inst/tinytest/test-S3methods.R

In longevity: Statistical Methods for the Analysis of Excess Lifetimes

# Check that plots work with both base R and with ggplot2

library(tinytest)
library(longevity)

set.seed(1234)
n <- 100L
x <- samp_elife(
  n = n,
  scale = 2,
  shape = 0.5,
  lower = low <- runif(n),
  upper = upp <- runif(n, min = 3, max = 15),
  type2 = "ltrc",
  family = "weibull"
)
fit <- fit_elife(
  time = x$dat,
  ltrunc = low,
  event = !x$rcens,
  family = "weibull",
  export = TRUE
)
fit2 <- fit_elife(
  time = x$dat,
  ltrunc = low,
  event = !x$rcens,
  family = "extweibull",
  export = TRUE
)
anova(fit, fit2)
plot(fit2, which.plot = "pp", plot.type = "base")
plot(fit2, which.plot = "qq", plot.type = "base")
# Warning because erp == pp w/o censoring
plot(fit2, which.plot = "erp", plot.type = "base")
plot(fit2, which.plot = "exp", plot.type = "base")
plot(fit2, which.plot = "tmd", plot.type = "base")
plot(fit2, which.plot = "dens", plot.type = "base")
plot(fit2, which.plot = "cdf", plot.type = "base")

plot(fit, which.plot = "pp", plot.type = "ggplot")
plot(fit, which.plot = "qq", plot.type = "ggplot")
plot(fit, which.plot = "erp", plot.type = "ggplot")
plot(fit, which.plot = "exp", plot.type = "ggplot")
plot(fit, which.plot = "tmd", plot.type = "ggplot")
plot(fit, which.plot = "dens", plot.type = "ggplot")
plot(fit, which.plot = "cdf", plot.type = "ggplot")

expect_true(isTRUE(all.equal(deviance(fit), as.numeric(logLik(fit)) * -2)))
expect_true(length(x$dat) == nobs(fit))

set.seed(1234)
n <- 100L
x <- samp_elife(
  n = n,
  scale = 2,
  shape = 0.5,
  lower = low <- runif(n),
  upper = upp <- runif(n, min = 3, max = 15),
  type2 = "ltrt",
  family = "weibull"
)
fit <- fit_elife(
  time = x,
  ltrunc = low,
  upper = upp,
  family = "weibull",
  export = TRUE
)
plot(fit, which.plot = "pp", plot.type = "base")
plot(fit, which.plot = "qq", plot.type = "base")
# Warning because erp == pp w/o censoring
expect_warning(plot(fit, which.plot = "erp", plot.type = "base"))
plot(fit, which.plot = "exp", plot.type = "base")
plot(fit, which.plot = "tmd", plot.type = "base")

plot(fit, which.plot = "pp", plot.type = "ggplot")
plot(fit, which.plot = "qq", plot.type = "ggplot")
expect_warning(plot(fit, which.plot = "erp", plot.type = "ggplot"))
plot(fit, which.plot = "exp", plot.type = "ggplot")
plot(fit, which.plot = "tmd", plot.type = "ggplot")
plot(fit, which.plot = "dens", plot.type = "ggplot")
plot(fit, which.plot = "cdf", plot.type = "ggplot")