Nothing
tests/testthat/test-ttestplots.R
In procs: Recreates Some 'SAS®' Procedures in 'R'
base_path <- file.path(getwd(), "tests/testthat")
data_dir <- base_path
base_path <- tempdir()
data_dir <- "."
cls <- read.table(header = TRUE, text = '
Name Sex Age Height Weight region
Alfred M 14 69.0 112.5 A
Alice F 13 56.5 84.0 A
Barbara F 13 65.3 98.0 A
Carol F 14 62.8 102.5 A
Henry M 14 63.5 102.5 A
James M 12 57.3 83.0 A
Jane F 12 59.8 84.5 A
Janet F 15 62.5 112.5 A
Jeffrey M 13 62.5 84.0 A
John M 12 59.0 99.5 B
Joyce F 11 51.3 50.5 B
Judy F 14 64.3 90.0 B
Louise F 12 56.3 77.0 B
Mary F 15 66.5 112.0 B
Philip M 16 72.0 150.0 B
Robert M 12 64.8 128.0 B
Ronald M 15 67.0 133.0 B
Thomas M 11 57.5 85.0 B
William M 15 66.5 112.0 B')
paird <- read.table(header = TRUE, text = '
subject_id before after region
1 12 15 A
2 14 16 A
3 10 11 A
4 15 18 A
5 18 20 A
6 20 22 B
7 11 12 B
8 13 14 B
9 16 17 B
10 9 13 B')
clsna <- read.table(header = TRUE, text = '
Name Sex Age Height Weight region
Alfred M 14 69.0 112.5 A
Alice F 13 56.5 84.0 A
Barbara F 13 65.3 98.0 A
Carol F 14 62.8 102.5 A
Henry M 14 63.5 102.5 A
James M 12 NA 83.0 A
Jane NA 12 59.8 84.5 A
Janet F 15 62.5 112.5 A
Jeffrey M 13 62.5 84.0 A
John M 12 59.0 99.5 B
Joyce F 11 51.3 50.5 B
Judy F 14 64.3 90.0 B
Louise F 12 56.3 NA B
Mary F 15 66.5 112.0 B
Philip M 16 72.0 150.0 B
Robert M 12 64.8 128.0 B
Ronald M 15 67.0 133.0 B
Thomas M 11 57.5 85.0 B
William M 15 66.5 112.0 B')
options("logr.output" = FALSE)
options("procs.print" = FALSE)
dev <- FALSE
test_that("ttestplot1: ttestplot() object works as expected.", {
# Defaults
res <- ttestplot()
res
expect_equal("ttestplot" %in% class(res), TRUE)
expect_equal(res$showh0, FALSE)
expect_equal(res$panel, TRUE)
expect_equal(res$type, c("default"))
# Assign something
res <- ttestplot(type = c("agreement", "boxplot", "histogram", 'interval', 'profiles'))
res
expect_equal("ttestplot" %in% class(res), TRUE)
expect_equal(res$type, c("agreement", "boxplot", "histogram", 'interval', 'profiles'))
})
test_that("ttestplot2: basic plot types.", {
# Histogram - OK
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Histogram - OK
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot - OK
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval - OK
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("interval"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# QQPlot - Line not correct. Dots look good.
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("qqplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
