Nothing
suppressPackageStartupMessages(library("ggplot2"))
suppressPackageStartupMessages(library("xpose"))
suppressPackageStartupMessages(library("ggforce"))
suppressPackageStartupMessages(library("onbrand"))
suppressPackageStartupMessages(library("nlmixr2rpt"))
# Objects used in the tests below:
rptyaml = system.file(package="nlmixr2rpt", "examples", "report_fit_test.yaml")
fit = fetch_fit_example()
obnd_test = read_template(
template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.docx"),
mapping = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))
test_that("Reading yaml", {
yaml_read_res = yaml_read_fit(
obnd = obnd_test,
rptyaml = rptyaml,
fit = fit)
expect_true(yaml_read_res$isgood)
})
test_that("build_figures", {
rptdetails = yaml_read_fit(
obnd = obnd_test,
rptyaml = rptyaml,
fit = fit)$rptdetails
bfres =
suppressWarnings(
suppressMessages(
invisible(
build_figures(obnd = obnd_test,
fit = fit,
verbose = FALSE,
rptdetails = rptdetails)
)
)
)
# Tests the overall build process:
expect_true(bfres$isgood)
# This should be a good figure so skip should be false and
# isgood should be true:
expect_false(bfres$rptfigs$dv_vs_pred$skip)
expect_true(bfres$rptfigs$dv_vs_pred$isgood)
# Catching broken figures:
expect_false(bfres$rptfigs$bad_figure$isgood)
# Catching skipped figures
expect_true(bfres$rptfigs$skip_figure$skip)
})
test_that("build_tables", {
rptdetails = yaml_read_fit(
obnd = obnd_test,
rptyaml = rptyaml,
fit = fit)$rptdetails
btres =
suppressWarnings(
suppressMessages(
invisible(
build_tables(obnd = obnd_test,
fit = fit,
verbose = FALSE,
rptdetails = rptdetails)
)
)
)
# Tests the overall build process:
expect_true(btres$isgood)
# This should be a good figure so skip should be false and
# isgood should be true:
expect_false(btres$rpttabs$pest_table$skip)
expect_true(btres$rpttabs$pest_table$isgood)
# Catching broken figures:
expect_false(btres$rpttabs$bad_table$isgood)
# Catching skipped figures
expect_true(btres$rpttabs$skip_table$skip)
})
test_that("PowerPoint Workflow", {
obnd_pptx = read_template(
template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.pptx"),
mapping = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))
obnd_pptx =
suppressMessages(
suppressWarnings(
invisible(
report_fit(
fit = fit,
obnd = obnd_pptx,
verbose = FALSE,
parameters = list(
TV_Vc = list(
md = "V~c~ (L)",
txt = "Vc (L)" ),
TV_ka = list(
md = "k~a~ (1/hr stuff)",
txt = "ka (1/hr stuff)" )),
placeholders = list(RUN="10"),
cat_covars = NULL, #c("SEX","SUBTYPE"),
cont_covars = NULL #c("WT")
)
)
)
)
expect_true(obnd_pptx$isgood)
save_res = save_report(obnd_pptx, tempfile(fileext=".pptx"))
expect_true(save_res$isgood)
})
test_that("Word Workflow", {
obnd_docx = read_template(
template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.docx"),
mapping = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))
obnd_docx =
suppressMessages(
suppressWarnings(
invisible(
report_fit(
fit = fit,
obnd = obnd_docx,
verbose = FALSE,
parameters = list(
TV_Vc = list(
md = "V~c~ (L)",
txt = "Vc (L)" ),
TV_ka = list(
md = "k~a~ (1/hr stuff)",
txt = "ka (1/hr stuff)" )),
placeholders = list(RUN="10"),
cat_covars = c("SEX","SUBTYPE"),
cont_covars = c("WT") )
)
)
)
expect_true(obnd_docx$isgood)
save_res = save_report(obnd_docx, tempfile(fileext=".docx"))
expect_true(save_res$isgood)
})
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