reconhub/incidence 1.5
Year: 2018
Type: article
Abstract: 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") + -7:6 setNames(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 week itue <- 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 week pmon <- 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 handled library(incidence) library(outbreaks) d <- ebola_sim_clean$linelist$date_of_onset h <- ebola_sim_clean$linelist$hospital plot(incidence(d, interval = "1 epiweek", group = h)) plot(incidence(d, interval = "2 epiweeks", group = h)) plot(incidence(d, interval = "3 epiweeks", group = h)) plot(incidence(d, interval = "2 months", group = h)) Created on 2019-03-14 by the [reprex package](https://reprex.tidyverse.org) (v0.2.1) Full set of changes NEW FEATURES Any interval seq.Date() can handle (e.g. "5 weeks") can be handled by incidence() (see https://github.com/reconhub/incidence/issues/67) Weekly intervals can start on any day of the week by allowing things like "epiweek", "isoweek", "wednesday week", "2 Saturday weeks", etc. (see https://github.com/reconhub/incidence/issues/55#issuecomment-405297526) the item $weeks is now added to the incidence object, which contains an "aweek" class plotting will now force the first tick to be the starting point of the incidence curve NEW FUNCTIONS make_breaks() will automatically calculate breaks from an incidence object for plotting. scale_x_incidence() will produce a ggplot2 "ScaleContinuous" object to add to a ggplot. DEPRECATED plot.incidence() argument labels_iso is deprecated in favor of labels_week Incidence objects will still have $isoweeks if the weeks are ISO 8601 standard, but users should rely intead on $weeks instead. The $isoweeks element will be removed in a future version of incidence. as.incidence() argument isoweeks has been deprecated in favour of standard DEPENDENCIES ISOweek import changed to aweek Documentation Vignettes have been updated with examples.
Source: Spiral (Imperial College London)
Authors: Jombart, Thibaut, Zhian N. Kamvar, Cai, Jun, Pulliam, Juliet, Chisholm, Sarah, FitzJohn, Rich, Bhatia, Sangeeta, Schumacher, Jakob, Schumacher, Dirk
Language: English
Topic: Data Analysis with R
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W6949528764