Package: MRFtools 0.0-6

Eric J. Pedersen

MRFtools: Tools for Constructing and Plotting Markov Random Fields in R for Graphical Data

Utility functions for using Markov Random Field smooths in Generalized Additive Models fitted with the 'mgcv' package.

Authors:Eric J. Pedersen [aut, cre], Gavin L. Simpson [aut], Valentin Lucet [ctb]

MRFtools_0.0-6.tar.gz
MRFtools_0.0-6.zip(r-4.7-any)MRFtools_0.0-6.zip(r-4.6-any)MRFtools_0.0-6.zip(r-4.5-any)
MRFtools_0.0-6.tgz(r-4.6-any)MRFtools_0.0-6.tgz(r-4.5-any)
MRFtools_0.0-6.tar.gz(r-4.7-any)MRFtools_0.0-6.tar.gz(r-4.6-any)
MRFtools_0.0-6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MRFtools/json (API)

# Install 'MRFtools' in R:

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

Bug tracker:https://github.com/gam-mafia/mrftools/issues

On CRAN:

generalized-additive-models markov-r mgcv spline quarto

5.46 score 24 stars 16 scripts 13 exports 96 dependencies

Last updated from:6e1d332d09. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	245
source / vignettes	OK	289
linux-release	OK	232
macos-release	OK	313
macos-oldrel	OK	264
windows-devel	OK	215
windows-release	OK	191
windows-oldrel	OK	211
wasm-release	OK	167

Exports:as_mrf_penalty get_config get_labels get_model get_mrf get_obj get_penalty get_type mrf_config mrf_penalty vis visualise visualize

Dependencies:ade4 ape askpass assertthat base64enc BH cachem class classInt cli colorspace cpp11 crayon curl DBI digest dplyr e1071 farver fastmap generics ggforce ggokabeito ggplot2 ggraph ggrepel glue graphlayouts gratia gridExtra gtable hms httr igraph isoband jsonlite KernSmooth labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime mirai mvnfast nanonext nlme openssl patchwork phylobase pillar pixmap pkgconfig plyr polyclip prettyunits progress proxy purrr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang rncl RNeXML s2 S7 scales sf sp statmod stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tweedie tweenr units utf8 uuid vctrs viridis viridisLite withr wk XML xml2

Vignette's Title

Installing MRFtools | Setup | Discrete random walks | Creating $\mathbf{S}$ | Creating the data | Fitting the model | Visualising the fitted smooth | Phylogenetic smooths | The role of internal nodes for phylogenetic smoothers | References

Rendered fromMRFtools.qmdusingquarto::html

Last update: 2026-04-24
Started: 2026-03-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create a '"mrf_penalty"' object from a matrix and a config	as_mrf_penalty
Convert a MRF penalty object to a matrix	as.matrix.mrf_penalty
Extract configuration details of an MRF penalty	get_config
Extract MRF node labels from an MRF penalty	get_labels
Extract the model type and parameters from an MRF penalty	get_model
Extract a fitted MRF	get_mrf get_mrf.bam get_mrf.gam get_mrf.gamm get_mrf.gamm4
Extract the original object used to construct an MRF penalty	get_obj get_obj.mrf_config get_obj.mrf_penalty
Extract a MRF penalty matrix	get_penalty get_penalty.mrf_penalty
Extract the type of MRF from the penalty	get_type get_type.mrf_config get_type.mrf_penalty
MRF penalty configuration data	mrf_config
Markov Random Field Penalty	mrf_penalty
MRF penalty from a dendrogram	mrf_penalty.dendrogram
Fully connected graph and random effect MRF penalties from a factor	mrf_penalty.factor
MRF penalty from a hclust object	mrf_penalty.hclust
Continuous-time random walk MRF penalty from a numeric vector	mrf_penalty.numeric
MRF penalty from a phylogeny	mrf_penalty.phylo
MRF penalty from a phylogeny from a phylo4 object	mrf_penalty.phylo4
MRF penalty from polygon or multi-polygon simple features	mrf_penalty.sf
MRF penalty from a SpatialPolygons	mrf_penalty.SpatialPolygons
MRF penalty from a SpatialPoylgonsDataFrame	mrf_penalty.SpatialPolygonsDataFrame
Visualize a data set or object	vis visualise
Visualizing penalty matrix or graph object for a cyclic 1D MRF	visualize.cyclic_mrf_penalty
Plot a thing	visualize.fully_connected_graph_mrf_penalty
Plot a thing	visualize.sequential_mrf_penalty
Plot a thing	visualize.tree_mrf_penalty