Package: mpoxseir 0.2.19

Lilith Whittles

mpoxseir: Stochastic compartmental model of mpox transmission

Stochastic compartmental model of mpox transmission in odin.dust.

Authors:Lilith Whittles [aut, cre], Ruth McCabe [aut], Charlie Whittaker [aut], Ed Knock [aut], Kieran Chopra [aut], Imperial College of Science, Technology and Medicine [cph]

mpoxseir_0.2.19.tar.gz
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mpoxseir.pdf |mpoxseir.html✨
mpoxseir/json (API)
NEWS

# Install 'mpoxseir' in R:

install.packages('mpoxseir', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

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

Uses libs:

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

On CRAN:

cpp openmp

4.21 score 2 stars 11 exports 88 dependencies

Last updated 15 hours agofrom:9a21b47286 (on main). Checks:1 OK, 11 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Apr 01 2025
R-4.5-win-x86_64	NOTE	Apr 01 2025
R-4.5-mac-x86_64	NOTE	Apr 01 2025
R-4.5-mac-aarch64	NOTE	Apr 01 2025
R-4.5-linux-x86_64	NOTE	Apr 01 2025
R-4.4-win-x86_64	NOTE	Apr 01 2025
R-4.4-mac-x86_64	NOTE	Apr 01 2025
R-4.4-mac-aarch64	NOTE	Apr 01 2025
R-4.4-linux-x86_64	NOTE	Apr 01 2025
R-4.3-win-x86_64	NOTE	Apr 01 2025
R-4.3-mac-x86_64	NOTE	Apr 01 2025
R-4.3-mac-aarch64	NOTE	Apr 01 2025

Exports:as_date as_mpoxseir_date get_age_bins get_compartment_indices model_targeted_vax mpoxseir_date mpoxseir_date_as_date parameters_demographic parameters_fixed run_mpoxSEIR_targetedVax_multiple run_mpoxSEIR_targetedVax_single

Dependencies:askpass cinterpolate cli clipr coda codetools colorspace cowplot cpp11 crayon credentials curl dde desc deSolve digest dplyr drjacoby dust2 fansi farver forcats fs furrr future generics gert GGally ggplot2 ggstats gh gitcreds globals glue gridExtra gtable hms httr2 ini isoband jsonlite labeling lattice lifecycle listenv magrittr MASS Matrix mgcv monty munsell mvtnorm nlme odin openssl parallelly patchwork pillar pkgconfig plyr prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp ring rlang rprojroot rstudioapi scales squire stringi stringr sys tibble tidyr tidyselect usethis utf8 vctrs viridis viridisLite whisker withr yaml zip

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Divide matrix by population	div_pop
Get age bins for use in the model	get_age_bins
Get compartment indices used throughout the model	get_compartment_indices
Process set of contact matrices -> mixing matrices	matrix_set
Stochastic compartmental transmission model of Mpox virus	model_targeted_vax
Date handling for mpoxseir	as_date as_mpoxseir_date mpoxseir_date mpoxseir_date_as_date
Get demographic parameters	parameters_demographic
Get fixed parameters for use in the model	parameters_fixed
Process a contact matrix	process_contact_matrix
Process a contact matrix with an extra	process_contact_matrix_scaled_age
calculate the proportion of each age group that lies between 'min_age' and 'max_age' (inclusive) based on uniform distribution within each age band	proportion_in_age_bins
Run multiple iterations of the model with different parameter values	run_mpoxSEIR_targetedVax_multiple
Run the model with single set of parameter values	run_mpoxSEIR_targetedVax_single