Nothing
tests/testthat/test-ttest.R
In procs: Recreates Some 'SAS®' Procedures in 'R'
base_path <- "c:/packages/procs/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_measure after_measure 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')
options("logr.output" = FALSE)
options("procs.print" = FALSE)
#options("procs.print" = NULL)
dev <- FALSE
test_that("ttest1: Get Output Specs works as expected.", {
res <- get_output_specs_ttest(mtcars, var = "mpg", paired = NULL, class = NULL,
opts = c("h0" = 20), output = "out" )
expect_equal(is.null(res), FALSE)
expect_equal("..mpg" %in% names(res$data), TRUE)
expect_equal(length(res$outreq) > 0, TRUE)
})
test_that("ttest2: Simple proc_ttest one variable works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$MEAN), 62.336842)
expect_equal(as.numeric(res$Statistics$STD), 5.1270752)
expect_equal(as.numeric(res$Statistics$STDERR), 1.17623173)
expect_equal(as.numeric(res$ConfLimits$LCLM), 59.8656709)
expect_equal(as.numeric(res$ConfLimits$UCLM), 64.808013)
expect_equal(as.numeric(res$TTests$DF), 18)
expect_equal(as.numeric(res$TTests$T), -2.2641439)
expect_equal(as.numeric(res$TTests$PROBT), 0.036152218)
})
test_that("ttest3: Simple proc_ttest with class works.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res <- proc_ttest(cls,
var = "Height",
class = "Sex")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
})
test_that("ttest4: Simple proc_ttest with paired variables works.", {
# data PairedData;
# input subject_id before_measure after_measure;
# datalines;
# 1 12 15
# 2 14 16
# 3 10 11
# 4 15 18
# 5 18 20
# 6 20 22
# 7 11 12
# 8 13 14
# 9 16 17
# 10 9 13
# ;
# run;
#
# proc ttest data=PairedData;
# paired before_measure * after_measure;
# run;
res <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$N), 10)
expect_equal(as.numeric(res$Statistics$MEAN), -2)
expect_equal(as.numeric(res$Statistics$STD), 1.05409255)
expect_equal(as.numeric(res$Statistics$STDERR), 0.33333333)
expect_equal(as.numeric(res$Statistics$MIN), -4)
expect_equal(as.numeric(res$Statistics$MAX), -1)
expect_equal(as.numeric(res$ConfLimits$UCLM), -1.2459476)
expect_equal(as.numeric(res$ConfLimits$LCLM), -2.7540524)
expect_equal(as.numeric(res$TTests$DF), 9)
expect_equal(as.numeric(res$TTests$T), -6)
expect_equal(as.numeric(res$TTests$PROBT), .000202499322)
})
test_that("ttest5: Simple proc_ttest weight var works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 100, "alpha" = 0.1),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$MEAN), 100.026316)
expect_equal(as.numeric(res$Statistics$STD), 22.7739335)
expect_equal(as.numeric(res$Statistics$STDERR), 5.2246987)
expect_equal(as.numeric(res$ConfLimits$LCLM), 90.966356)
expect_equal(as.numeric(res$ConfLimits$UCLM), 109.086276)
expect_equal(as.numeric(res$TTests$DF), 18)
expect_equal(as.numeric(res$TTests$T), 0.00503680521)
expect_equal(as.numeric(res$TTests$PROBT), 0.99603663)
})
test_that("ttest6: Simple proc_ttest log with one variable works.", {
if (dev) {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
library(logr)
options("logr.output" = TRUE)
options("logr.autolog" = TRUE)
lf <- log_open(file.path(base_path, "test.log"))
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
log_close()
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(file.exists(lf), TRUE)
#file.show(lf)
options("logr.output" = FALSE)
options("logr.autolog" = FALSE)
} else {
expect_equal(TRUE, TRUE)
}
})
test_that("ttest7: Simple proc_ttest with by and noprint works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), by = c("Sex"),
options = c("h0" = 65, "alpha" = 0.05, "noprint"),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
expect_equal(as.numeric(res$TTests$DF[1]), 8)
expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest8: Simple proc_ttest with report works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), output = "report",
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
# expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
# expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
# expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
# expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
# expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
# expect_equal(as.numeric(res$TTests$DF[1]), 8)
# expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
# expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest9: Simple proc_ttest with by and print works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Height"), by = "Sex",
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
# expect_equal(as.numeric(res$Statistics$MEAN), 62.336842)
# expect_equal(as.numeric(res$Statistics$STD), 5.1270752)
# expect_equal(as.numeric(res$Statistics$STDERR), 1.17623173)
# expect_equal(as.numeric(res$ConfLimits$LCLM), 59.8656709)
# expect_equal(as.numeric(res$ConfLimits$UCLM), 64.808013)
# expect_equal(as.numeric(res$TTests$DF), 18)
# expect_equal(as.numeric(res$TTests$T), -2.2641439)
# expect_equal(as.numeric(res$TTests$PROBT), 0.036152218)
})
test_that("ttest10: Simple proc_ttest with report and by works noprint.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), output = "report", by = "Sex",
options = c("h0" = 65, "alpha" = 0.05, "noprint"),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
# expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
# expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
# expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
# expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
# expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
# expect_equal(as.numeric(res$TTests$DF[1]), 8)
# expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
# expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest11: Simple proc_ttest with report and by works with print", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), output = "report", by = "Sex",
options = c("h0" = 65, "alpha" = 0.05))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
# expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
# expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
# expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
# expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
# expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
# expect_equal(as.numeric(res$TTests$DF[1]), 8)
# expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
# expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest12: proc_ttest with paired and by variables works.", {
# data PairedData;
# input subject_id before_measure after_measure region $9;
# datalines;
# 1 12 15 A
# 2 14 16 A
# 3 10 11 A
# 4 15 18 A
# 5 18 20 A
# 6 20 22 B
# 7 11 12 B
# 8 13 14 B
# 9 16 17 B
# 10 9 13 B
# ;
# run;
#
# proc ttest data=PairedData;
# paired before_measure * after_measure;
# run;
res <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
by = region)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$N[2]), 5)
expect_equal(as.numeric(res$Statistics$MEAN[2]), -1.8)
expect_equal(as.numeric(res$Statistics$STD[2]), 1.303840481)
expect_equal(as.numeric(res$Statistics$STDERR[2]), 0.583095189)
expect_equal(as.numeric(res$Statistics$MIN[2]), -4)
expect_equal(as.numeric(res$Statistics$MAX[2]), -1)
expect_equal(as.numeric(res$ConfLimits$UCLM[2]), -0.181068215)
expect_equal(as.numeric(res$ConfLimits$LCLM[2]), -3.41893178)
expect_equal(as.numeric(res$TTests$DF[2]), 4)
expect_equal(as.numeric(res$TTests$T[2]), -3.08697453)
expect_equal(as.numeric(res$TTests$PROBT[2]), 0.03668198940)
})
test_that("ttest13: get_class_ttest with paired and by variables works.", {
res <- get_class_ttest(cls, "Height", "Sex")
res
expect_equal(length(res), 4)
expect_equal(names(res), c("Statistics", "ConfLimits", "TTests", "Equality"))
res <- get_class_ttest(cls, "Height", "Sex", report = FALSE)
res
expect_equal(length(res), 4)
expect_equal("VAR" %in% names(res$Statistics), TRUE)
})
test_that("ttest14: Simple proc_ttest with class and by works.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res <- proc_ttest(cls,
by = "region",
var = "Height",
class = "Sex",
options = c(alpha = 0.1))
res
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 8)
expect_equal(nrow(res$ConfLimits), 8)
expect_equal(nrow(res$TTests), 4)
expect_equal(nrow(res$Equality), 2)
})
# test_that("test15: One sample test with sides parameter.", {
#
#
# # data time;
# # input time @@;
# # datalines;
# # 43 90 84 87 116 95 86 99 93 92
# # 121 71 66 98 79 102 60 112 105 98
# # ;
# #
# # proc ttest h0=80 plots(showh0) sides=u alpha=0.1;
# # var time;
# # run;
#
# v1 <- c(43, 90, 84, 87, 116, 95, 86, 99, 93, 92,
# 121, 71, 66, 98, 79, 102, 60, 112, 105, 98)
#
# dat <- data.frame(time = v1, stringsAsFactors = FALSE)
#
# res <- proc_ttest(dat, var = time, options = c("h0"=80, alpha = .1))
#
# expect_equal(res$Statistics
#
#
# })
test_that("ttest16: proc_ttest output options work.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report)
res
expect_equal("VAR" %in% names(res$Statistics), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 1)
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = long)
res
expect_equal(nrow(res$Statistics), 6)
expect_equal(ncol(res$Statistics), 2)
res <- proc_ttest(cls,
var = c("Height"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = long)
res
expect_equal(nrow(res$Statistics), 12)
expect_equal(ncol(res$Statistics), 3)
res <- proc_ttest(cls,
var = c("Height"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = c("out", "report"))
res
expect_equal(names(res), c("out", "report"))
expect_equal(nrow(res$out$Statistics), 2)
expect_equal(nrow(res$report$`Sex=F`$Statistics), 1)
})
test_that("ttest17: Multiple variables work with shaping options", {
res <- proc_ttest(cls,
var = c("Height", "Weight"),
#by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = out) #v(out, report, wide))
res
expect_equal(nrow(res$Statistics), 2)
expect_equal(ncol(res$Statistics), 7)
expect_equal(res$Statistics$VAR[1], "Height")
expect_equal(res$Statistics$VAR[2], "Weight")
res <- proc_ttest(cls,
var = c("Height", "Weight"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = out) #v(out, report, wide))
res
expect_equal(nrow(res$Statistics), 4)
expect_equal(ncol(res$Statistics), 8)
expect_equal(res$Statistics$VAR[1], "Height")
expect_equal(res$Statistics$VAR[2], "Weight")
res <- proc_ttest(cls,
var = c("Height", "Weight"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = c("out", "stacked"))
res
expect_equal(nrow(res$Statistics), 24)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = c("out", "long"))
res
expect_equal(nrow(res$Statistics), 12)
})
test_that("ttest18: Two by variables one var works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 4)
expect_equal(all(c("BY1", "BY2") %in% names(res$Statistics)), TRUE)
# Test report
res <- proc_ttest(cls,
var = c("Height"), by = c("region", "Sex"), output = "report",
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
# expect_equal(length(res), 3)
# expect_equal(nrow(res$Statistics), 4)
# expect_equal(all(c("BY1", "BY2") %in% names(res$Statistics)), TRUE)
})
test_that("ttest19: One by variable two vars works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("Sex"),
options = c("h0" = 65, "alpha" = 0.05))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 4)
expect_equal(all(c("BY") %in% names(res$Statistics)), TRUE)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("Sex"), output = report,
options = c("h0" = 65, "alpha" = 0.05))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
expect_equal(nrow(res[[1]][[1]]), 1)
})
test_that("ttest20: Two by variables two vars works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 8)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05), output = report,
