Imperial College London
Alternate

DrThibautJombart

Faculty of Medicine, School of Public Health

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 3658t.jombart Website

 
 
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Location

 

UG11Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@misc{Jombart:2019,
author = {Jombart, T and Kamvar, ZN and Cai, J and Pulliam, J and Chisholm, S and Fitzjohn, R and Schumacher, J and Bhatia, S},
title = {reconhub/incidence: Incidence version 1.7.0},
type = {Software},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - GEN
AB  - Incidence can now handle standardised weeks starting on any day thanks to the aweek package :tada:library(incidence)library(ggplot2)library(cowplot)d <- as.Date("2019-03-11") + -7:6setNames(d, weekdays(d))#>       Monday      Tuesday    Wednesday     Thursday       Friday #> "2019-03-04" "2019-03-05" "2019-03-06" "2019-03-07" "2019-03-08" #>     Saturday       Sunday       Monday      Tuesday    Wednesday #> "2019-03-09" "2019-03-10" "2019-03-11" "2019-03-12" "2019-03-13" #>     Thursday       Friday     Saturday       Sunday #> "2019-03-14" "2019-03-15" "2019-03-16" "2019-03-17"imon <- incidence(d, "mon week") # also ISO weekitue <- incidence(d, "tue week")iwed <- incidence(d, "wed week")ithu <- incidence(d, "thu week")ifri <- incidence(d, "fri week")isat <- incidence(d, "sat week")isun <- incidence(d, "sun week") # also MMWR week and EPI weekpmon <- plot(imon, show_cases = TRUE, labels_week = FALSE)ptue <- plot(itue, show_cases = TRUE, labels_week = FALSE)pwed <- plot(iwed, show_cases = TRUE, labels_week = FALSE)pthu <- plot(ithu, show_cases = TRUE, labels_week = FALSE)pfri <- plot(ifri, show_cases = TRUE, labels_week = FALSE)psat <- plot(isat, show_cases = TRUE, labels_week = FALSE)psun <- plot(isun, show_cases = TRUE, labels_week = FALSE)s <- scale_x_date(limits = c(as.Date("2019-02-26"), max(d) + 7L))plot_grid(pmon + s,ptue + s,pwed + s,pthu + s,pfri + s,psat + s,psun + s)multi-weeks/months/years can now be handledlibrary(incidence)library(outbreaks)d <- ebola_sim_clean$linelist$date_of_onseth <- ebola_sim_clean$linelist$hospitalplot(incidence(d, interval = "1 epiweek", group = h))plot(incidence(d, interval = "2 epiweeks", group = h))plot(incide
AU  - Jombart,T
AU  - Kamvar,ZN
AU  - Cai,J
AU  - Pulliam,J
AU  - Chisholm,S
AU  - Fitzjohn,R
AU  - Schumacher,J
AU  - Bhatia,S
PY  - 2019///
TI  - reconhub/incidence: Incidence version 1.7.0
ER  -
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