tests/testthat/test-plot.R
In OutbreakResources/incidence: Compute, Handle, Plot and Model Incidence of Dated Events
context("Test plotting")
test_that("plot for incidence object", {
skip_on_cran()
set.seed(1)
# dat <- sample(1:50, 200, replace = TRUE, prob = 1 + exp(1:50 * 0.1))
dat <- readRDS("data_cache/mfdat.rds")[1:200]
dat2 <- as.Date("2016-01-02") + dat
dat3 <- as.POSIXct(dat2)
sex <- c(1, 1, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1,
2, 2, 2, 1, 1, 1, 2, 1, 1, 1, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 1,
1, 1, 1, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 1, 2, 2, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 2, 2, 1,
1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 1, 2, 1, 1, 1, 1,
2, 2, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1,
1, 2, 1, 2, 2, 1, 2, 2, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2,
1, 1, 2, 2, 1, 2, 1, 1, 2, 2, 1, 1, 2, 1, 1, 1)
sex <- ifelse(sex == 1, "female", "male")
dat4 <- c(dat2,
sample(dat2, replace = TRUE) + 50,
sample(dat2, replace = TRUE) + 100
)
# constructing data
i <- incidence(dat)
iog <- incidence(dat, groups = rep("this group", 200))
i.3 <- incidence(dat, 3L)
i.14 <- incidence(dat, 14L)
i.sex <- incidence(dat, 7L, groups = sex)
# Dates ---------------------------------------------------------------------
i.POSIX <- incidence(as.POSIXct(dat2, tz = "GMT"))
i.isoweek <- incidence(dat2, 7L, standard = TRUE)
# character intervals -------------------------------------------------------
# Weekly intervals ------------------------------------------
i.epiweek <- incidence(dat2, "1 epiweek", standard = TRUE)
i.twoepiweek <- incidence(dat2, "2 epiweeks", standard = TRUE)
i.sunweek <- incidence(dat2, "1 sunday week")
i.monweek <- incidence(dat2, "1 monday week")
i.tueweek <- incidence(dat2, "1 tuesday week")
i.wedweek <- incidence(dat2, "1 wednesday week")
i.thuweek <- incidence(dat2, "1 thursday week")
i.friweek <- incidence(dat2, "1 friday week")
i.satweek <- incidence(dat2, "1 saturday week")
expect_identical(i.epiweek, i.sunweek)
expect_identical(i.isoweek$weeks, i.monweek$weeks)
expect_identical(get_counts(i.isoweek), get_counts(i.monweek))
# months and quarters ---------------------------------------
i.sexmonth <- incidence(dat4, "1 month", groups = rep(sex, 3))
i.sexquarter <- incidence(dat4, "1 quarter", groups = rep(sex, 3))
# special case for fit_optim_split:
i.sex.o <- incidence(c(dat, abs(dat - 45) + 45), 7L, groups = c(sex, rev(sex)))
fit.i <- suppressWarnings(fit(i))
fit.i.2 <- suppressWarnings(fit(i, split = 30))
fit.i.3 <- suppressWarnings(fit(i.3[5:13]))
fit.POSIX <- suppressWarnings(fit(i.POSIX))
fit.sex <- suppressWarnings(fit(i.sex))
fit.sex.o <- suppressWarnings(fit_optim_split(i.sex.o))
fit.o <- suppressWarnings(fit_optim_split(pool(i.sex.o)))
p.fit.i <- plot(fit.i)
p.fit.i.2 <- plot(i, fit = fit.i.2, color = "lightblue")
p.fit.sex <- plot(fit.sex)
p.optim.sex <- fit.sex.o$plot
p.optim.sex.fit <- plot(fit.sex.o$fit)
p.optim <- fit.o$plot
p.i <- plot(i)
p.i.cum <- plot(cumulate(i))
p.i.square <- plot(i, show_cases = TRUE)
p.i.14 <- plot(i.14)
p.i.2 <- plot(i, color = "blue", alpha = .2)
p.i.3 <- plot(i.3, fit = fit.i.3, color = "red")
p.sex <- plot(i.sex)
p.sex.cum <- plot(cumulate(i.sex))
p.sex.2 <- plot(i.sex, fit = fit.sex)
suppressMessages(p.sex.o <- plot(i.sex, fit = fit.sex.o$fit))
p.sex.3 <- plot(i.sex, fit = fit.sex, col_pal = rainbow)
