Incidence release v1.7.5

• No user facing changes.

Incidence release v1.7.4

• No user facing changes (just fixes for CRAN notes).

Incidence version 1.7.2

This is a minor release that reverts a kludge to prevent a {ggplot2} bug (see #126 and #119 for details)

Incidence version 1.7.0

Incidence can now handle standardised weeks starting on any day thanks to the aweek package 🎉

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 (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 #67)
• Weekly intervals can start on any day of the week by allowing things like
  "epiweek", "isoweek", "wednesday week", "2 Saturday weeks", etc.
  (see #55 (comment))
• 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.

Incidence version 1.6.0

The changes in this version are small, but the impact changes the behavior, so the minor version number is bumped. This updates first_date to NOT override standard = TRUE. This changes behavior because first_date used to automatically set standard = FALSE.

The change to having standard supersede first_date is more consistent with normal behavior and gives users more freedom in the end. Much thanks goes to @caijun for pointing this out and elaborating patiently.

To alert users to the change while minimizing annoyance, a one-time warning is now issued if standard is not specified with first_date. This can be explicitly turned off by setting an the incidence.warn.first_date option to FALSE (as described in the warning):

library("incidence")
d <- Sys.Date() + sample(-3:10, 10, replace = TRUE)
Sys.Date() - 10
#> [1] "2019-02-23"

If both standard and first_datespecified, no warning

incidence(d, interval = "week", first_date = Sys.Date() - 10, standard = TRUE)
#> <incidence object>
#> [10 cases from days 2019-02-18 to 2019-03-11]
#> [10 cases from ISO weeks 2019-W08 to 2019-W11]
#> 
#> $counts: matrix with 4 rows and 1 columns
#> $n: 10 cases in total
#> $dates: 4 dates marking the left-side of bins
#> $interval: 1 week
#> $timespan: 22 days
#> $cumulative: FALSE

warning issued if standard not specified

incidence(d, interval = "week", first_date = Sys.Date() - 10)
#> Warning in incidence.Date(d, interval = "week", first_date = Sys.Date() - : 
#> 
#> As of incidence version 1.6.0, the default behavior has been modified so that `first_date` no longer overrides `standard`. If you want to use Sys.Date() - 10 as the precise `first_date`, set `standard = FALSE`.
#> 
#> To remove this warning in the future,  explicitly set the `standard` argument OR use `options(incidence.warn.first_date = FALSE)`
#> <incidence object>
#> [10 cases from days 2019-02-18 to 2019-03-11]
#> [10 cases from ISO weeks 2019-W08 to 2019-W11]
#> 
#> $counts: matrix with 4 rows and 1 columns
#> $n: 10 cases in total
#> $dates: 4 dates marking the left-side of bins
#> $interval: 1 week
#> $timespan: 22 days
#> $cumulative: FALSE

no warning issued the second time around.

incidence(d, interval = "week", first_date = Sys.Date() - 10)
#> <incidence object>
#> [10 cases from days 2019-02-18 to 2019-03-11]
#> [10 cases from ISO weeks 2019-W08 to 2019-W11]
#> 
#> $counts: matrix with 4 rows and 1 columns
#> $n: 10 cases in total
#> $dates: 4 dates marking the left-side of bins
#> $interval: 1 week
#> $timespan: 22 days
#> $cumulative: FALSE

^{Created on 2019-03-05 by the reprex package (v0.2.1)}

Full changes detailed below:

---

BEHAVIORAL CHANGE

• incidence() will no longer allow a non-standard first_date to override
  standard = TRUE. The first call to incidence() specifying first_date
  without standard will issue a warning. To use non-standard first dates,
  specify standard = FALSE. To remove the warning, use
  options(incidence.warn.first_date = FALSE). See
  #87 for details.

