Nothing
suppressPackageStartupMessages(library(dplyr))
data("usz_13c")
data = usz_13c %>%
dplyr::filter( patient_id %in%
c("norm_001", "norm_002", "norm_004", "norm_007", "pat_004", "pat_012", "pat_023")) %>%
cleanup_data()
fit = nls_fit(data)
cm = comment(fit$data)
test_that("Result with default parameters is tbl_df with required columns",{
cf = coef_diff_by_group(fit)
expect_s3_class(cf, "tbl_df")
expect_s3_class(cf, "coef_diff_by_group")
expect_identical(ncol(cf), 7L)
expect_identical(nrow(cf), 54L)
expect_lt(min(cf$p.value), 5e-8)
expect_equal(length(unique(cf$groups)), 6)
expect_equal(comment(cf), cm)
})
test_that("Result with Dunnett contrast only returns 3 groups",{
cf = coef_diff_by_group(fit, mcp_group = "Dunnett")
expect_s3_class(cf, "tbl_df")
expect_s3_class(cf, "coef_diff_by_group")
expect_identical(ncol(cf), 7L)
expect_identical(nrow(cf), 27L)
expect_lt(min(cf$p.value), 5.e-8)
expect_equal(unique(cf$groups),
c("liquid_patient - liquid_normal", "solid_normal - liquid_normal",
"solid_patient - liquid_normal" ))
})
test_that("Only Dunnett and Tukey are allowed for mcp_group",{
expect_error(coef_diff_by_group(fit, mcp_group = "blub"))
})
test_that("Fit must be of class breathtestfit",{
expect_error(coef_diff_by_group(NULL))
})
test_that("Correct Dunnett contrast when reference value is given",{
coef(fit)$group
cf = coef_diff_by_group(fit, mcp_group = "Dunnett", reference_group = "solid_patient")
expect_equal(unique(cf$groups),
c("liquid_normal - solid_patient",
"liquid_patient - solid_patient",
"solid_normal - solid_patient"))
})
test_that("nlme_fit can be used to compute coefficients",{
skip_on_cran()
fit = nlme_fit(data)
cf = coef_diff_by_group(fit)
expect_s3_class(cf, "tbl_df")
expect_s3_class(cf, "coef_diff_by_group")
})
digs = function(x){
nchar(stringr::str_replace_all(paste(abs(x)), "[0\\.]",""))
}
test_that("Options digits is served",{
options(digits = 4)
cf = coef_diff_by_group(fit)
expect_s3_class(cf, "tbl_df")
expect_lte(digs(cf[[1,"estimate"]]) ,4L)
expect_lte(digs(cf[[1,"conf.low"]]), 4L)
expect_lte(digs(cf[[1,"conf.high"]]),4L)
})
test_that("NULL returned if there is only one group", {
data = usz_13c %>%
dplyr::filter( patient_id %in%
c("pat_001", "pat_002","pat_003")) %>%
cleanup_data()
fit = nls_fit(data)
cf = coef_diff_by_group(fit)
expect_null(cf)
})
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