titles = "My first Frequency Table")
res
expect_equal(length(res), 4)
expect_equal(nrow(res[[1]][[1]]), 1)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05), output = long,
titles = "My first Frequency Table")
res
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 24)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05), output = stacked,
titles = "My first Frequency Table")
res
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 48)
})
test_that("ttest21: proc_ttest with two paired variables works.", {
# data PairedData;
# input subject_id before_measure after_measure region $9;
# datalines;
# 1 12 15 A
# 2 14 16 A
# 3 10 11 A
# 4 15 18 A
# 5 18 20 A
# 6 20 22 B
# 7 11 12 B
# 8 13 14 B
# 9 16 17 B
# 10 9 13 B
# ;
# run;
#
# proc ttest data=PairedData;
# paired before_measure * after_measure after_measure * before_measure;
# run;
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
options = c(alpha = .1)
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 2)
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
by = region,
options = c(alpha = .1)
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 4)
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
by = region,
options = c(alpha = .1),
output = long
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 12)
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
by = region,
options = c(alpha = .1),
output = stacked
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 24)
})
test_that("ttest22: proc_ttest with two vars and class works.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = "report")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 8)
expect_equal(nrow(res$`Height:Statistics`), 4)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "out")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 8)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "long")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 16)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "stacked")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 32)
expect_equal(nrow(res$Equality), 8)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
by = "region",
output = "out")
res
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 16)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
by = "region",
output = "long")
res
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 32)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
by = "region",
output = "stacked")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 64)
expect_equal(nrow(res$Equality), 16)
})
test_that("ttest23: shape_ttest_data works as expected.", {
r1 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "wide")
dat1 <- r1$Statistics[c(3, 4), ]
res1 <- shape_ttest_data(dat1, "long")
res1
expect_equal(nrow(res1), 12)
dat2 <- r1$Statistics[c(3, 4, 7, 8), ]
res2 <- shape_ttest_data(dat2, "stacked")
res2
expect_equal(nrow(res2), 24)
})
test_that("ttest24: test parameter checks.", {
expect_error(proc_ttest("fork", var = "Height"))
expect_error(proc_ttest(cls[0, ], var = "Height"))
expect_error(proc_ttest(cls, var = "fork"))
expect_error(proc_ttest(cls, var = "Height", options = "bork"))
expect_error(proc_ttest(cls, var = "Height", options = c("bork"= 2)))
expect_error(proc_ttest(cls, var = "Height", options = c("bork"= 2, "spork")))
expect_error(proc_ttest(cls, paired = "bork * spork"))
expect_error(proc_ttest(cls, paired = "bork * Height"))
expect_error(proc_ttest(cls, paired = c("Weight * Height", "spork * Weight")))
expect_error(proc_ttest(cls, var = "Height", class = c("Sex", "region")))
})
test_that("ttest25: Internal consistency checks with class.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = c("out", "report"))
res1
expect_equal(res1$out$TTests$PROBT[1], res1$report$`Height:TTests`$PROBT[1])
expect_equal(res1$out$TTests$PROBT[3], res1$report$`Weight:TTests`$PROBT[1])
res2 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = c("out", "long"))
res2
expect_equal(res1$out$TTests$PROBT[1], res2$TTests$Height[3])
expect_equal(res1$out$TTests$PROBT[3], res2$TTests$Weight[3])
res3 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = c("out", "stacked"))
res3
expect_equal(res1$out$TTests$PROBT[1], res3$TTests$VALUES[3])
expect_equal(res1$out$TTests$PROBT[3], res3$TTests$VALUES[9])
})
test_that("ttest25: Internal consistency checks with single variable.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(cls,
var = c("Height", "Weight"),
# options = "noprint",
output = c("out", "report"),
options = c(h0 = 65))
res1
expect_equal(res1$out$TTests$PROBT[1], res1$report$`Height:TTests`$PROBT[1])
expect_equal(res1$out$TTests$PROBT[2], res1$report$`Weight:TTests`$PROBT[1])
res2 <- proc_ttest(cls,
var = c("Height", "Weight"),
# options = "noprint",
output = c("out", "long"),
options = c(h0 = 65))
res2
expect_equal(res1$out$TTests$PROBT[1], res2$TTests$Height[3])
expect_equal(res1$out$TTests$PROBT[2], res2$TTests$Weight[3])
res3 <- proc_ttest(cls,
var = c("Height", "Weight"), # VAR bad on all
# options = "noprint",
output = c("out", "stacked"),
options = c(h0 = 65))
res3
expect_equal(res1$out$TTests$PROBT[1], res3$TTests$VALUES[3])
expect_equal(res1$out$TTests$PROBT[3], res3$TTests$VALUES[9])
})
test_that("ttest26: Internal consistency checks with paired", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table",
output = c("out", "report"))
res1
expect_equal(res1$out$TTests$PROBT[1], res1$report$`diff1:TTests`$PROBT[1])
res2 <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table",
output = c("out", "long"))
res2
expect_equal(res1$out$TTests$PROBT[1], res2$TTests$DIFF1[3])
res3 <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table",
output = c("out", "stacked"))
res3
expect_equal(res1$out$TTests$PROBT[1], res3$TTests$VALUES[3])
expect_equal(res1$out$TTests$PROBT[3], res3$TTests$VALUES[9])
})
