Package: sircovid 0.15.1

Marc Baguelin

sircovid: SIR Model for COVID-19

Mechanistic models of transmission of the SARS-Cov-2 (COVID-19) virus implemented as stochastic compartmental models in odin and dust. Uses mcstate to perfom Bayesian evidence synthesis from several surveillance data streams through the estimation of transmission parameters.

Authors:Marc Baguelin [aut, cre], Sangeeta Bhatia [ctb], Edward Knock [aut], Lilith Whittles [aut], Rich FitzJohn [aut], John Lees [aut], OJ Watson [ctb], Anne Cori [aut], Pablo Perez-Guzman [aut], Raphael Sonabend [aut], Yasin Elmaci [aut]

sircovid_0.15.1.tar.gz
sircovid_0.15.1.zip(r-4.7)sircovid_0.15.1.zip(r-4.6)sircovid_0.15.1.zip(r-4.5)
sircovid_0.15.1.tgz(r-4.6-x86_64)sircovid_0.15.1.tgz(r-4.6-arm64)sircovid_0.15.1.tgz(r-4.5-x86_64)sircovid_0.15.1.tgz(r-4.5-arm64)
sircovid_0.15.1.tar.gz(r-4.7-arm64)sircovid_0.15.1.tar.gz(r-4.7-x86_64)sircovid_0.15.1.tar.gz(r-4.6-arm64)sircovid_0.15.1.tar.gz(r-4.6-x86_64)
sircovid_0.15.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sircovid/json (API)

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

Bug tracker:https://github.com/mrc-ide/sircovid/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

cppopenmp

4.48 score 29 stars 15 scripts 53 exports 55 dependencies

Last updated from:5492e5a47e (on master). Checks:11 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING257
linux-devel-x86_64WARNING287
source / vignettesOK294
linux-release-arm64WARNING308
linux-release-x86_64WARNING330
macos-release-arm64WARNING237
macos-release-x86_64WARNING392
macos-oldrel-arm64WARNING239
macos-oldrel-x86_64WARNING607
windows-develWARNING346
windows-releaseWARNING309
windows-oldrelWARNING312
wasm-releaseOK156

Exports:add_trajectory_incidenceas_dateas_sircovid_datebasicbasic_comparebasic_indexbasic_initialbasic_parameterscheck_sircovid_modelcombine_rtcombine_rt_epiestimcombine_trajectoriescompile_gpudrop_trajectory_incidenceget_sample_rankinflate_state_strainsinflate_state_vacc_classeslancelotlancelot_check_datalancelot_check_severitylancelot_comparelancelot_ifr_excl_immunitylancelot_indexlancelot_initiallancelot_parameterslancelot_parameters_observationlancelot_parameters_progressionlancelot_parameters_sens_and_speclancelot_parameters_severitylancelot_Rtlancelot_Rt_trajectorieslancelot_rt_trajectories_epiestimmodify_severityregionsreorder_rt_ifrreorder_samplerotate_strainssircovid_datesircovid_date_as_datesircovid_modelssircovid_parameters_expand_stepsircovid_parameters_piecewise_constantsircovid_parameters_piecewise_linearsircovid_parameters_severityupgrade_statevaccine_eligibilityvaccine_priority_populationvaccine_priority_proportionvaccine_remap_statevaccine_schedulevaccine_schedule_from_datavaccine_schedule_futurevaccine_schedule_scenario

Dependencies:askpassbackportscachemcallrcheckmateclicountrycodecpp11crayoncurldata.tabledescdusteigen1fastmapfsgenericsgluehmshttrjsonlitelifecyclelubridatemagrittrmcstatememoisemimeoaiopensslotelpillarpkgbuildpkgconfigpkgloadplyrprettyunitsprocessxprogresspspurrrR6Rcpprlangrprojrootsocialmixrstringistringrsystibbletimechangeutf8vctrswithrwpp2017xml2

Readme and manuals

Help Manual

Help pageTopics
Add incidence to trajectoriesadd_trajectory_incidence drop_trajectory_incidence
The basic sircovid modelbasic
Compare observed and modelled data for the basic modelbasic_compare
Index of basic modelbasic_index
Initial conditions for the basic modelbasic_initial
Parameters for the basic modelbasic_parameters
Check a model typecheck_sircovid_model
Combine Rt estimatescombine_rt
Combine Rt estimates from EpiEstimcombine_rt_epiestim
Combine trajectoriescombine_trajectories
Create GPU modelcompile_gpu
Get the ranking of sample by a given variable, e.g. infectionsget_sample_rank
Inflate strains in model stateinflate_state_strains
Inflate vacc classes in model stateinflate_state_vacc_classes
The lancelot sircovid modellancelot
Check data for particle filterlancelot_check_data
Check severity parameterslancelot_check_severity
Compare observed and modelled data for the lancelot modellancelot_compare
Compute "IFR" excluding immunitylancelot_ifr_excl_immunity
Index of lancelot modellancelot_index
Initial conditions for the lancelot modellancelot_initial
Parameters for the lancelot modellancelot_parameters
Lancelot observation parameterslancelot_parameters_observation
Lancelot progression parameterslancelot_parameters_progression
Lancelot sensitivity and specificity parameterslancelot_parameters_sens_and_spec
Lancelot severity parameterslancelot_parameters_severity
Compute "Rt"lancelot_Rt
Compute Rt for a set of trajectorieslancelot_Rt_trajectories
Compute Rt using EpiEstim for a set of trajectorieslancelot_rt_trajectories_epiestim
Modify severity and transmission of variantsmodify_severity
Regionsregions
Reorder Rt or IFR trajectoriesreorder_rt_ifr
Reorder samplesreorder_sample
Rotate strainsrotate_strains
Date handling for sircovidas_date as_sircovid_date sircovid_date sircovid_date_as_date
Available sircovid Modelssircovid_models
Expand beta stepssircovid_parameters_expand_step
Construct piecewise constant arraysircovid_parameters_piecewise_constant
Construct piecewise linear arraysircovid_parameters_piecewise_linear
Process severity datasircovid_parameters_severity
Upgrade model state after changeupgrade_state
Create vaccine eligibility vectorvaccine_eligibility
Compute vaccination ordervaccine_priority_population vaccine_priority_proportion
Remap state to include vaccinationvaccine_remap_state
Create vaccine schedulevaccine_schedule
Create historical vaccine schedulevaccine_schedule_from_data
Create vaccination schedulevaccine_schedule_future
High-level vaccine scenario creationvaccine_schedule_scenario