# Nice!
test_that("ttestplot3: multiple plot types.", {
# Combined
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot(c("histogram", "boxplot", "interval", "qqplot")))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
# OK
test_that("ttestplot4: summary plot type.", {
# Summary
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary - 90% Confidence
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary "unpacked"
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("summary", panel = FALSE))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[4]][[2]]), TRUE)
})
# OK
test_that("ttestplot5: summary plot type by groups.", {
# Summary
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
by = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
expect_equal("plot_spec" %in% class(res[[1]][[4]][[1]]), TRUE)
})
# OK
test_that("ttestplot6: multiple variables.", {
# Summary
res <- proc_ttest(cls,
var = c("Height", "Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
# by = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 8)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[8]][[1]]), TRUE)
# Multiple vars with by
res <- proc_ttest(cls,
var = c("Height", "Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
by = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
expect_equal("plot_spec" %in% class(res[[1]][[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[2]][[4]][[1]]), TRUE)
})
# OK
test_that("ttestplot7: class analysis.", {
# Boxplot with class
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("boxplot"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Interval with class - Mean of Difference
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
class = Sex,
plots = ttestplot("interval"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Histogram with class
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot with class
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# QQPlot with class
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("qqplot"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Summary with class
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot8: boxplot outliers are working as expected.", {
dt1 <- cls[cls$Sex == "F", ]
# Single chart outliers
res <- proc_ttest(dt1,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Double chart outliers
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.1),
class = "Sex",
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot8: edge cases.", {
# Boxplot - 90% confidence, and possibly outliers
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
plots = ttestplot("boxplot", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary2 scale off on this data - OK Now
res <- proc_ttest(sleep,
var = extra,
class = group,
output = report,
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot9: Paired analysis.", {
# Profiles
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("profiles"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Agreement
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("agreement"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Profiles - with by variables and multiple plot types
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
by = "Sex",
plots = ttestplot(c("profiles", "agreement")))
expect_equal(length(res), 2)
expect_equal("plot_spec" %in% class(res[[1]][[4]][[1]]), TRUE)
# Summary
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Histogram
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("histogram"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("interval"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# QQPlot
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("qqplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot10: plots = TRUE.", {
# One Sample
res <- proc_ttest(cls,
var = "Weight",
options = c(h0 = 80),
output = report,
plots = TRUE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[4]][[2]]), TRUE)
# Two Samples
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plots = TRUE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[5]][[2]]), TRUE)
# Paired
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = TRUE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Two Samples
res <- proc_ttest(cls,
var = "Weight",
class = "region",
output = report,
plots = TRUE)
# Paired
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plots = TRUE)
})
test_that("ttestplot11: plots = 'all'", {
# One Sample
res <- proc_ttest(cls,
var = "Weight",
options = c(h0 = 80),
output = report,
plots = "all")
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal(length(res[[4]]), 5)
# Two Samples
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plots = "all")
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
expect_equal(length(res[[5]]), 5)
# Paired
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plots = "all")
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal(length(res[[4]]), 7)
})
test_that("ttestplot12: Documentation examples", {
res <- proc_ttest(paird, paired = "before * after",
output = report,
plots = TRUE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal(length(res[[4]]), 4)
})
# Also check that x scale adjusts if h0 is outsize confidence intervals
test_that("ttestplot13: showh0 parameter", {
# Boxplot1
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 75, "alpha" = 0.05),
output = report,
plots = ttestplot("boxplot", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval 1
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 63, "alpha" = 0.05),
output = report,
plots = ttestplot("interval", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary 1
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 63, "alpha" = 0.05),
output = report,
plots = ttestplot("summary", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval2
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 0, "alpha" = 0.05),
class = "Sex",
output = report,
plots = ttestplot("interval", showh0 = TRUE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
# Work on this
test_that("ttestplot14: troublesome plots match SAS", {
# qqplot1 - Got it!
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("qqplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# qqplot2 - Hurray!
res <- proc_ttest(cls,
var = c("Height"),
class = "Sex",
output = report,
plot = TRUE,
options = c("alpha" = 0.1))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# histogram - Good enough
res <- proc_ttest(cls,
var = c("Age"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("histogram"))
# Boxplot1 - needs outlier. Got it!
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = "boxplot")
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot2 - needs outlier. Got it!