test_that("ttest27: Check F Values for different var and class combinations.", {
# SAS appears to pick the different variables for test or control
# depending on what is going on in the data. Best guess is that it is
# picking the combination with highest F Value. This is to run a few
# comparisons against SAS and just make sure everything is coming out OK.
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(cls,
by = "region",
var = "Height",
class = "Sex",
options = c(alpha = 0.1))
res1
expect_equal(as.numeric(res1$Equality$NDF), c(3, 3))
expect_equal(as.numeric(res1$Equality$DDF), c(4, 5))
expect_equal(as.numeric(res1$Equality$FVAL), c(2.04584557, 1.70834286))
res2 <- proc_ttest(cls,
by = "region",
var = "Weight",
class = "Sex",
options = c(alpha = 0.1))
res2
expect_equal(as.numeric(res2$Equality$NDF), c(3, 3))
expect_equal(as.numeric(res2$Equality$DDF), c(4, 5))
expect_equal(as.numeric(res2$Equality$FVAL), c(1.4055752, 1.1721952))
res3 <- proc_ttest(cls,
by = "region",
var = "Age",
class = "Sex",
options = c(alpha = 0.1))
res3
expect_equal(as.numeric(res3$Equality$NDF), c(4, 5))
expect_equal(as.numeric(res3$Equality$DDF), c(3, 3))
expect_equal(as.numeric(res3$Equality$FVAL), c(1.41818182, 1.290000))
res4 <- proc_ttest(cls,
by = "region",
var = c("Height", "Weight", "Age"),
class = "Sex",
options = c(alpha = 0.1))
res4
})
test_that("ttest28: Data with no rows generates error.", {
cls2 <- cls[0, ]
expect_error(proc_ttest(cls2, var = c("Height")))
})
# Not sure how to do this. Can't get lognormal dist to match SAS.
# test_that("ttest28: Paired ttest with lognormal data works.", {
#
#
#
# auc <- read.table(header = TRUE, text = '
# TestAUC RefAUC
# 103.4 90.11
# 59.92 77.71
# 68.17 77.71
# 94.54 97.51
# 69.48 58.21
# 72.17 101.3
# 74.37 79.84
# 84.44 96.06
# 96.74 89.30
# 94.26 97.22
# 48.52 61.62
# 95.68 85.80')
#
# t.test(auc$TestAUC, paired = FALSE, var.equal = FALSE)
#
# t.test(auc$TestAUC, auc$RefAUC, paired = TRUE, var.equal = TRUE)
#
# t.test(auc$TestAUC, auc$RefAUC, paired = FALSE, var.equal = FALSE)
#
#
# t.test(auc$RefAUC, auc$TestAUC, data = auc, paired = TRUE, var.equal = TRUE)
#
# t.test(auc$RefAUC, auc$TestAUC, data = auc, paired = TRUE, var.equal = FALSE)
#
# res <- proc_ttest(auc,
# paired = "TestAUC * RefAUC")
#
# res
#
# expect_equal(is.null(res), FALSE)
# expect_equal(length(res), 3)
#
# # expect_equal(as.numeric(res$Statistics$MEAN), 62.336842)
# # expect_equal(as.numeric(res$Statistics$STD), 5.1270752)
# # expect_equal(as.numeric(res$Statistics$STDERR), 1.17623173)
# # expect_equal(as.numeric(res$ConfLimits$LCLM), 59.8656709)
# # expect_equal(as.numeric(res$ConfLimits$UCLM), 64.808013)
# # expect_equal(as.numeric(res$TTests$DF), 18)
# # expect_equal(as.numeric(res$TTests$T), -2.2641439)
# # expect_equal(as.numeric(res$TTests$PROBT), 0.036152218)
#
# })
# CO2
# t.test(uptake ~ Treatment, CO2)
#
#
# t.test(uptake ~ Treatment, CO2, var.equal = TRUE)
#
# mean(auc$TestAUC)
# mean(auc$RefAUC)
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base_path <- "c:/packages/procs/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_measure after_measure 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')
options("logr.output" = FALSE)
options("procs.print" = FALSE)
#options("procs.print" = NULL)
dev <- FALSE
test_that("ttest1: Get Output Specs works as expected.", {
res <- get_output_specs_ttest(mtcars, var = "mpg", paired = NULL, class = NULL,
opts = c("h0" = 20), output = "out" )
expect_equal(is.null(res), FALSE)
expect_equal("..mpg" %in% names(res$data), TRUE)
expect_equal(length(res$outreq) > 0, TRUE)
})
test_that("ttest2: Simple proc_ttest one variable works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$MEAN), 62.336842)
expect_equal(as.numeric(res$Statistics$STD), 5.1270752)
expect_equal(as.numeric(res$Statistics$STDERR), 1.17623173)
expect_equal(as.numeric(res$ConfLimits$LCLM), 59.8656709)
expect_equal(as.numeric(res$ConfLimits$UCLM), 64.808013)
expect_equal(as.numeric(res$TTests$DF), 18)
expect_equal(as.numeric(res$TTests$T), -2.2641439)
expect_equal(as.numeric(res$TTests$PROBT), 0.036152218)
})
test_that("ttest3: Simple proc_ttest with class works.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res <- proc_ttest(cls,
var = "Height",
class = "Sex")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
})
test_that("ttest4: Simple proc_ttest with paired variables works.", {
# data PairedData;
# input subject_id before_measure after_measure;
# datalines;
# 1 12 15
# 2 14 16
# 3 10 11
# 4 15 18
# 5 18 20
# 6 20 22
# 7 11 12
# 8 13 14
# 9 16 17
# 10 9 13
# ;
# run;
#
# proc ttest data=PairedData;
# paired before_measure * after_measure;
# run;
res <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$N), 10)
expect_equal(as.numeric(res$Statistics$MEAN), -2)
expect_equal(as.numeric(res$Statistics$STD), 1.05409255)
expect_equal(as.numeric(res$Statistics$STDERR), 0.33333333)
expect_equal(as.numeric(res$Statistics$MIN), -4)
expect_equal(as.numeric(res$Statistics$MAX), -1)
expect_equal(as.numeric(res$ConfLimits$UCLM), -1.2459476)
expect_equal(as.numeric(res$ConfLimits$LCLM), -2.7540524)
expect_equal(as.numeric(res$TTests$DF), 9)
expect_equal(as.numeric(res$TTests$T), -6)
expect_equal(as.numeric(res$TTests$PROBT), .000202499322)
})
test_that("ttest5: Simple proc_ttest weight var works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Weight"),
