Package: IDSpatialStats 0.4.0

IDSpatialStats: Estimate Global Clustering in Infectious Disease

Implements various novel and standard clustering statistics and other analyses useful for understanding the spread of infectious disease.

Authors:John Giles [aut, ctb], Henrik Salje [aut, ctb], Justin Lessler [aut, cre], Timothy Willard [ctb]

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manual.pdf |manual.html✨
card.svg |card.png
IDSpatialStats/json (API)

# Install 'IDSpatialStats' in R:
install.packages('IDSpatialStats', repos = c('https://jlessler.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • DengueSimR01 - Simulated dataset of dengue transmission with basic reproductive number of 1
  • DengueSimR02 - Simulated dataset of dengue cases with basic reproductive number of 2
  • DengueSimRepresentative - Simulated dataset of dengue cases with representative underlying population

On CRAN:

Conda:

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

2.69 score 1 stars 33 scripts 182 downloads 3 mentions 33 exports 28 dependencies

Last updated from:a9be20d91e. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK130
linux-devel-x86_64OK173
source / vignettesOK179
linux-release-arm64OK145
linux-release-x86_64OK176
macos-release-arm64OK130
macos-release-x86_64OK242
macos-oldrel-arm64OK146
macos-oldrel-x86_64OK479
windows-develOK113
windows-releaseOK137
windows-oldrelOK95
wasm-releaseOK104

Exports:est.transdistest.transdist.bootstrap.ciest.transdist.temporalest.transdist.temporal.bootstrap.ciest.transdist.theta.weightsest.wt.matrixest.wt.matrix.weightsget.cross.Kget.cross.PCFget.piget.pi.bootstrapget.pi.ciget.pi.permuteget.pi.typedget.pi.typed.bootstrapget.pi.typed.permuteget.tauget.tau.bootstrapget.tau.ciget.tau.permuteget.tau.typedget.tau.typed.bootstrapget.tau.typed.permuteget.thetaget.theta.bootstrapget.theta.ciget.theta.permuteget.theta.typedget.theta.typed.bootstrapget.theta.typed.permuteget.transdist.thetasim.epidemicsim.plot

Dependencies:abindclicodetoolscpp11deldirdoParallelforeachgluegoftestigraphiteratorslatticelifecyclemagrittrMatrixnlmepkgconfigpolycliprlangspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilstensorvctrs

Readme and manuals

Help Manual

Help pageTopics
Simulated dataset of dengue transmission with basic reproductive number of 1DengueSimR01
Simulated dataset of dengue cases with basic reproductive number of 2DengueSimR02
Simulated dataset of dengue cases with representative underlying populationDengueSimRepresentative
Estimate transmission distanceest.transdist
Bootstrap mean transmission distance valuesest.transdist.bootstrap.ci
Change in mean transmission distance over timeest.transdist.temporal
Bootstrapped confidence intervals for the change in mean transmission distance over timeest.transdist.temporal.bootstrap.ci
Estimate transmission distance theta values by replicationest.transdist.theta.weights
Calculate the Infector-Infectee Wallinga-Teunis matrixest.wt.matrix
Estimate matrix of basic Wallinga-Teunis weightsest.wt.matrix.weights
Cross type K function using homotypic and heterotypic case typesget.cross.K
Cross type Pair Correlation Function using homotypic and heterotypic case typesget.cross.PCF
Generalized version of 'get.pi'get.pi
Bootstrap 'get.pi' values.get.pi.bootstrap
Calculate bootstrapped confidence intervals for 'get.pi' values.get.pi.ci
get the null distribution of the 'get.pi' functionget.pi.permute
Optimized version of 'get.pi' for typed data.get.pi.typed
runs bootstrapping on 'get.pi.typed'get.pi.typed.bootstrap
get the null distribution of the get.pi.typed functionget.pi.typed.permute
generalized version of 'get.tau'get.tau
Bootstrap 'get.tau' values.get.tau.bootstrap
Bootstrap confidence interval for the 'get.tau' valuesget.tau.ci
get the null distribution of the 'get.tau' functionget.tau.permute
Optimized version of 'get.tau' for typed dataget.tau.typed
runs bootstrapping for 'get.tau.typed'get.tau.typed.bootstrap
get the null distribution for the 'get.tau.typed' functionget.tau.typed.permute
Generalized version of 'get.theta'get.theta
Bootstrap 'get.theta' values.get.theta.bootstrap
Calculate bootstrapped confidence intervals for 'get.theta' values.get.theta.ci
get the null distribution of the 'get.theta' functionget.theta.permute
Optimized version of 'get.theta' for typed data.get.theta.typed
runs bootstrapping on 'get.theta.typed'get.theta.typed.bootstrap
get the null distribution of the get.theta.typed functionget.theta.typed.permute
Get weights of transmission distance thetaget.transdist.theta
Simulation of an epidemic in space and timesim.epidemic
Plot output of simulated epidemicsim.plot