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = "boxplot")
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Different data with class - Fixed
res <- proc_ttest(sleep,
var = "extra",
class = "group",
output = "report",
plots = c("summary", "histogram", "boxplot"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
# Good
test_that("ttestplot15: Label and ID parameters work as expected.", {
# Boxplot1 - label FALSE
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = FALSE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot1 - label TRUE
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot1 - id value
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE, id = "Name"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot2 - label FALSE
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = FALSE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot2 - label TRUE
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot2 - id value
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE, id = "Name"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot16: plots with freq parameter.", {
# One sample with freq
cls_freq <- cls
cls_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
res <- proc_ttest(cls_freq, var = "Height",
freq = "FreqVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Two sample (class) with freq
res <- proc_ttest(cls_freq, var = "Height",
class = "Sex",
freq = "FreqVar",
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Paired with freq
paird_freq <- paird
paird_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1)
res <- proc_ttest(paird_freq,
paired = "before * after",
freq = "FreqVar",
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot17: plots with weight parameter.", {
# One sample with weight, add some strange value to show difference
cls_wgt <- cls
cls_wgt$WgtVar <- c(1.5, 2.0, 0.8, 1.2, 1.0, 1.5, 2.0, 0.8, 1.2, 1.0,
1.5, 2.0, 0.8, 1.2, 1.0, 1.5, 200, 80, 120)
res <- proc_ttest(cls_wgt, var = "Height",
weight = "WgtVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot(c("summary", "qqplot")))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
#freq and weight together
cls_wgt$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
res <- proc_ttest(cls_wgt, var = "Height",
freq = "FreqVar",
weight = "WgtVar",
output = "report",
plots = ttestplot("summary"))
# Two sample (class) with weight
res <- proc_ttest(cls_wgt, var = "Height",
class = "Sex",
weight = "WgtVar",
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Paired with weight
paird_wgt <- paird
paird_wgt$WgtVar <- c(1.5, 2.0, 0.8, 1.2, 1.0, 1.5, 2.0, 0.8, 1.2, 1.0)
res <- proc_ttest(paird_wgt,
paired = "before * after",
weight = "WgtVar",
output = "report",
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Multiple plot types with weight
res <- proc_ttest(cls_wgt, var = "Height",
weight = "WgtVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot(c("summary", "histogram", "boxplot")))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot18: plots with sides parameter (one-sample).", {
# Summary plot with sides = 'U'
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary plot with sides = 'L'
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "L"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval plot with sides option
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = ttestplot("interval"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot19: plots with sides parameter (two-sample).", {
# Summary plot with sides = 'U' and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot with sides = 'L' and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(sides = "L"),
output = "report",
plots = ttestplot("boxplot"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Interval plot with sides and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(sides = "U", alpha = 0.1),
output = "report",
plots = ttestplot("interval"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot20: plots with sides parameter (paired).", {
# Profiles plot with sides = 'U'
res <- proc_ttest(paird, paired = "before * after",
options = c(sides = "U"),
output = "report",
plots = ttestplot("profiles"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Agreement plot with sides = 'L'
res <- proc_ttest(paird, paired = "before * after",
options = c(sides = "L"),
output = "report",
plots = ttestplot("agreement"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary with paired and sides
res <- proc_ttest(paird, paired = "before * after",
options = c(sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot21: plots with freq and sides together.", {
cls_freq <- cls
cls_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
# One sample with freq and sides
res <- proc_ttest(cls_freq, var = "Height",
freq = "FreqVar",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Two sample with freq and sides
res <- proc_ttest(cls_freq, var = "Height",
class = "Sex",
freq = "FreqVar",
options = c(sides = "L"),
output = "report",
plots = ttestplot(c("summary", "boxplot")))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot22: multiple plot types with freq and sides.", {
cls_freq <- cls
cls_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
# Multiple plots with freq
res <- proc_ttest(cls_freq, var = "Height",
