Nothing
context("plotreg")
suppressPackageStartupMessages(library("texreg"))
skip_if_not_installed("ggplot2")
require("ggplot2")
test_that("plotreg works", {
skip_if_not_installed("ggplot2", minimum_version = "3.3.1")
# linear model p-values
ctl <- c(4.17, 5.58, 5.18, 6.11, 4.50, 4.61, 5.17, 4.53, 5.33, 5.14)
trt <- c(4.81, 4.17, 4.41, 3.59, 5.87, 3.83, 6.03, 4.89, 4.32, 4.69)
group <- gl(2, 10, 20, labels = c("Ctl", "Trt"))
weight <- c(ctl, trt)
m1 <- lm(weight ~ group)
m2 <- lm(weight ~ group - 1)
p1 <- plotreg(list(m1, m2))
p2 <- plotreg(list(m1, m2), ci.force = TRUE)
p3 <- plotreg(list(m1, m2), custom.title = "My plot")
p4 <- plotreg(list(m1, m2), custom.note = "My note")
expect_true(ggplot2::is.ggplot(p1))
expect_true(ggplot2::is.ggplot(p2))
expect_true(ggplot2::is.ggplot(p3))
expect_true(ggplot2::is.ggplot(p4))
expect_s3_class(p1$data, "data.frame")
expect_s3_class(p1, "gg")
expect_equal(dim(p1$data), dim(readRDS("../files/PlotDataFrame.RDS"))) # test if data frame is correctly constructed
#saveRDS(p1$data, "../files/PlotDataFrame.RDS")
expect_identical(p1$labels$y, "Bars denote SEs (95%). Circle points denote significance.")# tests if it is printing the correct xlab
expect_identical(p2$labels$y, "Bars denote CIs (95%) computed from SEs. Circle points denote significance.") # tests if it is printing the correct xlab
expect_identical(p3$labels$title, "My plot") # test if title is printed
expect_identical(p4$labels$y, "My note") # test if note is printed
})
test_that("plotreg works with confidence intervals using the biglm package", {
skip_if_not_installed("ggplot2", minimum_version = "3.3.1")
skip_if_not_installed("biglm")
require("biglm")
skip_if_not_installed("DBI")
data("trees")
ff <- log(Volume) ~ log(Girth) + log(Height)
a <- biglm::bigglm(ff, data = trees, chunksize = 10, sandwich = TRUE)
gg <- log(Volume) ~ log(Girth) + log(Height) + offset(2 * log(Girth) + log(Height))
b <- biglm::bigglm(gg, data = trees, chunksize = 10, sandwich = TRUE)
p6 <- plotreg(list(a, b))
expect_true(ggplot2::is.ggplot(p6))
expect_equal(dim(p6$data), dim(readRDS("../files/PlotDataFrameCI.RDS")))
# saveRDS(p6$data, "../files/PlotDataFrameCI.RDS")
expect_identical(p6$labels$y, "Bars denote SEs (95%). Circle points denote significance.")
})
test_that("plotreg -odds ratio", {
skip_if_not_installed("ggplot2", minimum_version = "3.3.1")
# linear model p-values
# the model is not actually suitable for odds ratio estimation, but it
# makes no difference for testing plotreg
ctl <- c(4.17, 5.58, 5.18, 6.11, 4.50, 4.61, 5.17, 4.53, 5.33, 5.14)
trt <- c(4.81, 4.17, 4.41, 3.59, 5.87, 3.83, 6.03, 4.89, 4.32, 4.69)
group <- gl(2, 10, 20, labels = c("Ctl", "Trt"))
weight <- c(ctl, trt)
m1 <- lm(weight ~ group)
p7 <- plotreg(m1, override.coef = exp(m1$coefficients), ci.force = TRUE, ci.test = 1)
expect_true(ggplot2::is.ggplot(p7))
expect_s3_class(p7$data, "data.frame")
expect_s3_class(p7, "gg")
expect_equal(dim(p7$data), dim(readRDS("../files/PlotDataFrameOR.RDS"))) # test if data frame is correctly constructed
#saveRDS(p1$data, "../files/PlotDataFrameOR.RDS")
class(p7$data$signif)
# tests if significance is computed according to the value provided with ci.test
expect_identical(as.character(p7$data$signif), as.character(c(TRUE, FALSE)))
})
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