Package: MRFcov 1.0.39

MRFcov: Markov Random Fields with Additional Covariates

Approximate node interaction parameters of Markov Random Fields graphical networks. Models can incorporate additional covariates, allowing users to estimate how interactions between nodes in the graph are predicted to change across covariate gradients. The general methods implemented in this package are described in Clark et al. (2018) <doi:10.1002/ecy.2221>.

Authors:Nicholas J Clark [aut, cre], Konstans Wells [aut], Oscar Lindberg [aut]

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MRFcov.pdf |MRFcov.html✨
MRFcov/json (API)
NEWS

# Install 'MRFcov' in R:

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

Bug tracker:https://github.com/nicholasjclark/mrfcov/issues

Datasets:

Bird.parasites - Blood parasite occurrences in New Caledonian birds.

On CRAN:

conditional-random-fields graphical-models machine-learning markov-random-field multivariate-analysis multivariate-statistics network-analysis networks

6.03 score 24 stars 30 scripts 299 downloads 11 exports 82 dependencies

Last updated 11 months agofrom:91d77124c0. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 20 2025
R-4.5-win	OK	Feb 20 2025
R-4.5-mac	OK	Feb 20 2025
R-4.5-linux	OK	Feb 20 2025
R-4.4-win	OK	Feb 20 2025
R-4.4-mac	OK	Feb 20 2025
R-4.3-win	OK	Feb 20 2025
R-4.3-mac	OK	Feb 20 2025

Exports:bootstrap_MRF cv_MRF_diag cv_MRF_diag_rep cv_MRF_diag_rep_spatial MRFcov MRFcov_spatial plotMRF_hm predict_MRF predict_MRFnetworks prep_MRF_covariates prep_MRF_covariates_spatial

Dependencies:caret class cli clock codetools colorspace cpp11 data.table diagram digest dplyr e1071 fansi farver foreach future future.apply generics ggplot2 glmnet globals glue gower gridExtra gtable hardhat igraph ipred isoband iterators KernSmooth labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix mgcv ModelMetrics munsell nlme nnet numDeriv parallelly pbapply pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp RcppEigen recipes reshape2 rlang rpart scales sfsmisc shape sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr

Gaussian and Poisson CRFs

Rendered fromGaussian_Poisson_CRFs.Rmdusingknitr::rmarkdownon Feb 20 2025.

Last update: 2023-01-12
Started: 2018-08-27

MRFs and CRFs for Bird.parasites data

Rendered fromBird_Parasite_CRF.Rmdusingknitr::rmarkdownon Feb 20 2025.

Last update: 2023-04-04
Started: 2018-03-04

Prepping datasets for CRF models

Rendered fromCRF_data_prep.Rmdusingknitr::rmarkdownon Feb 20 2025.

Last update: 2023-01-12
Started: 2018-03-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Blood parasite occurrences in New Caledonian birds.	Bird.parasites
Bootstrap observations to estimate MRF parameter coefficients	bootstrap_MRF
MRF cross validation and assessment of predictive performance	cv_MRF_diag cv_MRF_diag_rep cv_MRF_diag_rep_spatial
Markov Random Fields with covariates	MRFcov
Spatially structured Markov Random Fields with covariates	MRFcov_spatial
Plot MRF interaction parameters as a heatmap	plotMRF_hm
Predict training observations from fitted MRFcov models	predict_MRF
Extract predicted network metrics for observations in a given dataset using equations from a fitted 'MRFcov' object	predict_MRFnetworks
Cross-multiply response and covariate variables	prep_MRF_covariates
Cross-multiply response and covariate variables and build spatial splines	prep_MRF_covariates_spatial