MISC

• citation("incidence") will now give the proper citation for our article in
  F1000 research and the global DOI for archived code. See
  https://github.com/reconhub/incidence/pulls/106
• Tests have been updated to avoid randomisation errors on R 3.6.0
  See #107

Incidence version 1.5.4

This is another small release of incidence that fixes a few bugs:

BUG FIX

• incidence() now returns an error when supplied a character vector that is not formatted as (yyyy-mm-dd). (See #88)
• fit() now returns correct coefficients when dates is POSIXt by converting to Date. (See #91)
• plot.incidence() now plots in UTC by default for POSIXt incidence objects. This prevents a bug where different time zones would cause a shift in the bars (See #99).

MISC

• A test that randomly failed on CRAN has been fixed. (See #95).
• Plotting tests have been updated for new version of vdiffr (See #96).
• POSIXct incidence are first passed through POSIXlt when initialized.
• A more informative error message is generated for non ISO 8601 formatted first_date and last_date parameters.

This also introduces new contributor @jrcpulliam! 🎉 🎉 🎉

Incidence version 1.5.3

This is a patch release that fixes an issue with handling single-group incidence curves.

You can install this version like so:

remotes::install_github("reconhub/[email protected]")

Incidence version 1.5.2

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"

^{Created on 2018-11-30 by the reprex package (v0.2.1)}

Incidence version 1.5.1

This version is a bug fix version:

BUG FIX

• Two bugs regarding the ordering of groups when the user specifies a factor/
  column order have been fixed. This affects plot.incidence(), incidence(),
  and as.data.frame.incidence() For details, see #79

incidence version 1.5.0

This release of incidence contains a couple of bug fixes, new accessor functions for incidence elements, and a new plotting parameter that highlights individual cases for small epicurves. Below are a couple of highlights:

Individual cases in epicurves

You can now use the option show_cases = TRUE to show individual cases on the epicurve:

library("incidence")
library("outbreaks") 
require("ggplot2")

onset <- ebola_sim$linelist$date_of_onset
sex <- ebola_sim$linelist$gender
inc.week.gender <- incidence(onset, interval = 7, groups = sex)

## show individual cases at the beginning of the epidemic
inc.week.8 <- subset(inc.week.gender, to = "2014-06-01")

plot(inc.week.8, show_cases = TRUE, border = "black")

Accessing and fixing group names

If you use a grouping factor that contains mistakes (i.e. a typo in a location column), you can correct those mistakes by using group_names():

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

Clearly "Eisengard" is supposed to be "Isengard" in this case. To correct it, we just have to correct the group names and re-assign them:

# fix Eisengard to Isengard
print(gnames <- group_names(i))
#> [1] "Eisengard" "Isengard"  "Mordor"    "Shire"
gnames[gnames == "Eisengard"] <- "Isengard"
print(gnames)
#> [1] "Isengard" "Isengard" "Mordor"   "Shire"
i.fix <- group_names(i, gnames)
plot(i.fix, show_cases = TRUE)

^{Created on 2018-11-01 by the reprex package (v0.2.1)}

Full Changeset for incidence 1.5.0

NEW FUNCTIONS

• group_names() allows the user to retrieve and set the group names.
• get_timespan() returns the $timespan element.
• get_n() returns the $n element.
• dim(), nrow(), and ncol() are now available for incidence objects,
  returning the dimensions of the number of bins and the number of groups.

NEW FEATURES

• A new argument to plot() called show_cases has been added to draw borders
  around individual cases for EPIET-style curves.
  See #72 for details.

DOCUMENTATION UPDATES

• An example of EPIET-style bars for small data sets has been added to the
  plot customisation vignette by @jakobschumacher.
  See #68 for details.
• The incidence class vignette has been updated to use the available accessors.

BUG FIX

• estimate_peak() no longer fails with integer dates
• incidence() no longer fails when providing both group information and a
  first_date or last_date parameter that is inside the bounds of the
  observed dates. Thanks to @mfaber for reporting this bug.
  See #70 for details.

MISC

• code has been spread out into a more logical file structure where the
  internal_checks.R file has been split into the relative components.
• A message is now printed if missing observations are present when
  creating the incidence object.