freq = "FreqVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot(c("summary", "histogram", "boxplot")))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# All plots with sides
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = "all")
expect_equal(length(res), 4)
expect_equal(length(res[[4]]), 5)
})
test_that("ttestplot23: plots with showh0 and sides together.", {
# showh0 with sides = 'U'
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 70, sides = "U"),
output = "report",
plots = ttestplot("summary", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# showh0 with sides = 'L' and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(h0 = 60, sides = "L"),
output = "report",
plots = ttestplot("interval", showh0 = TRUE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
# These now match SAS
test_that("ttestplot24: qqplot works as expected with weight.", {
scrs <- read.table(header = TRUE, text = '
Group Score Frequency
Online 85 10
Online 90 25
Online 92 15
InPerson 88 12
InPerson 91 30
InPerson 95 18
')
# Two charts
res <- proc_ttest(scrs,
var = "Score",
class = "Group",
weight = "Frequency",
output = "report",
plot = TRUE)
expect_equal(length(res), 5)
# expect_true(is.finite(as.numeric(res2$ConfLimits$LCLM[3])))
# Single chart
res <- proc_ttest(scrs,
var = "Score",
weight = "Frequency",
output = "report",
plot = TRUE,
options = c(h0 = 80))
expect_equal(length(res), 4)
})
test_that("ttestplot25: plots work with NAs in data.", {
# Histogram with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "histogram")
expect_equal(length(res), 5)
# Boxplot with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "boxplot")
expect_equal(length(res), 5)
# Summary with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "summary")
expect_equal(length(res), 5)
# QQplot with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "qqplot")
expect_equal(length(res), 5)
# Agreement with NA
res <- proc_ttest(clsna,
paired = "Height * Weight",
output = "report",
plots = "agreement")
expect_equal(length(res), 4)
# Paired all with NA
res <- proc_ttest(clsna,
paired = "Height * Weight",
output = "report",
plots = "all")
# Two sample all with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "all")
# One sample all with NA
res <- proc_ttest(clsna,
var = "Height",
output = "report",
options = c(h0 = 65),
plots = "all")
# One sample all with NA
res <- proc_ttest(clsna,
var = "Height",
by = "Sex",
output = "report",
options = c(h0 = 65),
plots = "all")
})
test_that("ttestplot26: More NA tests", {
# What is grey stuff at top of histogram? Fixed
proc_ttest(airquality,
paired = "Ozone * Solar.R",
plots = c("summary", "histogram"))
# Fixed
proc_ttest(airquality,
var = "Ozone",
options = c(h0 = 50),
plots = c("summary", "histogram"))
# Fixed
proc_ttest(airquality[airquality$Month %in% c(8,9), ],
var = "Ozone",
class = "Month",
plots = c("boxplot"))
expect_equal(TRUE, TRUE)
})
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base_path <- file.path(getwd(), "tests/testthat")
data_dir <- base_path
base_path <- tempdir()
data_dir <- "."
cls <- read.table(header = TRUE, text = '
Name Sex Age Height Weight region
Alfred M 14 69.0 112.5 A
Alice F 13 56.5 84.0 A
Barbara F 13 65.3 98.0 A
Carol F 14 62.8 102.5 A
Henry M 14 63.5 102.5 A
James M 12 57.3 83.0 A
Jane F 12 59.8 84.5 A
Janet F 15 62.5 112.5 A
Jeffrey M 13 62.5 84.0 A
John M 12 59.0 99.5 B
Joyce F 11 51.3 50.5 B
Judy F 14 64.3 90.0 B
Louise F 12 56.3 77.0 B
Mary F 15 66.5 112.0 B
Philip M 16 72.0 150.0 B
Robert M 12 64.8 128.0 B
Ronald M 15 67.0 133.0 B
Thomas M 11 57.5 85.0 B
William M 15 66.5 112.0 B')
paird <- read.table(header = TRUE, text = '
subject_id before after region
1 12 15 A
2 14 16 A
3 10 11 A
4 15 18 A
5 18 20 A
6 20 22 B
7 11 12 B
8 13 14 B
9 16 17 B
10 9 13 B')
clsna <- read.table(header = TRUE, text = '
Name Sex Age Height Weight region
Alfred M 14 69.0 112.5 A
Alice F 13 56.5 84.0 A
Barbara F 13 65.3 98.0 A
Carol F 14 62.8 102.5 A
Henry M 14 63.5 102.5 A
James M 12 NA 83.0 A
Jane NA 12 59.8 84.5 A
Janet F 15 62.5 112.5 A
Jeffrey M 13 62.5 84.0 A
John M 12 59.0 99.5 B
Joyce F 11 51.3 50.5 B
Judy F 14 64.3 90.0 B
Louise F 12 56.3 NA B
Mary F 15 66.5 112.0 B
Philip M 16 72.0 150.0 B
Robert M 12 64.8 128.0 B
Ronald M 15 67.0 133.0 B
Thomas M 11 57.5 85.0 B
William M 15 66.5 112.0 B')
options("logr.output" = FALSE)
options("procs.print" = FALSE)
dev <- FALSE
test_that("ttestplot1: ttestplot() object works as expected.", {
# Defaults
res <- ttestplot()
res
expect_equal("ttestplot" %in% class(res), TRUE)
expect_equal(res$showh0, FALSE)
expect_equal(res$panel, TRUE)
expect_equal(res$type, c("default"))
# Assign something
res <- ttestplot(type = c("agreement", "boxplot", "histogram", 'interval', 'profiles'))
res
expect_equal("ttestplot" %in% class(res), TRUE)
expect_equal(res$type, c("agreement", "boxplot", "histogram", 'interval', 'profiles'))
})
test_that("ttestplot2: basic plot types.", {
# Histogram - OK
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Histogram - OK
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot - OK
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval - OK
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("interval"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# QQPlot - Line not correct. Dots look good.