p.sex.4 <- plot(i.sex, fit = fit.sex,
color = c(male = "salmon3", female = "gold2"))
p.isoweek <- plot(i.isoweek)
p.isoweek.2 <- plot(i.isoweek, labels_week = FALSE)
p.epiweek <- plot(i.epiweek)
p.epiweek.2 <- plot(i.epiweek, labels_week = FALSE)
p.epiweek.b <- plot(i.epiweek, labels_week = FALSE, n_breaks = nrow(i.epiweek))
p.twoepiweek <- plot(i.twoepiweek, n_breaks = nrow(i.twoepiweek))
p.sunweek <- plot(i.sunweek)
expect_warning({
p.sunweek.2 <- plot(i.sunweek, labels_iso = FALSE)
}, "labels_iso is deprecated. Use `labels_week` instead")
p.monweek <- plot(i.monweek)
expect_warning({
p.monweek.2 <- plot(i.monweek, labels_week = FALSE, labels_iso = TRUE)
}, "labels_iso is deprecated. The value of `labels_week` will be used")
p.tueweek <- plot(i.tueweek)
p.tueweek.2 <- plot(i.tueweek, labels_week = FALSE)
p.wedweek <- plot(i.wedweek)
p.wedweek.2 <- plot(i.wedweek, labels_week = FALSE)
p.thuweek <- plot(i.thuweek)
p.thuweek.2 <- plot(i.thuweek, labels_week = FALSE)
p.friweek <- plot(i.friweek)
p.friweek.2 <- plot(i.friweek, labels_week = FALSE)
p.satweek <- plot(i.satweek)
p.satweek.2 <- plot(i.satweek, labels_week = FALSE)
p.POSIX <- plot(i.POSIX)
p.POSIX.f <- plot(i.POSIX, fit = fit.POSIX)
p.month <- plot(i.sexmonth)
p.quarter <- plot(i.sexquarter)
## messages
expect_message(plot(i.sex, show_cases = TRUE, stack = FALSE),
"`show_cases` requires the argument `stack = TRUE`")
expect_message(p.iog <- plot(iog, color = c("this group" = "blue", "that group" = "red")),
"1 colors were not used: \"that group\" = \"red\"")
## errors
expect_error(plot(i, fit = "tamere"),
"Fit must be a 'incidence_fit' object, or a list of these")
expect_error(plot(i, fit = list(fit.i, "tamere")),
"The 2-th item in 'fit' is not an 'incidence_fit' object, but a character")
## Normal plots
vdiffr::expect_doppelganger("incidence fit", p.fit.i)
vdiffr::expect_doppelganger("incidence plot with two fitting models", p.fit.i.2)
vdiffr::expect_doppelganger("grouped incidence fit", p.fit.sex)
vdiffr::expect_doppelganger("incidence plot with default interval", p.i)
vdiffr::expect_doppelganger("incidence plot with default interval, cumulative", p.i.cum)
vdiffr::expect_doppelganger("incidence plot with interval of 14 days", p.i.14)
vdiffr::expect_doppelganger("incidence plot with specified color and alpha", p.i.2)
vdiffr::expect_doppelganger("incidence plot with interval of 3 days, fit and specified color", p.i.3)
vdiffr::expect_doppelganger("grouped incidence plot", p.sex)
vdiffr::expect_doppelganger("grouped incidence plot with one group", p.iog)
vdiffr::expect_doppelganger("grouped incidence plot, cumulative", p.sex.cum)
vdiffr::expect_doppelganger("grouped incidence plot with fit", p.sex.2)
vdiffr::expect_doppelganger("grouped incidence plot with color palette", p.sex.3)
vdiffr::expect_doppelganger("grouped incidence plot with specified color", p.sex.4)
vdiffr::expect_doppelganger("incidence plot from POSIXct data", p.POSIX)
vdiffr::expect_doppelganger("incidence plot from POSIXct data with fit", p.POSIX.f)
vdiffr::expect_doppelganger("incidence plot with isoweek labels", p.isoweek)
vdiffr::expect_doppelganger("incidence plot without isoweek labels", p.isoweek.2)
vdiffr::expect_doppelganger("incidence plot by month", p.month)
vdiffr::expect_doppelganger("incidence plot by quarter", p.quarter)
vdiffr::expect_doppelganger("incidence fit plot with split", p.sex.o)
