Package: MetricGraph 1.6.0.9000

MetricGraph: Random Fields on Metric Graphs

Facilitates creation and manipulation of metric graphs, such as street or river networks. Further facilitates operations and visualizations of data on metric graphs, and the creation of a large class of random fields and stochastic partial differential equations on such spaces. These random fields can be used for simulation, prediction and inference. In particular, linear mixed effects models including random field components can be fitted to data based on computationally efficient sparse matrix representations. Interfaces to the R packages 'INLA' and 'inlabru' are also provided, which facilitate working with Bayesian statistical models on metric graphs. The main references for the methods are Bolin, Simas and Wallin (2024) <doi:10.3150/23-BEJ1647>, Bolin, Kovacs, Kumar and Simas (2023) <doi:10.1090/mcom/3929> and Bolin, Simas and Wallin (2023) <doi:10.48550/arXiv.2304.03190> and <doi:10.48550/arXiv.2304.10372>.

Authors:David Bolin [cre, aut], Alexandre Simas [aut], Jonas Wallin [aut]

MetricGraph_1.6.0.9000.tar.gz
MetricGraph_1.6.0.9000.zip(r-4.7)MetricGraph_1.6.0.9000.zip(r-4.6)MetricGraph_1.6.0.9000.zip(r-4.5)
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manual.pdf |manual.html
card.svg |card.png
MetricGraph/json (API)
NEWS

# Install 'MetricGraph' in R:
install.packages('MetricGraph', repos = c('https://davidbolin.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/davidbolin/metricgraph/issues

Pkgdown/docs site:https://davidbolin.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • pems - Traffic speed data from San Jose, California
  • pems_repl - Traffic speed data with replicates from San Jose, California

On CRAN:

Conda:

cpp

6.80 score 22 stars 358 scripts 380 downloads 44 exports 64 dependencies

Last updated from:91d1d6425d. Checks:10 WARNING, 2 ERROR, 1 OK. Indexed: yes.

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macos-release-arm64WARNING797
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macos-oldrel-arm64WARNING580
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wasm-releaseOK229

Exports:%>%augmentCholeskycross_validationdrop_naexp_covariancefiltergg_dfglancegraph_bru_process_datagraph_componentsgraph_data_spdegraph_lgcp_simgraph_lmegraph_spdegraph_spde_basisgraph_spde_make_Agraph_starting_valueslgcp_graphlinnet.to.graphlogo_linesmake_Q_eulermake_Q_spacetimematch_mesh_datametric_graphmutateposterior_crossvalidationposterior_crossvalidation_looprecompute_lgcp_graphprocess_rspde_predictionspsp.to.graphsample_spdeselectselected_invsimulate_parallelsimulate_spacetimespde_covariancespde_metric_graph_resultspde_precisionspde_variancestlpp.to.graphsummarisetupdate_graph

Dependencies:backportsbroomclassclassIntclicodetoolscpp11DBIdeldirdoParalleldplyre1071farverfmesherforeachgenericsggnewscaleggplot2gluegtableigraphisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixpillarpkgconfigpolyclipproxypurrrR6RANNRColorBrewerRcppRcppEigenrlangrSPDEs2S7scalessfspspatstat.dataspatstat.geomspatstat.univarspatstat.utilssplancsstringistringrtibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkzoo