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("qqplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
# Nice!
test_that("ttestplot3: multiple plot types.", {
# Combined
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot(c("histogram", "boxplot", "interval", "qqplot")))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
# OK
test_that("ttestplot4: summary plot type.", {
# Summary
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary - 90% Confidence
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary "unpacked"
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("summary", panel = FALSE))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[4]][[2]]), TRUE)
})
# OK
test_that("ttestplot5: summary plot type by groups.", {
# Summary
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
by = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
expect_equal("plot_spec" %in% class(res[[1]][[4]][[1]]), TRUE)
})
# OK
test_that("ttestplot6: multiple variables.", {
# Summary
res <- proc_ttest(cls,
var = c("Height", "Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
# by = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 8)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[8]][[1]]), TRUE)
# Multiple vars with by
res <- proc_ttest(cls,
var = c("Height", "Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
by = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
expect_equal("plot_spec" %in% class(res[[1]][[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[2]][[4]][[1]]), TRUE)
})
# OK
test_that("ttestplot7: class analysis.", {
# Boxplot with class
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("boxplot"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Interval with class - Mean of Difference
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
class = Sex,
plots = ttestplot("interval"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Histogram with class
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot with class
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("histogram"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# QQPlot with class
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("qqplot"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Summary with class
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
class = Sex,
plots = ttestplot("summary"))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot8: boxplot outliers are working as expected.", {
dt1 <- cls[cls$Sex == "F", ]
# Single chart outliers
res <- proc_ttest(dt1,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Double chart outliers
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.1),
class = "Sex",
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot8: edge cases.", {
# Boxplot - 90% confidence, and possibly outliers
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 65, "alpha" = 0.1),
output = report,
plots = ttestplot("boxplot", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary2 scale off on this data - OK Now
res <- proc_ttest(sleep,
var = extra,
class = group,
output = report,
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot9: Paired analysis.", {
# Profiles
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("profiles"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Agreement
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("agreement"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Profiles - with by variables and multiple plot types
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
by = "Sex",
plots = ttestplot(c("profiles", "agreement")))
expect_equal(length(res), 2)
expect_equal("plot_spec" %in% class(res[[1]][[4]][[1]]), TRUE)
# Summary
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Histogram
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("histogram"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("interval"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# QQPlot
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = ttestplot("qqplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot10: plots = TRUE.", {
# One Sample
res <- proc_ttest(cls,
var = "Weight",
options = c(h0 = 80),
output = report,
plots = TRUE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[4]][[2]]), TRUE)
# Two Samples
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plots = TRUE)
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
expect_equal("plot_spec" %in% class(res[[5]][[2]]), TRUE)
# Paired
res <- proc_ttest(cls,
paired = "Weight * Height",
output = report,
plots = TRUE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Two Samples
res <- proc_ttest(cls,
var = "Weight",
class = "region",
output = report,
plots = TRUE)
# Paired
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plots = TRUE)
})
test_that("ttestplot11: plots = 'all'", {
# One Sample
res <- proc_ttest(cls,
var = "Weight",
options = c(h0 = 80),
output = report,
plots = "all")
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal(length(res[[4]]), 5)
# Two Samples
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plots = "all")
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
expect_equal(length(res[[5]]), 5)
# Paired
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plots = "all")
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal(length(res[[4]]), 7)
})
test_that("ttestplot12: Documentation examples", {
res <- proc_ttest(paird, paired = "before * after",
output = report,
plots = TRUE)
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
expect_equal(length(res[[4]]), 4)
})
# Also check that x scale adjusts if h0 is outsize confidence intervals
test_that("ttestplot13: showh0 parameter", {
# Boxplot1
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 75, "alpha" = 0.05),
output = report,
plots = ttestplot("boxplot", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval 1
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 63, "alpha" = 0.05),
output = report,
plots = ttestplot("interval", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary 1
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 63, "alpha" = 0.05),
output = report,
plots = ttestplot("summary", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval2
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 0, "alpha" = 0.05),
class = "Sex",
output = report,
plots = ttestplot("interval", showh0 = TRUE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
# Work on this
test_that("ttestplot14: troublesome plots match SAS", {
# qqplot1 - Got it!
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("qqplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# qqplot2 - Hurray!