vdiffr::expect_doppelganger("incidence fit list plot with split", p.optim.sex.fit)
vdiffr::expect_doppelganger("split optimum plot", p.optim.sex)
vdiffr::expect_doppelganger("split optimum plot pooled", p.optim)
vdiffr::expect_doppelganger("epiquares single plot", p.i.square)
## Weekly plots
vdiffr::expect_doppelganger("sun weekly incidence with labels", p.sunweek)
vdiffr::expect_doppelganger("sun weekly incidence with labels", p.epiweek)
vdiffr::expect_doppelganger("sun weekly incidence with dates", p.sunweek.2)
vdiffr::expect_doppelganger("sun weekly incidence with dates", p.epiweek.2)
vdiffr::expect_doppelganger("sun weekly incidence with dates and full breaks", p.epiweek.b)
vdiffr::expect_doppelganger("sun semi-weekly incidence with dates and full breaks", p.twoepiweek)
vdiffr::expect_doppelganger("mon weekly incidence with labels", p.monweek)
vdiffr::expect_doppelganger("mon weekly incidence with dates", p.monweek.2)
vdiffr::expect_doppelganger("tue weekly incidence with labels", p.tueweek)
vdiffr::expect_doppelganger("tue weekly incidence with dates", p.tueweek.2)
vdiffr::expect_doppelganger("wed weekly incidence with labels", p.wedweek)
vdiffr::expect_doppelganger("wed weekly incidence with dates", p.wedweek.2)
vdiffr::expect_doppelganger("thu weekly incidence with labels", p.thuweek)
vdiffr::expect_doppelganger("thu weekly incidence with dates", p.thuweek.2)
vdiffr::expect_doppelganger("fri weekly incidence with labels", p.friweek)
vdiffr::expect_doppelganger("fri weekly incidence with dates", p.friweek.2)
vdiffr::expect_doppelganger("sat weekly incidence with labels", p.satweek)
vdiffr::expect_doppelganger("sat weekly incidence with dates", p.satweek.2)
})
OutbreakResources/incidence documentation built on Nov. 13, 2020, 2:49 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("Test plotting")
test_that("plot for incidence object", {
skip_on_cran()
set.seed(1)
# dat <- sample(1:50, 200, replace = TRUE, prob = 1 + exp(1:50 * 0.1))
dat <- readRDS("data_cache/mfdat.rds")[1:200]
dat2 <- as.Date("2016-01-02") + dat
dat3 <- as.POSIXct(dat2)
sex <- c(1, 1, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1,
2, 2, 2, 1, 1, 1, 2, 1, 1, 1, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 1,
1, 1, 1, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 1, 2, 2, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 2, 2, 1,
1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 1, 2, 1, 1, 1, 1,
2, 2, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1,
1, 2, 1, 2, 2, 1, 2, 2, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2,
1, 1, 2, 2, 1, 2, 1, 1, 2, 2, 1, 1, 2, 1, 1, 1)
sex <- ifelse(sex == 1, "female", "male")
dat4 <- c(dat2,
sample(dat2, replace = TRUE) + 50,
sample(dat2, replace = TRUE) + 100
)
# constructing data
i <- incidence(dat)
iog <- incidence(dat, groups = rep("this group", 200))
i.3 <- incidence(dat, 3L)
i.14 <- incidence(dat, 14L)
i.sex <- incidence(dat, 7L, groups = sex)
# Dates ---------------------------------------------------------------------
i.POSIX <- incidence(as.POSIXct(dat2, tz = "GMT"))
i.isoweek <- incidence(dat2, 7L, standard = TRUE)
# character intervals -------------------------------------------------------
# Weekly intervals ------------------------------------------
i.epiweek <- incidence(dat2, "1 epiweek", standard = TRUE)
i.twoepiweek <- incidence(dat2, "2 epiweeks", standard = TRUE)
i.sunweek <- incidence(dat2, "1 sunday week")