options = c("h0" = 100, "alpha" = 0.1),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$MEAN), 100.026316)
expect_equal(as.numeric(res$Statistics$STD), 22.7739335)
expect_equal(as.numeric(res$Statistics$STDERR), 5.2246987)
expect_equal(as.numeric(res$ConfLimits$LCLM), 90.966356)
expect_equal(as.numeric(res$ConfLimits$UCLM), 109.086276)
expect_equal(as.numeric(res$TTests$DF), 18)
expect_equal(as.numeric(res$TTests$T), 0.00503680521)
expect_equal(as.numeric(res$TTests$PROBT), 0.99603663)
})
test_that("ttest6: Simple proc_ttest log with one variable works.", {
if (dev) {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
library(logr)
options("logr.output" = TRUE)
options("logr.autolog" = TRUE)
lf <- log_open(file.path(base_path, "test.log"))
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
log_close()
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(file.exists(lf), TRUE)
#file.show(lf)
options("logr.output" = FALSE)
options("logr.autolog" = FALSE)
} else {
expect_equal(TRUE, TRUE)
}
})
test_that("ttest7: Simple proc_ttest with by and noprint works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), by = c("Sex"),
options = c("h0" = 65, "alpha" = 0.05, "noprint"),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
expect_equal(as.numeric(res$TTests$DF[1]), 8)
expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest8: Simple proc_ttest with report works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), output = "report",
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
# expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
# expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
# expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
# expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
# expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
# expect_equal(as.numeric(res$TTests$DF[1]), 8)
# expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
# expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest9: Simple proc_ttest with by and print works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Height"), by = "Sex",
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
# expect_equal(as.numeric(res$Statistics$MEAN), 62.336842)
# expect_equal(as.numeric(res$Statistics$STD), 5.1270752)
# expect_equal(as.numeric(res$Statistics$STDERR), 1.17623173)
# expect_equal(as.numeric(res$ConfLimits$LCLM), 59.8656709)
# expect_equal(as.numeric(res$ConfLimits$UCLM), 64.808013)
# expect_equal(as.numeric(res$TTests$DF), 18)
# expect_equal(as.numeric(res$TTests$T), -2.2641439)
# expect_equal(as.numeric(res$TTests$PROBT), 0.036152218)
})
test_that("ttest10: Simple proc_ttest with report and by works noprint.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), output = "report", by = "Sex",
options = c("h0" = 65, "alpha" = 0.05, "noprint"),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
# expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
# expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
# expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
# expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
# expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
# expect_equal(as.numeric(res$TTests$DF[1]), 8)
# expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
# expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest11: Simple proc_ttest with report and by works with print", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), output = "report", by = "Sex",
options = c("h0" = 65, "alpha" = 0.05))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
# expect_equal(as.numeric(res$Statistics$MEAN[1]), 60.5888888888889)
# expect_equal(as.numeric(res$Statistics$STD[1]), 5.0183275)
# expect_equal(as.numeric(res$Statistics$STDERR[1]), 1.67277584)
# expect_equal(as.numeric(res$ConfLimits$LCLM[1]), 56.7314609)
# expect_equal(as.numeric(res$ConfLimits$UCLM[1]), 64.446317)
# expect_equal(as.numeric(res$TTests$DF[1]), 8)
# expect_equal(as.numeric(res$TTests$T[1]), -2.6370007)
# expect_equal(as.numeric(res$TTests$PROBT[1]), 0.02985198)
})
test_that("ttest12: proc_ttest with paired and by variables works.", {
# data PairedData;
# input subject_id before_measure after_measure region $9;
# datalines;
# 1 12 15 A
# 2 14 16 A
# 3 10 11 A
# 4 15 18 A
# 5 18 20 A
# 6 20 22 B
# 7 11 12 B
# 8 13 14 B
# 9 16 17 B
# 10 9 13 B
# ;
# run;
#
# proc ttest data=PairedData;
# paired before_measure * after_measure;
# run;
res <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
by = region)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(as.numeric(res$Statistics$N[2]), 5)
expect_equal(as.numeric(res$Statistics$MEAN[2]), -1.8)
expect_equal(as.numeric(res$Statistics$STD[2]), 1.303840481)
expect_equal(as.numeric(res$Statistics$STDERR[2]), 0.583095189)
expect_equal(as.numeric(res$Statistics$MIN[2]), -4)
expect_equal(as.numeric(res$Statistics$MAX[2]), -1)
expect_equal(as.numeric(res$ConfLimits$UCLM[2]), -0.181068215)
expect_equal(as.numeric(res$ConfLimits$LCLM[2]), -3.41893178)
expect_equal(as.numeric(res$TTests$DF[2]), 4)
expect_equal(as.numeric(res$TTests$T[2]), -3.08697453)
expect_equal(as.numeric(res$TTests$PROBT[2]), 0.03668198940)
})
test_that("ttest13: get_class_ttest with paired and by variables works.", {
res <- get_class_ttest(cls, "Height", "Sex")
res
