Package: ggoutbreak 0.3.1

Robert Challen

ggoutbreak: Estimate Incidence, Proportions and Exponential Growth Rates

Simple statistical models and visualisations for calculating the incidence, proportion, exponential growth rate, and reproduction number of infectious disease case timeseries. This toolkit was largely developed during the COVID-19 pandemic.

Authors:Robert Challen [aut, cre, cph]

ggoutbreak_0.3.1.tar.gz
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ggoutbreak_0.3.1.tgz(r-4.4-any)ggoutbreak_0.3.1.tgz(r-4.3-any)
ggoutbreak_0.3.1.tar.gz(r-4.5-noble)ggoutbreak_0.3.1.tar.gz(r-4.4-noble)
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ggoutbreak.pdf |ggoutbreak.html✨
ggoutbreak/json (API)

# Install 'ggoutbreak' in R:

install.packages('ggoutbreak', repos = c('https://ai4ci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ai4ci/ggoutbreak/issues

Datasets:

covid_infectivity_profile - The covid_infectivity_profile dataframe structure specification
england_consensus_growth_rate - The SPI-M-O England consensus growth rate
england_consensus_rt - The SPI-M-O England consensus reproduction number
england_covid - Daily COVID-19 case counts by age group in England
england_covid_pcr_positivity - England COVID-19 PCR test positivity
england_covid_proportion - England COVID by age group for ascertainment
england_demographics - England demographics
england_events - Key dated in the COVID-19 response in England
england_nhs_app - NHS COVID-19 app data
england_ons_infection_survey - The england_ons_infection_survey dataset
england_variants - Counts of COVID-19 variants
germany_covid - Weekly COVID-19 case counts by age group in Germany
germany_demographics - Germany demographics

On CRAN:

41 exports 1 stars 0.91 score 79 dependencies

Last updated 1 months agofrom:20be3651c0 (on 0.3.1). Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 15 2024
R-4.5-win	NOTE	Sep 15 2024
R-4.5-linux	NOTE	Sep 15 2024
R-4.4-win	NOTE	Sep 15 2024
R-4.4-mac	NOTE	Sep 15 2024
R-4.3-win	NOTE	Sep 15 2024
R-4.3-mac	NOTE	Sep 15 2024

Exports:.test_multinomial %>%as.time_period breaks_log1p cut_date date_seq date_to_time doubling_time fdmy geom_events is.Date is.time_period logit_trans max_date min_date multinomial_nnet_model normalise_incidence normalise_incidence.incidence normalise_incidence.proportion normalise_proportion plot_growth_phase plot_growth_rate plot_incidence plot_multinomial plot_proportion plot_rt poisson_glm_model poisson_locfit_model proportion_glm_model proportion_locfit_model reband_discrete rt_epiestim rt_from_growth_rate rt_from_incidence scale_y_log1p scale_y_logit time_aggregate time_summarise time_to_date type.time_period wallinga_lipsitch

Dependencies:aweek brew callr cli coarseDataTools coda colorspace commonmark cpp11 desc digest dplyr EpiEstim evaluate fansi farver fitdistrplus forcats fs generics ggplot2 glue gridExtra gtable highr incidence interfacer isoband knitr labeling lattice lifecycle locfit lubridate magrittr MASS Matrix MatrixModels mcmc MCMCpack mgcv munsell nlme nnet pillar pkgbuild pkgconfig pkgload plyr processx ps purrr quantreg R6 ragg RColorBrewer Rcpp reshape2 rlang roxygen2 rprojroot scales SparseM stringi stringr survival systemfonts textshaping tibble tidyr tidyselect timechange utf8 vctrs viridisLite withr xfun xml2 yaml

Data wrangling and working with ggoutbreak

Rendered fromtime-periods.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2024-08-02
Started: 2023-12-24

England COVID-19 cases

Rendered fromcovid-timeseries.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2024-08-15
Started: 2023-12-24

Estimating the reproduction number from modelled incidence

Rendered fromrt-from-incidence.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2024-08-15
Started: 2024-01-05

Multinomial proportions models for genomic variants

Rendered fromvariant-proportions.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2024-08-02
Started: 2022-10-23

Population comparisons and incidence

Rendered fromincidence-trends.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2024-08-02
Started: 2023-12-24

Simulation tests for growth rate estimators

Rendered fromestimators-example.Rmdusingknitr::rmarkdownon Sep 15 2024.

Last update: 2024-08-15
Started: 2022-10-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate a multinomial outbreak defined by per class growth rates and a poisson model	.test_multinomial
Convert time period to dates	as.Date.time_period as.POSIXct.time_period
Convert to a time period class	as.time_period c.time_period is.time_period print.time_period [.time_period [<-.time_period [[.time_period [[<-.time_period
A scales breaks generator for log1p scales	breaks_log1p
The covid_infectivity_profile dataframe structure specification	covid_infectivity_profile
Places a set of dates within a regular time series	cut_date
Create the full sequence of values in a vector	date_seq
Expand a date vector to the full range of possible dates	date_seq.Date
Create the full sequence of values in a vector	date_seq.numeric
Expand a 'time_period' vector to the full range of possible times	date_seq.time_period
Convert a set of dates to numeric timepoints	date_to_time
Doubling time from growth rate	doubling_time
The SPI-M-O England consensus growth rate	england_consensus_growth_rate
The SPI-M-O England consensus reproduction number	england_consensus_rt
Daily COVID-19 case counts by age group in England	england_covid
England COVID-19 PCR test positivity	england_covid_pcr_positivity
England COVID by age group for ascertainment	england_covid_proportion
England demographics	england_demographics
Key dated in the COVID-19 response in England	england_events
NHS COVID-19 app data	england_nhs_app
The england_ons_infection_survey dataset	england_ons_infection_survey
Counts of COVID-19 variants	england_variants
Format date as dmy	fdmy
Add time series event markers to a timeseries plot.	geom_events
Weekly COVID-19 case counts by age group in Germany	germany_covid
Germany demographics	germany_demographics
Check whether vector is a date	is.Date
Label a time period	labels.time_period
logit scale	logit_trans
The maximum of a set of dates	max_date
The minimum of a set of dates	min_date
Multinomial time-series model.	multinomial_nnet_model
Calculate a normalised incidence rate per capita	normalise_incidence
Calculate a normalised incidence rate per capita	normalise_incidence.incidence
Calculate a normalised incidence rate per capita	normalise_incidence.proportion
Calculate a normalised risk ration from proportions	normalise_proportion
Plot an incidence or proportion vs. growth phase diagram	plot_growth_phase
Growth rate timeseries diagram	plot_growth_rate
Plot an incidence timeseries	plot_incidence
Plot a multinomial proportions mode	plot_multinomial
Plot a proportions timeseries	plot_proportion
Reproduction number timeseries diagram	plot_rt
Poisson time-series model.	poisson_glm_model
Poisson time-series model.	poisson_locfit_model
Binomial time-series model.	proportion_glm_model
A binomial proportion estimate and associated exponential growth rate	proportion_locfit_model
Reband any discrete distribution	reband_discrete
EpiEstim reproduction number	rt_epiestim
Wallinga-Lipsitch reproduction number	rt_from_growth_rate
Reproduction number from modelled incidence	rt_from_incidence
A log1p y scale	scale_y_log1p
A logit y scale	scale_y_logit
Aggregate time series data preserving the time series	time_aggregate
Summarise data from a line list to a time-series of counts.	time_summarise
Convert a set of timepoints to dates	time_to_date
Type coercion to a 'time_period' class	type.time_period
Calculate the reproduction number from a growth rate estimate and an infectivity profile	wallinga_lipsitch