Package: MRFtools 0.0-3

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]

# Install 'MRFtools' in R:

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

On CRAN:

Last updated from:1193d58ed7. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	239
source / vignettes	OK	280
linux-release	OK	244
macos-release	OK	231
macos-oldrel	OK	187
windows-devel	OK	179
windows-release	OK	159
windows-oldrel	OK	209
wasm-release	OK	170

Last update: 2026-03-25
Started: 2026-03-25

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.list
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 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.dendrogram_mrf_penalty
Plot a thing	visualize.fully_connected_graph_mrf_penalty
Plot a thing	visualize.sequential_mrf_penalty