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Package: squire 0.7.1

OJ Watson

squire: SEIR transmission model of COVID-19

An extended model of the SEIR model used in the Imperial College London Report into the global impact of COVID-19 and strategies for mitigation and suppression (https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-12-global-impact-covid-19/). Extensions now include healthcare treatment pathways and excess mortality.

Authors:OJ Watson [aut, cre], Patrick Walker [aut], Charlie Whittaker [aut], Peter Winskill [aut], Giovanni Charles [aut], Imperial College of Science, Technology and Medicine [cph]

squire_0.7.1.tar.gz
squire_0.7.1.zip(r-4.7)squire_0.7.1.zip(r-4.6)squire_0.7.1.zip(r-4.5)
squire_0.7.1.tgz(r-4.6-x86_64)squire_0.7.1.tgz(r-4.6-arm64)squire_0.7.1.tgz(r-4.5-x86_64)squire_0.7.1.tgz(r-4.5-arm64)
squire_0.7.1.tar.gz(r-4.7-arm64)squire_0.7.1.tar.gz(r-4.7-x86_64)squire_0.7.1.tar.gz(r-4.6-arm64)squire_0.7.1.tar.gz(r-4.6-x86_64)
squire_0.7.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
squire/json (API)

# Install 'squire' in R:

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

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

Datasets:

contact_matrices - Contact matrices
country_specific_healthcare_capacity - Country specific healthcare capacity
elderly_pop - Elderly Population
income_group - Income group
income_strata_healthcare_capacity - Income strata healthcare capacity
population - Population

On CRAN:

6.95 score 53 stars 1 packages 141 scripts 32 exports 77 dependencies

Last updated from:9fd16c495b (on master). Checks:11 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	ERROR	352
linux-devel-x86_64	ERROR	377
source / vignettes	OK	259
linux-release-arm64	ERROR	364
linux-release-x86_64	ERROR	359
macos-release-arm64	ERROR	203
macos-release-x86_64	ERROR	439
macos-oldrel-arm64	ERROR	199
macos-oldrel-x86_64	ERROR	442
windows-devel	ERROR	393
windows-release	ERROR	396
windows-oldrel	ERROR	393
wasm-release	OK	128

Exports:adjusted_eigen align beta_est_explicit beta_est_simple calibrate create_master_chain default_durations default_probs drjacoby_mcmc explicit_model extract_deaths extract_hospital_occ extract_ICU_occ extract_infection_incidence format_deterministic_output format_output format_output_simple_model get_elderly_population get_healthcare_capacity get_lmic_countries get_mixing_matrix get_population parameters_explicit_SEEIR parameters_simple_SEEIR pmcmc projection_plotting projections run_deterministic_SEIR_model run_explicit_SEEIR_model run_simple_SEEIR_model sample_drjacoby trigger_projections

Dependencies:askpass cinterpolate cli clipr coda codetools cowplot cpp11 crayon credentials curl dde desc deSolve digest dplyr drjacoby farver forcats fs furrr future generics gert GGally ggplot2 ggstats gitcreds globals glue gridExtra gtable hms httr2 ini isoband jsonlite labeling lattice lifecycle listenv magrittr mvtnorm odin openssl parallelly patchwork pillar pkgconfig prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp ring rlang rprojroot rstudioapi S7 scales stringi stringr sys tibble tidyr tidyselect usethis utf8 vctrs viridis viridisLite whisker withr yaml zip

Model Parameters

Age-Specific Parameters

Rendered fromparameters.Rmdusingknitr::rmarkdown

Last update: 2022-09-08
Started: 2020-05-01

Help page	Topics
Compute age-adjusted eigenvalue for mixing matrix	adjusted_eigen
Align deaths	align
Estimate beta for a squire model using model parameters	beta_est
Estimate beta parameter for explicit model	beta_est_explicit
Estimate beta parameter	beta_est_simple
Calibrate via particle filter grid search using time series of deaths	calibrate
Check object is an squire_simulation	check_squire
Check time change inputs are correct	check_time_change
Compare model to death data	compare_output
Handles simulating replicates within 'projections'	conduct_replicate
Contact matrices	contact_matrices
Country specific healthcare capacity	country_specific_healthcare_capacity
create a master chain from a pmcmc_list object	create_master_chain
Return the default hospital durations for modelling	default_durations
Return the default probabilities for modelling	default_probs
Simple SEEIR model creation. We will use this structure to ensure that model fitting is flexible in the future as more models are added	deterministic_model
Divide matrix by population	div_pop
Run an MCMC Sampler using drjacoby	drjacoby_mcmc
Elderly Population	elderly_pop
Explicit SEEIR model creation. We will use this structure to ensure that model fitting is flexible in the future as more models are added	explicit_model
Extract deaths from model output	extract_deaths
Extract hospital bed occupancy from model output	extract_hospital_occ
Extract ICU bed occupancy from model output	extract_ICU_occ
Extract infection incidence from model output	extract_infection_incidence
Format deterministic model output as data.frame	format_deterministic_output
Format model output as data.frame	format_output
Format model output from simple as data.frame	format_output_simple_model
Get elderly population data (5 year age-breakdown for 80-84, 85-89 and 90+)	get_elderly_population
Get healthcare capacity data	get_healthcare_capacity
Get supported LMIC countries	get_lmic_countries
Get mixing matrix	get_mixing_matrix
Get population data	get_population
Income group	income_group
Income strata healthcare capacity	income_strata_healthcare_capacity
Check and set up initial values	init_check
Check and set up initial values for explicit model	init_check_explicit
Prepare intervention timing for odin	intervention_dates_for_odin
update_sigma	jc_prop_update
Check dimensions of inputs	matrix_check
Process set of contact matrices -> mixing matrices	matrix_set
Parmaters for explicit SEEIR model	parameters_explicit_SEEIR
Parmeters for the simple SEEIR model	parameters_simple_SEEIR
Parse country severity parameters	parse_country_severity
Run a particle filter	particle_filter
Prepare particle filter data	particle_filter_data
squire scan plot	plot.squire_scan
squire simulation plot	plot.squire_simulation
Run a Particle MCMC Sampler within the Squire Framework	pmcmc
Population	population
Check argument is a single positive numeric	pos_num
squire simulation print	print.squire_simulation
Process a contact matrix	process_contact_matrix
Process a contact matrix with an extra	process_contact_matrix_scaled_age
Plot projections against each other	projection_plotting
Provide projections from calibrated simulations by changing RO, contact matrices or bed availability.	projections
Run Deterministic model comparison	run_deterministic_comparison
Run the deterministic explicit SEIR model	run_deterministic_SEIR_model
Run the explicit SEEIR model	run_explicit_SEEIR_model
Run particle filter	run_particle_filter
Run the SEEIR model	run_simple_SEEIR_model
Sample Grid Scan	sample_3d_grid_scan
Sample from a drjacoby mcmc	sample_drjacoby
Sample Grid Scan	sample_grid_scan
Sample PMCMC	sample_pmcmc
Grid search of R0 and start date	scan_R0_date
Grid search of R0 and start date	scan_R0_date_Meff
Simple SEEIR model creation. We will use this structure to ensure that model fitting is flexible in the future as more models are added	simple_model
squire simulation summary	summary.squire_simulation
Project lockdowns based on triggering	trigger_projections

Package: squire 0.7.1

squire: SEIR transmission model of COVID-19

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