Readme and manuals

Help Manual

Help pageTopics
Gaussian processes on metric graphsMetricGraph-package MetricGraph
Augment data with information from a 'graph_lme' objectaugment augment.graph_lme
Metric graph 'inlabru' mapperbru_get_mapper.inla_metric_graph_spde bru_mapper.inla_metric_graph_spde ibm_jacobian.bru_mapper_inla_metric_graph_spde ibm_n.bru_mapper_inla_metric_graph_spde ibm_values.bru_mapper_inla_metric_graph_spde
Perform cross-validation on a list of fitted inlabru models on metric graphs.cross_validation
A version of 'tidyr::drop_na()' function for datasets on metric graphsdrop_na drop_na.metric_graph_data
Exponential covariance functionexp_covariance
A version of 'dplyr::filter()' function for datasets on metric graphsfilter filter.metric_graph_data
Data frame for metric_graph_spde_result objects to be used in 'ggplot2'gg_df gg_df.metric_graph_spde_result
Glance at a 'graph_lme' objectglance glance.graph_lme
Prepare data frames or data lists to be used with 'inlabru' in metric graphsgraph_bru_process_data
Data extraction for 'spde' modelsgraph_data_spde
Simulate log-Gaussian Cox processes on metric graphsgraph_lgcp_sim
Metric graph linear mixed effects modelsgraph_lme
'INLA' implementation of Whittle-Matérn fields for metric graphsgraph_spde
Deprecated - Observation/prediction matrices for 'SPDE' modelsgraph_spde_basis
Deprecated - Observation/prediction matrices for 'SPDE' modelsgraph_spde_make_A
Starting values for random field models on metric graphsgraph_starting_values
Fit log-Gaussian Cox process models on metric graphslgcp_graph
Convert a 'linnet' object to a metric graph objectlinnet.to.graph
Create lines for package namelogo_lines
Space-time precision operator Euler discretizationmake_Q_euler
Space-time precision operator discretizationmake_Q_spacetime
Match Data Frame Rows to Graph Mesh Ordermatch_mesh_data
Metric graphmetric_graph
A version of 'dplyr::mutate()' function for datasets on metric graphsmutate mutate.metric_graph_data
Traffic speed data from San Jose, Californiapems
Traffic speed data with replicates from San Jose, Californiapems_repl
Plot of predicted values with 'inlabru'plot.graph_bru_pred
Plot of processed predicted values with 'inlabru'plot.graph_bru_proc_pred
Cross-validation for 'graph_lme' models assuming observations at the vertices of metric graphsposterior_crossvalidation
Leave-one-out pseudo-crossvalidation for 'graph_lme' models assuming observations at the vertices of metric graphsposterior_crossvalidation_loo
Precompute expensive quantities for efficient LGCP model fittingprecompute_lgcp_graph
Prediction for a mixed effects regression model on a metric graphpredict.graph_lme
Predict method for 'inlabru' fits on Metric Graphspredict.inla_metric_graph_spde
Predict method for 'inlabru' fits on Metric Graphs for 'rSPDE' modelspredict.rspde_metric_graph
Process predictions of 'rspde_metric_graph' objects obtained by using 'inlabru'process_rspde_predictions
Convert a 'psp' object to a metric graph objectpsp.to.graph
Samples a Whittle-Matérn field on a metric graphsample_spde
A version of 'dplyr::select()' function for datasets on metric graphsselect select.metric_graph_data
Selected Inverse Calculationselected_inv
Parallel simulation of a Whittle-Matérn field on a metric graphsimulate_parallel
space-time simulation based on implicit Euler discretization in timesimulate_spacetime
Simulation of models on metric graphssimulate.graph_lme
Simulate a Whittle-Matérn field on a metric graphsimulate.metric_graph
Covariance function for Whittle-Matérn fieldsspde_covariance
Metric graph SPDE result extraction from 'INLA' estimation resultsspde_metric_graph_result
Precision matrix for Whittle-Matérn fieldsspde_precision
Variancefor Whittle-Matérn fieldsspde_variance
Convert an 'stlpp' object to a metric graph objectstlpp.to.graph
A version of 'dplyr::summarise()' function for datasets on metric graphssummarise summarise.metric_graph_data
Summary Method for 'graph_lme' Objectssummary.graph_lme
Summary Method for 'metric_graph' Objectssummary.metric_graph
Summary for posteriors of field parameters for an 'inla_rspde' model from a 'rspde.result' objectsummary.metric_graph_spde_result
Update an older version metric graph to the current package versionupdate_graph