res <- proc_ttest(cls,
var = c("Height"),
class = "Sex",
output = report,
plot = TRUE,
options = c("alpha" = 0.1))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# histogram - Good enough
res <- proc_ttest(cls,
var = c("Age"),
options = c("h0" = 65, "alpha" = 0.05),
output = report,
plots = ttestplot("histogram"))
# Boxplot1 - needs outlier. Got it!
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = "boxplot")
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot2 - needs outlier. Got it!
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = "boxplot")
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Different data with class - Fixed
res <- proc_ttest(sleep,
var = "extra",
class = "group",
output = "report",
plots = c("summary", "histogram", "boxplot"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
# Good
test_that("ttestplot15: Label and ID parameters work as expected.", {
# Boxplot1 - label FALSE
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = FALSE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot1 - label TRUE
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot1 - id value
res <- proc_ttest(cls,
paired = "Height * Weight",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE, id = "Name"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Boxplot2 - label FALSE
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = FALSE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot2 - label TRUE
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot2 - id value
res <- proc_ttest(cls,
var = "Weight",
class = "Sex",
output = report,
plot = ttestplot(c("summary", "boxplot"),
label = TRUE, id = "Name"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot16: plots with freq parameter.", {
# One sample with freq
cls_freq <- cls
cls_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
res <- proc_ttest(cls_freq, var = "Height",
freq = "FreqVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Two sample (class) with freq
res <- proc_ttest(cls_freq, var = "Height",
class = "Sex",
freq = "FreqVar",
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Paired with freq
paird_freq <- paird
paird_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1)
res <- proc_ttest(paird_freq,
paired = "before * after",
freq = "FreqVar",
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot17: plots with weight parameter.", {
# One sample with weight, add some strange value to show difference
cls_wgt <- cls
cls_wgt$WgtVar <- c(1.5, 2.0, 0.8, 1.2, 1.0, 1.5, 2.0, 0.8, 1.2, 1.0,
1.5, 2.0, 0.8, 1.2, 1.0, 1.5, 200, 80, 120)
res <- proc_ttest(cls_wgt, var = "Height",
weight = "WgtVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot(c("summary", "qqplot")))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
#freq and weight together
cls_wgt$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
res <- proc_ttest(cls_wgt, var = "Height",
freq = "FreqVar",
weight = "WgtVar",
output = "report",
plots = ttestplot("summary"))
# Two sample (class) with weight
res <- proc_ttest(cls_wgt, var = "Height",
class = "Sex",
weight = "WgtVar",
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Paired with weight
paird_wgt <- paird
paird_wgt$WgtVar <- c(1.5, 2.0, 0.8, 1.2, 1.0, 1.5, 2.0, 0.8, 1.2, 1.0)
res <- proc_ttest(paird_wgt,
paired = "before * after",
weight = "WgtVar",
output = "report",
plots = ttestplot("boxplot"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Multiple plot types with weight
res <- proc_ttest(cls_wgt, var = "Height",
weight = "WgtVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot(c("summary", "histogram", "boxplot")))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot18: plots with sides parameter (one-sample).", {
# Summary plot with sides = 'U'
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary plot with sides = 'L'
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "L"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Interval plot with sides option
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = ttestplot("interval"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot19: plots with sides parameter (two-sample).", {
# Summary plot with sides = 'U' and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Boxplot with sides = 'L' and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(sides = "L"),
output = "report",
plots = ttestplot("boxplot"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
# Interval plot with sides and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(sides = "U", alpha = 0.1),
output = "report",
plots = ttestplot("interval"))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot20: plots with sides parameter (paired).", {
