Package: rts2 1.0.3

rts2: Log-Gaussian Cox Process Models with Approximations

Supports modelling case data to facilitate. The package provides automated computational grid generation over an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts, and predictions and visualisation. Monte Carlo maximum likelihood is the main fitting method with a low-rank approximation for Gaussian processes described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and a stochastic partial differential equation approximation. Bayesian methods are also provided for some methods. Log-Gaussian Cox Processes are described by Diggle et al. (2013) <doi:10.1214/13-STS441>.

Authors:Sam Watson [aut, cre]

rts2_1.0.3.tar.gz
rts2_1.0.3.zip(r-4.7)rts2_1.0.3.zip(r-4.6)rts2_1.0.3.zip(r-4.5)
rts2_1.0.3.tgz(r-4.6-x86_64)rts2_1.0.3.tgz(r-4.6-arm64)rts2_1.0.3.tgz(r-4.5-x86_64)rts2_1.0.3.tgz(r-4.5-arm64)
rts2_1.0.3.tar.gz(r-4.7-arm64)rts2_1.0.3.tar.gz(r-4.7-x86_64)rts2_1.0.3.tar.gz(r-4.6-arm64)rts2_1.0.3.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html
card.svg |card.png
rts2/json (API)

# Install 'rts2' in R:
install.packages('rts2', repos = c('https://samueliwatson.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

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

cpp

2.54 score 2 scripts 183 downloads 6 exports 78 dependencies

Last updated from:6899cb62b2. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK501
linux-devel-x86_64OK501
source / vignettesOK562
linux-release-arm64OK435
linux-release-x86_64OK464
macos-release-arm64OK499
macos-release-x86_64OK793
macos-oldrel-arm64OK569
macos-oldrel-x86_64OK833
windows-develOK623
windows-releaseOK477
windows-oldrelOK645
wasm-releaseFAIL182

Exports:covariance.parameterscreate_pointsfixed.effectsgridprogress_barrandom.effects

Dependencies:abindbackportsBHbootcallrcheckmateclassclassIntclicpp11DBIdeldirdescdistributionaldplyre1071farverfmesherFNNgenericsggplot2glmmrBasegluegridExtragtableinlineisobandKernSmoothlabelinglatticelifecycleloolubridatemagrittrMASSMatrixmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxproxypsquadprogQuickJSRR6rasterRColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolss2S7scalessfspspDataspdepsplancsStanHeadersstarstensorAterratibbletidyselecttimechangeunitsutf8vctrsviridisLitewithrwk

Readme and manuals

Help Manual

Help pageTopics
Log-Gaussian Cox Process Models with Approximationsrts2-package rts2
Birmingham crime databirmingham_crime
Boundary polygon for Birmingham, UKboundary
Extracts fixed effect coefficients from a rtsFit objectcoef.rtsFit
Fixed effect confidence intervals for a 'rtsFit' objectconfint.rtsFit
Extracts the estimates of the covariance parameterscovariance.parameters
Create sf object from point location datacreate_points
Disaggregate regional means to fine grid, preserving aggregate meansdisaggregate_covariate
Disaggregation function for strictly positive covariatesdisaggregate_positive
Simulated point data for running single-period examplesexample_points
Extracts the family from a 'grid' object.family.grid
Extracts the family from a 'rtsFit' object.family.rtsFit
Fitted values from a 'rtsFit' objectfitted.rtsFit
Extracts the fixed effect estimatesfixed.effects
Simple flat disaggregationflat_disaggregate
Extracts the formula from a 'grid' object.formula.grid
Extracts the formula from a 'rtsFit' object.formula.rtsFit
An rts grid objectgrid
Extracts the log-likelihood from an rtsFit objectlogLik.rtsFit
Extract predictions from a 'grid' objectpredict.grid
Predict from a 'rtsFit' objectpredict.rtsFit
Prints an rtsFit fit outputprint.rtsFit
Prints an rtsFitSummary fit outputprint.rtsFitSummary
Generates a progress barprogress_bar
Extracts the random effect estimatesrandom.effects
Residuals method for a 'grid' objectresiduals.grid
Residuals method for a 'rtsFit' objectresiduals.rtsFit
Summarizes a 'grid' objectsummary.grid
Summary method for class "rtsFit"summary.rtsFit
Calculate Variance-Covariance matrix for a maximum likelihood object stored in 'grid'vcov.grid
Extract the Variance-Covariance matrix for a 'rtsFit' objectvcov.rtsFit