expect_equal(length(res), 4)
expect_equal(names(res), c("Statistics", "ConfLimits", "TTests", "Equality"))
res <- get_class_ttest(cls, "Height", "Sex", report = FALSE)
res
expect_equal(length(res), 4)
expect_equal("VAR" %in% names(res$Statistics), TRUE)
})
test_that("ttest14: Simple proc_ttest with class and by works.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res <- proc_ttest(cls,
by = "region",
var = "Height",
class = "Sex",
options = c(alpha = 0.1))
res
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 8)
expect_equal(nrow(res$ConfLimits), 8)
expect_equal(nrow(res$TTests), 4)
expect_equal(nrow(res$Equality), 2)
})
# test_that("test15: One sample test with sides parameter.", {
#
#
# # data time;
# # input time @@;
# # datalines;
# # 43 90 84 87 116 95 86 99 93 92
# # 121 71 66 98 79 102 60 112 105 98
# # ;
# #
# # proc ttest h0=80 plots(showh0) sides=u alpha=0.1;
# # var time;
# # run;
#
# v1 <- c(43, 90, 84, 87, 116, 95, 86, 99, 93, 92,
# 121, 71, 66, 98, 79, 102, 60, 112, 105, 98)
#
# dat <- data.frame(time = v1, stringsAsFactors = FALSE)
#
# res <- proc_ttest(dat, var = time, options = c("h0"=80, alpha = .1))
#
# expect_equal(res$Statistics
#
#
# })
test_that("ttest16: proc_ttest output options work.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# run;
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = report)
res
expect_equal("VAR" %in% names(res$Statistics), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 1)
res <- proc_ttest(cls,
var = c("Height"),
options = c("h0" = 65, "alpha" = 0.05),
output = long)
res
expect_equal(nrow(res$Statistics), 6)
expect_equal(ncol(res$Statistics), 2)
res <- proc_ttest(cls,
var = c("Height"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = long)
res
expect_equal(nrow(res$Statistics), 12)
expect_equal(ncol(res$Statistics), 3)
res <- proc_ttest(cls,
var = c("Height"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = c("out", "report"))
res
expect_equal(names(res), c("out", "report"))
expect_equal(nrow(res$out$Statistics), 2)
expect_equal(nrow(res$report$`Sex=F`$Statistics), 1)
})
test_that("ttest17: Multiple variables work with shaping options", {
res <- proc_ttest(cls,
var = c("Height", "Weight"),
#by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = out) #v(out, report, wide))
res
expect_equal(nrow(res$Statistics), 2)
expect_equal(ncol(res$Statistics), 7)
expect_equal(res$Statistics$VAR[1], "Height")
expect_equal(res$Statistics$VAR[2], "Weight")
res <- proc_ttest(cls,
var = c("Height", "Weight"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = out) #v(out, report, wide))
res
expect_equal(nrow(res$Statistics), 4)
expect_equal(ncol(res$Statistics), 8)
expect_equal(res$Statistics$VAR[1], "Height")
expect_equal(res$Statistics$VAR[2], "Weight")
res <- proc_ttest(cls,
var = c("Height", "Weight"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = c("out", "stacked"))
res
expect_equal(nrow(res$Statistics), 24)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
by = Sex,
options = c("h0" = 65, "alpha" = 0.05),
output = c("out", "long"))
res
expect_equal(nrow(res$Statistics), 12)
})
test_that("ttest18: Two by variables one var works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 4)
expect_equal(all(c("BY1", "BY2") %in% names(res$Statistics)), TRUE)
# Test report
res <- proc_ttest(cls,
var = c("Height"), by = c("region", "Sex"), output = "report",
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(is.null(res), FALSE)
# expect_equal(length(res), 3)
# expect_equal(nrow(res$Statistics), 4)
# expect_equal(all(c("BY1", "BY2") %in% names(res$Statistics)), TRUE)
})
test_that("ttest19: One by variable two vars works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("Sex"),
options = c("h0" = 65, "alpha" = 0.05))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 4)
expect_equal(all(c("BY") %in% names(res$Statistics)), TRUE)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("Sex"), output = report,
options = c("h0" = 65, "alpha" = 0.05))
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 2)
expect_equal(nrow(res[[1]][[1]]), 1)
})
test_that("ttest20: Two by variables two vars works.", {
# proc ttest data=sashelp.class
# h0=65 /* Null hypothesis mean of 65 */
# alpha=0.05; /* Significance level of 0.05 */
# var height; /* Specify the variable to test */
# by sex;
# run;
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05),
titles = "My first Frequency Table")
res
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 8)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05), output = report,
titles = "My first Frequency Table")
res
expect_equal(length(res), 4)
expect_equal(nrow(res[[1]][[1]]), 1)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05), output = long,
titles = "My first Frequency Table")
res
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 24)
res <- proc_ttest(cls,
var = c("Height", "Weight"), by = c("region", "Sex"),
options = c("h0" = 65, "alpha" = 0.05), output = stacked,
titles = "My first Frequency Table")
res
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 48)
})
test_that("ttest21: proc_ttest with two paired variables works.", {
# data PairedData;
# input subject_id before_measure after_measure region $9;
# datalines;
# 1 12 15 A
# 2 14 16 A
# 3 10 11 A
# 4 15 18 A
# 5 18 20 A
# 6 20 22 B
# 7 11 12 B
# 8 13 14 B
# 9 16 17 B
# 10 9 13 B
# ;
# run;
#
# proc ttest data=PairedData;
# paired before_measure * after_measure after_measure * before_measure;
# run;
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