i.monweek <- incidence(dat2, "1 monday week")
i.tueweek <- incidence(dat2, "1 tuesday week")
i.wedweek <- incidence(dat2, "1 wednesday week")
i.thuweek <- incidence(dat2, "1 thursday week")
i.friweek <- incidence(dat2, "1 friday week")
i.satweek <- incidence(dat2, "1 saturday week")
expect_identical(i.epiweek, i.sunweek)
expect_identical(i.isoweek$weeks, i.monweek$weeks)
expect_identical(get_counts(i.isoweek), get_counts(i.monweek))
# months and quarters ---------------------------------------
i.sexmonth <- incidence(dat4, "1 month", groups = rep(sex, 3))
i.sexquarter <- incidence(dat4, "1 quarter", groups = rep(sex, 3))
# special case for fit_optim_split:
i.sex.o <- incidence(c(dat, abs(dat - 45) + 45), 7L, groups = c(sex, rev(sex)))
fit.i <- suppressWarnings(fit(i))
fit.i.2 <- suppressWarnings(fit(i, split = 30))
fit.i.3 <- suppressWarnings(fit(i.3[5:13]))
fit.POSIX <- suppressWarnings(fit(i.POSIX))
fit.sex <- suppressWarnings(fit(i.sex))
fit.sex.o <- suppressWarnings(fit_optim_split(i.sex.o))
fit.o <- suppressWarnings(fit_optim_split(pool(i.sex.o)))
p.fit.i <- plot(fit.i)
p.fit.i.2 <- plot(i, fit = fit.i.2, color = "lightblue")
p.fit.sex <- plot(fit.sex)
p.optim.sex <- fit.sex.o$plot
p.optim.sex.fit <- plot(fit.sex.o$fit)
p.optim <- fit.o$plot
p.i <- plot(i)
p.i.cum <- plot(cumulate(i))
p.i.square <- plot(i, show_cases = TRUE)
p.i.14 <- plot(i.14)
p.i.2 <- plot(i, color = "blue", alpha = .2)
p.i.3 <- plot(i.3, fit = fit.i.3, color = "red")
p.sex <- plot(i.sex)
p.sex.cum <- plot(cumulate(i.sex))
p.sex.2 <- plot(i.sex, fit = fit.sex)
suppressMessages(p.sex.o <- plot(i.sex, fit = fit.sex.o$fit))
p.sex.3 <- plot(i.sex, fit = fit.sex, col_pal = rainbow)
p.sex.4 <- plot(i.sex, fit = fit.sex,
color = c(male = "salmon3", female = "gold2"))
p.isoweek <- plot(i.isoweek)
p.isoweek.2 <- plot(i.isoweek, labels_week = FALSE)
p.epiweek <- plot(i.epiweek)
p.epiweek.2 <- plot(i.epiweek, labels_week = FALSE)
p.epiweek.b <- plot(i.epiweek, labels_week = FALSE, n_breaks = nrow(i.epiweek))
p.twoepiweek <- plot(i.twoepiweek, n_breaks = nrow(i.twoepiweek))
p.sunweek <- plot(i.sunweek)
expect_warning({
p.sunweek.2 <- plot(i.sunweek, labels_iso = FALSE)
}, "labels_iso is deprecated. Use `labels_week` instead")
p.monweek <- plot(i.monweek)
expect_warning({
p.monweek.2 <- plot(i.monweek, labels_week = FALSE, labels_iso = TRUE)
}, "labels_iso is deprecated. The value of `labels_week` will be used")
p.tueweek <- plot(i.tueweek)
p.tueweek.2 <- plot(i.tueweek, labels_week = FALSE)
p.wedweek <- plot(i.wedweek)
p.wedweek.2 <- plot(i.wedweek, labels_week = FALSE)
p.thuweek <- plot(i.thuweek)
p.thuweek.2 <- plot(i.thuweek, labels_week = FALSE)
p.friweek <- plot(i.friweek)
p.friweek.2 <- plot(i.friweek, labels_week = FALSE)
p.satweek <- plot(i.satweek)
p.satweek.2 <- plot(i.satweek, labels_week = FALSE)
p.POSIX <- plot(i.POSIX)
p.POSIX.f <- plot(i.POSIX, fit = fit.POSIX)
p.month <- plot(i.sexmonth)
p.quarter <- plot(i.sexquarter)
## messages
expect_message(plot(i.sex, show_cases = TRUE, stack = FALSE),
"`show_cases` requires the argument `stack = TRUE`")
expect_message(p.iog <- plot(iog, color = c("this group" = "blue", "that group" = "red")),
"1 colors were not used: \"that group\" = \"red\"")
## errors
expect_error(plot(i, fit = "tamere"),
"Fit must be a 'incidence_fit' object, or a list of these")
expect_error(plot(i, fit = list(fit.i, "tamere")),