# Profiles plot with sides = 'U'
res <- proc_ttest(paird, paired = "before * after",
options = c(sides = "U"),
output = "report",
plots = ttestplot("profiles"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Agreement plot with sides = 'L'
res <- proc_ttest(paird, paired = "before * after",
options = c(sides = "L"),
output = "report",
plots = ttestplot("agreement"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Summary with paired and sides
res <- proc_ttest(paird, paired = "before * after",
options = c(sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
})
test_that("ttestplot21: plots with freq and sides together.", {
cls_freq <- cls
cls_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
# One sample with freq and sides
res <- proc_ttest(cls_freq, var = "Height",
freq = "FreqVar",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = ttestplot("summary"))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# Two sample with freq and sides
res <- proc_ttest(cls_freq, var = "Height",
class = "Sex",
freq = "FreqVar",
options = c(sides = "L"),
output = "report",
plots = ttestplot(c("summary", "boxplot")))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
test_that("ttestplot22: multiple plot types with freq and sides.", {
cls_freq <- cls
cls_freq$FreqVar <- c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1)
# Multiple plots with freq
res <- proc_ttest(cls_freq, var = "Height",
freq = "FreqVar",
options = c(h0 = 65),
output = "report",
plots = ttestplot(c("summary", "histogram", "boxplot")))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# All plots with sides
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 65, sides = "U"),
output = "report",
plots = "all")
expect_equal(length(res), 4)
expect_equal(length(res[[4]]), 5)
})
test_that("ttestplot23: plots with showh0 and sides together.", {
# showh0 with sides = 'U'
res <- proc_ttest(cls, var = "Height",
options = c(h0 = 70, sides = "U"),
output = "report",
plots = ttestplot("summary", showh0 = TRUE))
expect_equal(length(res), 4)
expect_equal("plot_spec" %in% class(res[[4]][[1]]), TRUE)
# showh0 with sides = 'L' and class
res <- proc_ttest(cls, var = "Height",
class = "Sex",
options = c(h0 = 60, sides = "L"),
output = "report",
plots = ttestplot("interval", showh0 = TRUE))
expect_equal(length(res), 5)
expect_equal("plot_spec" %in% class(res[[5]][[1]]), TRUE)
})
# These now match SAS
test_that("ttestplot24: qqplot works as expected with weight.", {
scrs <- read.table(header = TRUE, text = '
Group Score Frequency
Online 85 10
Online 90 25
Online 92 15
InPerson 88 12
InPerson 91 30
InPerson 95 18
')
# Two charts
res <- proc_ttest(scrs,
var = "Score",
class = "Group",
weight = "Frequency",
output = "report",
plot = TRUE)
expect_equal(length(res), 5)
# expect_true(is.finite(as.numeric(res2$ConfLimits$LCLM[3])))
# Single chart
res <- proc_ttest(scrs,
var = "Score",
weight = "Frequency",
output = "report",
plot = TRUE,
options = c(h0 = 80))
expect_equal(length(res), 4)
})
test_that("ttestplot25: plots work with NAs in data.", {
# Histogram with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "histogram")
expect_equal(length(res), 5)
# Boxplot with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "boxplot")
expect_equal(length(res), 5)
# Summary with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "summary")
expect_equal(length(res), 5)
# QQplot with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "qqplot")
expect_equal(length(res), 5)
# Agreement with NA
res <- proc_ttest(clsna,
paired = "Height * Weight",
output = "report",
plots = "agreement")
expect_equal(length(res), 4)
# Paired all with NA
res <- proc_ttest(clsna,
paired = "Height * Weight",
output = "report",
plots = "all")
# Two sample all with NA
res <- proc_ttest(clsna,
var = "Height",
class = "Sex",
output = "report",
plots = "all")
# One sample all with NA
res <- proc_ttest(clsna,
var = "Height",
output = "report",
options = c(h0 = 65),
plots = "all")
# One sample all with NA
res <- proc_ttest(clsna,
var = "Height",
by = "Sex",
output = "report",
options = c(h0 = 65),
plots = "all")
})
test_that("ttestplot26: More NA tests", {
# What is grey stuff at top of histogram? Fixed
proc_ttest(airquality,
paired = "Ozone * Solar.R",
plots = c("summary", "histogram"))
# Fixed
proc_ttest(airquality,
var = "Ozone",
options = c(h0 = 50),
plots = c("summary", "histogram"))
# Fixed
proc_ttest(airquality[airquality$Month %in% c(8,9), ],
var = "Ozone",
class = "Month",
plots = c("boxplot"))
expect_equal(TRUE, TRUE)
})
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