options = c(alpha = .1)
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 2)
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
by = region,
options = c(alpha = .1)
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 4)
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
by = region,
options = c(alpha = .1),
output = long
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 12)
res <- proc_ttest(paird,
paired = c("before_measure * after_measure",
"after_measure * before_measure"),
by = region,
options = c(alpha = .1),
output = stacked
)
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 3)
expect_equal(nrow(res$Statistics), 24)
})
test_that("ttest22: proc_ttest with two vars and class works.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = "report")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 8)
expect_equal(nrow(res$`Height:Statistics`), 4)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "out")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 8)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "long")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 16)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "stacked")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 32)
expect_equal(nrow(res$Equality), 8)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
by = "region",
output = "out")
res
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 16)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
by = "region",
output = "long")
res
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 32)
res <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
by = "region",
output = "stacked")
res
expect_equal(is.null(res), FALSE)
expect_equal(length(res), 4)
expect_equal(nrow(res$Statistics), 64)
expect_equal(nrow(res$Equality), 16)
})
test_that("ttest23: shape_ttest_data works as expected.", {
r1 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
output = "wide")
dat1 <- r1$Statistics[c(3, 4), ]
res1 <- shape_ttest_data(dat1, "long")
res1
expect_equal(nrow(res1), 12)
dat2 <- r1$Statistics[c(3, 4, 7, 8), ]
res2 <- shape_ttest_data(dat2, "stacked")
res2
expect_equal(nrow(res2), 24)
})
test_that("ttest24: test parameter checks.", {
expect_error(proc_ttest("fork", var = "Height"))
expect_error(proc_ttest(cls[0, ], var = "Height"))
expect_error(proc_ttest(cls, var = "fork"))
expect_error(proc_ttest(cls, var = "Height", options = "bork"))
expect_error(proc_ttest(cls, var = "Height", options = c("bork"= 2)))
expect_error(proc_ttest(cls, var = "Height", options = c("bork"= 2, "spork")))
expect_error(proc_ttest(cls, paired = "bork * spork"))
expect_error(proc_ttest(cls, paired = "bork * Height"))
expect_error(proc_ttest(cls, paired = c("Weight * Height", "spork * Weight")))
expect_error(proc_ttest(cls, var = "Height", class = c("Sex", "region")))
})
test_that("ttest25: Internal consistency checks with class.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = c("out", "report"))
res1
expect_equal(res1$out$TTests$PROBT[1], res1$report$`Height:TTests`$PROBT[1])
expect_equal(res1$out$TTests$PROBT[3], res1$report$`Weight:TTests`$PROBT[1])
res2 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = c("out", "long"))
res2
expect_equal(res1$out$TTests$PROBT[1], res2$TTests$Height[3])
expect_equal(res1$out$TTests$PROBT[3], res2$TTests$Weight[3])
res3 <- proc_ttest(cls,
var = c("Height", "Weight"),
class = "Sex",
# options = "noprint",
output = c("out", "stacked"))
res3
expect_equal(res1$out$TTests$PROBT[1], res3$TTests$VALUES[3])
expect_equal(res1$out$TTests$PROBT[3], res3$TTests$VALUES[9])
})
test_that("ttest25: Internal consistency checks with single variable.", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(cls,
var = c("Height", "Weight"),
# options = "noprint",
output = c("out", "report"),
options = c(h0 = 65))
res1
expect_equal(res1$out$TTests$PROBT[1], res1$report$`Height:TTests`$PROBT[1])
expect_equal(res1$out$TTests$PROBT[2], res1$report$`Weight:TTests`$PROBT[1])
res2 <- proc_ttest(cls,
var = c("Height", "Weight"),
# options = "noprint",
output = c("out", "long"),
options = c(h0 = 65))
res2
expect_equal(res1$out$TTests$PROBT[1], res2$TTests$Height[3])
expect_equal(res1$out$TTests$PROBT[2], res2$TTests$Weight[3])
res3 <- proc_ttest(cls,
var = c("Height", "Weight"), # VAR bad on all
# options = "noprint",
output = c("out", "stacked"),
options = c(h0 = 65))
res3
expect_equal(res1$out$TTests$PROBT[1], res3$TTests$VALUES[3])
expect_equal(res1$out$TTests$PROBT[3], res3$TTests$VALUES[9])
})
test_that("ttest26: Internal consistency checks with paired", {
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table",
output = c("out", "report"))
res1
expect_equal(res1$out$TTests$PROBT[1], res1$report$`diff1:TTests`$PROBT[1])
res2 <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table",
output = c("out", "long"))
res2
expect_equal(res1$out$TTests$PROBT[1], res2$TTests$DIFF1[3])
res3 <- proc_ttest(paird,
paired = c("before_measure * after_measure"),
titles = "My first TTest Table",
output = c("out", "stacked"))
res3
expect_equal(res1$out$TTests$PROBT[1], res3$TTests$VALUES[3])
expect_equal(res1$out$TTests$PROBT[3], res3$TTests$VALUES[9])
})
