Package: growthrates 0.2.0

Robert Challen

growthrates: 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]

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growthrates.pdf |growthrates.html✨
growthrates/json (API)

# Install 'growthrates' in R:
install.packages('growthrates', repos = c('https://bristol-vaccine-centre.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bristol-vaccine-centre/growthrates/issues

Datasets:

On CRAN:

6.25 score 2 stars 98 scripts 452 downloads 6 mentions 39 exports 79 dependencies

Last updated 4 months agofrom:334d6f6450 (on 0.2.0). Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winOKNov 18 2024
R-4.5-linuxOKNov 18 2024
R-4.4-winNOTENov 18 2024
R-4.4-macNOTENov 18 2024
R-4.3-winNOTENov 18 2024
R-4.3-macNOTENov 18 2024

Exports:%>%as.time_periodbreaks_log1pcut_datedate_seqdate_to_timedoubling_timefdmygeom_eventsis.Dateis.time_periodlogit_transmax_datemin_datemultinomial_nnet_modelnormalise_incidencenormalise_incidence.incidencenormalise_incidence.proportionnormalise_proportionplot_growth_phaseplot_growth_rateplot_incidenceplot_multinomialplot_proportionplot_rtpoisson_glm_modelpoisson_locfit_modelproportion_glm_modelproportion_locfit_modelreband_discretert_epiestimrt_from_growth_ratert_from_incidencescale_y_log1pscale_y_logittime_aggregatetime_summarisetime_to_datewallinga_lipsitch

Dependencies:aweekbrewcallrclicoarseDataToolscodacolorspacecommonmarkcpp11descdigestdplyrEpiEstimevaluatefansifarverfitdistrplusforcatsfsgenericsggplot2gluegridExtragtablehighrincidenceinterfacerisobandknitrlabelinglatticelifecyclelocfitlubridatemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmennetpillarpkgbuildpkgconfigpkgloadplyrprocessxpspurrrquantregR6raggRColorBrewerRcppreshape2rlangroxygen2rprojrootscalesSparseMstringistringrsurvivalsystemfontstextshapingtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithrxfunxml2yaml

Data wrangling and working with growthrates

Rendered fromtime-periods.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-04-26
Started: 2023-12-24

England COVID-19 cases

Rendered fromcovid-timeseries.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-04-25
Started: 2023-12-24

Estimating the reproduction number from modelled incidence

Rendered fromrt-from-incidence.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Multinomial proportions models for genomic variants

Rendered fromvariant-proportions.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-04-26
Started: 2022-10-23

Population comparisons and incidence

Rendered fromincidence-trends.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-08-01
Started: 2023-12-24

Simulation tests for growth rate estimators

Rendered fromestimators-example.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-04-26
Started: 2022-10-23

Readme and manuals

Help Manual

Help pageTopics
Convert time period to datesas.Date.time_period as.POSIXct.time_period
Convert to a time period classas.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 scalesbreaks_log1p
The covid_infectivity_profile dataframe structure specificationcovid_infectivity_profile
Places a set of dates within a regular time seriescut_date
Create the full sequence of values in a vectordate_seq
Expand a date vector to the full range of possible datesdate_seq.Date
Create the full sequence of values in a vectordate_seq.numeric
Expand a 'time_period' vector to the full range of possible timesdate_seq.time_period
Convert a set of dates to numeric timepointsdate_to_time
Doubling time from growth ratedoubling_time
The SPI-M-O England consensus growth rateengland_consensus_growth_rate
The SPI-M-O England consensus reproduction numberengland_consensus_rt
Daily COVID-19 case counts by age group in Englandengland_covid
England COVID-19 PCR test positivityengland_covid_pcr_positivity
England COVID by age group for ascertainmentengland_covid_proportion
England demographicsengland_demographics
Key dated in the COVID-19 response in Englandengland_events
NHS COVID-19 app dataengland_nhs_app
The england_ons_infection_survey datasetengland_ons_infection_survey
Counts of COVID-19 variantsengland_variants
Format date as dmyfdmy
Add time series event markers to a timeseries plot.geom_events
Weekly COVID-19 case counts by age group in Germanygermany_covid
Germany demographicsgermany_demographics
Check whether vector is a dateis.Date
Label a time periodlabels.time_period
logit scalelogit_trans
The maximum of a set of datesmax_date
The minimum of a set of datesmin_date
Multinomial time-series model.multinomial_nnet_model
Calculate a normalised incidence rate per capitanormalise_incidence
Calculate a normalised incidence rate per capitanormalise_incidence.incidence
Calculate a normalised incidence rate per capitanormalise_incidence.proportion
Calculate a normalised risk ration from proportionsnormalise_proportion
Plot an incidence or proportion vs. growth phase diagramplot_growth_phase
Growth rate timeseries diagramplot_growth_rate
Plot an incidence timeseriesplot_incidence
Plot a multinomial proportions modeplot_multinomial
Plot a proportions timeseriesplot_proportion
Reproduction number timeseries diagramplot_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 rateproportion_locfit_model
Reband any discrete distributionreband_discrete
EpiEstim reproduction numberrt_epiestim
Wallinga-Lipsitch reproduction numberrt_from_growth_rate
Reproduction number from modelled incidencert_from_incidence
A log1p y scalescale_y_log1p
A logit y scalescale_y_logit
Aggregate time series data preserving the time seriestime_aggregate
Summarise data from a line list to a time-series of counts.time_summarise
Convert a set of timepoints to datestime_to_date
Calculate the reproduction number from a growth rate estimate and an infectivity profilewallinga_lipsitch