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reconhub/incidence: Incidence version 1.5.2

Thibaut Jombart; Zhian N. Kamvar; Jun Cai; Sarah Chisholm; Rich FitzJohn; Jakob Schumacher; Sangeeta Bhatia

This release of incidence includes a couple of bug fixes and also updates the incidence demo. This is the first CRAN version since 1.5.0. For incidence > 1.5.0, the way the object is constructed and plotted differs. Mainly, the ordering of the groups in the epicurve will match the ordering of the groups in the incidence object (previously, they were ordered alphabetically):

library("incidence")
set.seed(2018-11-01)
dat <- rpois(200, 10)
me  <- c("Mordor", "Shire", "Isengard", "Eisengard")
grp <- sample(me, 
              200,
              replace = TRUE,
              prob = c(1, 1, 1, 0.05))
i   <- incidence(dat, group = grp)
plot(i, show_cases = TRUE)

i   <- incidence(dat, group = factor(grp, me))
plot(i, show_cases = TRUE)

group_names(i)
#> [1] "Mordor"    "Shire"     "Isengard"  "Eisengard"

<sup>Created on 2018-11-30 by the [reprex package](https://reprex.tidyverse.org) (v0.2.1)</sup>

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