test_that("ttest27: Check F Values for different var and class combinations.", {
# SAS appears to pick the different variables for test or control
# depending on what is going on in the data. Best guess is that it is
# picking the combination with highest F Value. This is to run a few
# comparisons against SAS and just make sure everything is coming out OK.
# proc ttest data=sashelp.class alpha=0.05;
# class sex /* Grouping Variable */;
# var height;
# run;
res1 <- proc_ttest(cls,
by = "region",
var = "Height",
class = "Sex",
options = c(alpha = 0.1))
res1
expect_equal(as.numeric(res1$Equality$NDF), c(3, 3))
expect_equal(as.numeric(res1$Equality$DDF), c(4, 5))
expect_equal(as.numeric(res1$Equality$FVAL), c(2.04584557, 1.70834286))
res2 <- proc_ttest(cls,
by = "region",
var = "Weight",
class = "Sex",
options = c(alpha = 0.1))
res2
expect_equal(as.numeric(res2$Equality$NDF), c(3, 3))
expect_equal(as.numeric(res2$Equality$DDF), c(4, 5))
expect_equal(as.numeric(res2$Equality$FVAL), c(1.4055752, 1.1721952))
res3 <- proc_ttest(cls,
by = "region",
var = "Age",
class = "Sex",
options = c(alpha = 0.1))
res3
expect_equal(as.numeric(res3$Equality$NDF), c(4, 5))
expect_equal(as.numeric(res3$Equality$DDF), c(3, 3))
expect_equal(as.numeric(res3$Equality$FVAL), c(1.41818182, 1.290000))
res4 <- proc_ttest(cls,
by = "region",
var = c("Height", "Weight", "Age"),
class = "Sex",
options = c(alpha = 0.1))
res4
})
test_that("ttest28: Data with no rows generates error.", {
cls2 <- cls[0, ]
expect_error(proc_ttest(cls2, var = c("Height")))
})
# Not sure how to do this. Can't get lognormal dist to match SAS.
# test_that("ttest28: Paired ttest with lognormal data works.", {
#
#
#
# auc <- read.table(header = TRUE, text = '
# TestAUC RefAUC
# 103.4 90.11
# 59.92 77.71
# 68.17 77.71
# 94.54 97.51
# 69.48 58.21
# 72.17 101.3
# 74.37 79.84
# 84.44 96.06
# 96.74 89.30
# 94.26 97.22
# 48.52 61.62
# 95.68 85.80')
#
# t.test(auc$TestAUC, paired = FALSE, var.equal = FALSE)
#
# t.test(auc$TestAUC, auc$RefAUC, paired = TRUE, var.equal = TRUE)
#
# t.test(auc$TestAUC, auc$RefAUC, paired = FALSE, var.equal = FALSE)
#
#
# t.test(auc$RefAUC, auc$TestAUC, data = auc, paired = TRUE, var.equal = TRUE)
#
# t.test(auc$RefAUC, auc$TestAUC, data = auc, paired = TRUE, var.equal = FALSE)
#
# res <- proc_ttest(auc,
# paired = "TestAUC * RefAUC")
#
# res
#
# expect_equal(is.null(res), FALSE)
# expect_equal(length(res), 3)
#
# # expect_equal(as.numeric(res$Statistics$MEAN), 62.336842)
# # expect_equal(as.numeric(res$Statistics$STD), 5.1270752)
# # expect_equal(as.numeric(res$Statistics$STDERR), 1.17623173)
# # expect_equal(as.numeric(res$ConfLimits$LCLM), 59.8656709)
# # expect_equal(as.numeric(res$ConfLimits$UCLM), 64.808013)
# # expect_equal(as.numeric(res$TTests$DF), 18)
# # expect_equal(as.numeric(res$TTests$T), -2.2641439)
# # expect_equal(as.numeric(res$TTests$PROBT), 0.036152218)
#
# })
# CO2
# t.test(uptake ~ Treatment, CO2)
#
#
# t.test(uptake ~ Treatment, CO2, var.equal = TRUE)
#
# mean(auc$TestAUC)
# mean(auc$RefAUC)
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