"The 2-th item in 'fit' is not an 'incidence_fit' object, but a character")
## Normal plots
vdiffr::expect_doppelganger("incidence fit", p.fit.i)
vdiffr::expect_doppelganger("incidence plot with two fitting models", p.fit.i.2)
vdiffr::expect_doppelganger("grouped incidence fit", p.fit.sex)
vdiffr::expect_doppelganger("incidence plot with default interval", p.i)
vdiffr::expect_doppelganger("incidence plot with default interval, cumulative", p.i.cum)
vdiffr::expect_doppelganger("incidence plot with interval of 14 days", p.i.14)
vdiffr::expect_doppelganger("incidence plot with specified color and alpha", p.i.2)
vdiffr::expect_doppelganger("incidence plot with interval of 3 days, fit and specified color", p.i.3)
vdiffr::expect_doppelganger("grouped incidence plot", p.sex)
vdiffr::expect_doppelganger("grouped incidence plot with one group", p.iog)
vdiffr::expect_doppelganger("grouped incidence plot, cumulative", p.sex.cum)
vdiffr::expect_doppelganger("grouped incidence plot with fit", p.sex.2)
vdiffr::expect_doppelganger("grouped incidence plot with color palette", p.sex.3)
vdiffr::expect_doppelganger("grouped incidence plot with specified color", p.sex.4)
vdiffr::expect_doppelganger("incidence plot from POSIXct data", p.POSIX)
vdiffr::expect_doppelganger("incidence plot from POSIXct data with fit", p.POSIX.f)
vdiffr::expect_doppelganger("incidence plot with isoweek labels", p.isoweek)
vdiffr::expect_doppelganger("incidence plot without isoweek labels", p.isoweek.2)
vdiffr::expect_doppelganger("incidence plot by month", p.month)
vdiffr::expect_doppelganger("incidence plot by quarter", p.quarter)
vdiffr::expect_doppelganger("incidence fit plot with split", p.sex.o)
vdiffr::expect_doppelganger("incidence fit list plot with split", p.optim.sex.fit)
vdiffr::expect_doppelganger("split optimum plot", p.optim.sex)
vdiffr::expect_doppelganger("split optimum plot pooled", p.optim)
vdiffr::expect_doppelganger("epiquares single plot", p.i.square)
## Weekly plots
vdiffr::expect_doppelganger("sun weekly incidence with labels", p.sunweek)
vdiffr::expect_doppelganger("sun weekly incidence with labels", p.epiweek)
vdiffr::expect_doppelganger("sun weekly incidence with dates", p.sunweek.2)
vdiffr::expect_doppelganger("sun weekly incidence with dates", p.epiweek.2)
vdiffr::expect_doppelganger("sun weekly incidence with dates and full breaks", p.epiweek.b)
vdiffr::expect_doppelganger("sun semi-weekly incidence with dates and full breaks", p.twoepiweek)
vdiffr::expect_doppelganger("mon weekly incidence with labels", p.monweek)
vdiffr::expect_doppelganger("mon weekly incidence with dates", p.monweek.2)
vdiffr::expect_doppelganger("tue weekly incidence with labels", p.tueweek)
vdiffr::expect_doppelganger("tue weekly incidence with dates", p.tueweek.2)
vdiffr::expect_doppelganger("wed weekly incidence with labels", p.wedweek)
vdiffr::expect_doppelganger("wed weekly incidence with dates", p.wedweek.2)
vdiffr::expect_doppelganger("thu weekly incidence with labels", p.thuweek)
vdiffr::expect_doppelganger("thu weekly incidence with dates", p.thuweek.2)
vdiffr::expect_doppelganger("fri weekly incidence with labels", p.friweek)
vdiffr::expect_doppelganger("fri weekly incidence with dates", p.friweek.2)
vdiffr::expect_doppelganger("sat weekly incidence with labels", p.satweek)
vdiffr::expect_doppelganger("sat weekly incidence with dates", p.satweek.2)
})
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