Nothing
library(joineR)
context("Plotting")
test_that("plot jointdata objects (longitudinal)", {
# load data
data(heart.valve)
heart.surv <- UniqueVariables(heart.valve,
var.col = c("fuyrs", "status"),
id.col = "num")
heart.long <- heart.valve[, c(1, 4, 5, 7, 8, 9, 10, 11)]
heart.jd <- jointdata(longitudinal = heart.long,
survival = heart.surv,
id.col = "num",
time.col = "time")
# tests
expect_silent(plot(heart.jd, Y.col = "grad", col = "grey"))
expect_silent(plot(heart.jd))
})
test_that("plot jointdata objects (joint plot)", {
# load data
data(heart.valve)
heart.surv <- UniqueVariables(heart.valve,
var.col = c("fuyrs", "status"),
id.col = "num")
heart.long <- heart.valve[, c("num", "time", "log.lvmi")]
heart.cov <- UniqueVariables(heart.valve,
c("age", "sex"),
id.col = "num")
heart.valve.jd <- jointdata(longitudinal = heart.long,
baseline = heart.cov,
survival = heart.surv,
id.col = "num",
time.col = "time")
# tests
expect_output(str(jointplot(heart.valve.jd, Y.col = "log.lvmi",
Cens.col = "status", lag = 5)),
"trellis")
expect_output(str(jointplot(heart.valve.jd, Y.col = "log.lvmi",
Cens.col = "status", lag = 5,
mean.profile = TRUE, split = FALSE)),
"trellis")
expect_output(str(jointplot(heart.valve.jd, Y.col = "log.lvmi",
Cens.col = "status", lag = 5,
mean.profile = FALSE, split = FALSE)),
"trellis")
})
test_that("points + lines added to a plot of jointdata", {
# data
data(heart.valve)
heart.surv <- UniqueVariables(heart.valve,
var.col = c("fuyrs", "status"),
id.col = "num")
heart.long <- heart.valve[, c(1, 4, 5, 7, 8, 9, 10, 11)]
heart.jd <- jointdata(longitudinal = heart.long,
survival = heart.surv,
id.col = "num",
time.col = "time")
# randomly select a pair of subjects to plot profiles of
set.seed(1)
take <- sample(1 : max(heart.jd$survival$num), 2)
heart.jd.1 <- subset(heart.jd, take[1])
heart.jd.2 <- subset(heart.jd, take[2])
ylim1 <- min(min(heart.jd.1$longitudinal$grad, na.rm = TRUE),
min(heart.jd.2$longitudinal$grad, na.rm = TRUE))
ylim2 <- max(max(heart.jd.1$longitudinal$grad, na.rm = TRUE),
max(heart.jd.2$longitudinal$grad, na.rm = TRUE))
# main plot
plot(heart.jd.1, Y.col = "grad", type = "p", ylim = c(ylim1, ylim2))
# tests
expect_silent(points(heart.jd.2, Y.col = "grad", col = "blue", pch = 20))
expect_silent(lines(heart.jd.2, Y.col = "grad", col = "blue", pch = 20))
})
test_that("variogram plot", {
# data + variogram
data(mental)
mental.unbalanced <- to.unbalanced(mental, id.col = 1,
times = c(0, 1, 2, 4, 6, 8),
Y.col = 2:7,
other.col = c(8, 10, 11))
names(mental.unbalanced)[3] <- "Y"
vgm <- variogram(indv = tail(mental.unbalanced[, 1], 30),
time = tail(mental.unbalanced[, 2], 30),
Y = tail(mental.unbalanced[, 3], 30))
# tests
expect_silent(plot(vgm))
})
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