintPlot viviBart viviBartMatrix viviBartPlot

Dependencies:backports BART bartMachine bartMachineJARs base64enc bslib ca cachem checkmate cli cluster codetools colorspace cowplot cpp11 dbarts DendSer digest doRNG dplyr evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs gclus gdtools generics ggforce ggiraph ggnewscale ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable highr htmltools htmlwidgets igraph isoband iterators itertools jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime missForest nlme patchwork permute pillar pkgconfig polyclip purrr qap R6 randomForest ranger rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack registry rJava rlang rmarkdown rngtools rrapply S7 sass scales seriation stringi stringr survival systemfonts tibble tidygraph tidyr tidyselect tinytex TSP tweenr utf8 vctrs vegan viridis viridisLite withr xfun yaml

Help page	Topics
acceptRate	acceptRate
bartClassifDiag	bartClassifDiag
bartDiag	bartDiag
bartRegrDiag	bartRegrDiag
bartReorder	bartReorder
Cluster Trees by Variable	clusterTrees
Update Dummy Variable Names	combineDummy
extractTreeData	extractTreeData
Determines the stump color for a legend based on its mean value	get_stump_colour_for_legend
Generate Child and Parent Node Relationships	getChildren
Get Observations Falling into Each Node	getObservations
Colourfan guide	guide_colorfan guide_colourfan
input_data	input_data
localProcedure	localProcedure
mdsBart	mdsBart
Calculate Node Depths in a Tree Data Frame	node_depth
Variance suppressing uncertainty palette	pal_vsup
permVimp	permVimp
permVint	permVint
plotProximity	plotProximity
plotSingleTree	plotSingleTree
Plot Trees with Customisations	plotTrees
print.hideHelper	print.hideHelper1
proximityMatrix	proximityMatrix
Constructor for bivariate range object	bivariate_range RangeBivariate
Constructor for bivariate scale object	bivariate_scale ScaleBivariate
Sort Trees by Maximum Depth	sort_trees_by_depthMax
splitDensity	splitDensity
Generate Terminal Node Indicator	terminalFunction
Train range for bivariate scale	train_bivariate
tree_data_example	tree_data_example
Transform tree data into a structured dataframe	tree_dataframe
Plot Frequency of Tree Structures	treeBarPlot
treeDepth	treeDepth
Generate a List of Tree Structures from BART Model Output	treeList
treeNodes	treeNodes
vimpBart	vimpBart
vimpPlot	vimpPlot
vintPlot	vintPlot
viviBart	viviBart
viviBartMatrix	viviBartMatrix
viviBartPlot	viviBartPlot

Package: bartMan 0.2.1

bartMan: Create Visualisations for BART Models

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)