Nothing
tests/testthat/test-plot_expirest_osle.R
In expirest: Expiry Estimation Procedures
context("Plot illustrating the ordinary shelf life estimation (osle)")
test_that("plot_expirest_osle_succeeds", {
re1 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 1, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("no", "no"),
shift = c(0, 0), sf_option = "loose", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re2 <-
expirest_osle(
data = exp4, response_vbl = "Conc", time_vbl = "Month",
batch_vbl = "Batch", sl = c(95.0, 105.0), sl_sf = c(3, 4),
srch_range = c(0, 500), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "no"), shift = c(0, 0), sf_option = "loose",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re3 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(1, 2),
srch_range = c(0, 500), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "no"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
re4 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = 1.5, sl_sf = 2, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("no", "no"),
shift = c(0, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "lower")
# <-><-><-><->
tmp1 <-
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = "%",
x_range = NULL, y_range = c(-0.01, 0.5), mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp2 <-
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = " mg/kg",
x_range = c(-1, 29), y_range = c(92, 107), mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp3 <-
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = NULL,
x_range = c(-1, 29), y_range = c(92, 107), mtbs = "verified",
plot_option = "full", ci_app = "ribbon")
suppressWarnings(tmp4 <-
plot_expirest_osle(
model = re2, show_grouping = "no", response_vbl_unit = NULL,
x_range = c(-1, 29), y_range = c(92, 107), mtbs = "verified",
plot_option = "full", ci_app = "ribbon"))
suppressWarnings(tmp5 <-
plot_expirest_osle(
model = re3, show_grouping = "no", response_vbl_unit = "% (w/w)",
x_range = NULL, y_range = c(0.2, 5.2), mtbs = "verified",
plot_option = "full", ci_app = "line"))
suppressWarnings(tmp6 <-
plot_expirest_osle(
model = re4, show_grouping = "no", response_vbl_unit = "% (w/w)",
x_range = NULL, y_range = c(0.2, 5.2), mtbs = "verified",
plot_option = "full", ci_app = "line"))
suppressWarnings(tmp7 <-
plot_expirest_osle(
model = re4, show_grouping = "no", response_vbl_unit = "% (w/w)",
x_range = NULL, y_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"))
# <-><-><-><->
expect_length(tmp1, 7)
expect_s3_class(tmp1$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp1[["text"]][, "Month"], 5), c(20.000, 19.018))
expect_equal(tmp1[["text"]][, "Related"], c(0.35, 0.39))
expect_equal(tmp1[["text"]][, "Label"], c("USL: 0.34%", "19.0"))
expect_equal(tmp1[["text"]][, "Colour"], c("black", "forestgreen"))
expect_equal(tmp1[["hlines"]][1, "Related"], 0.34)
expect_equal(tmp1[["hlines"]][1, "Item"], "USL")
expect_equal(tmp1[["hlines"]][1, "Colour"], "black")
expect_equal(tmp1[["hlines"]][1, "Type"], "dotted")
expect_equal(signif(tmp1[["vlines"]][, "Month"], 5), 19.018)
expect_equal(tmp1[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp1[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp1[["vlines"]][, "Type"], "dotdash")
expect_length(tmp2, 7)
expect_s3_class(tmp2$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp2[["text"]][, "Month"], 5), c(29.000, 29.000, 23.698))
expect_equal(tmp2[["text"]][, "Conc"], c(94.45, 105.54, 92.45))
expect_equal(tmp2[["text"]][, "Label"],
c("LSL: 94.95 mg/kg", "USL: 105.04 mg/kg", "23.7"))
expect_equal(tmp2[["text"]][, "Colour"], c("black", "black", "forestgreen"))
expect_equal(tmp2[["hlines"]][, "Conc"], c(94.95, 105.04))
expect_equal(tmp2[["hlines"]][, "Item"], c("LSL", "USL"))
expect_equal(tmp2[["hlines"]][, "Colour"], c("black", "black"))
expect_equal(tmp2[["hlines"]][, "Type"], c("dotted", "dotted"))
expect_equal(signif(tmp2[["vlines"]][, "Month"], 5), 23.698)
expect_equal(tmp2[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp2[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp2[["vlines"]][, "Type"], "dotdash")
expect_equal(tmp3[["text"]][, "Label"],
c("LSL: 94.95", "USL: 105.04", "23.7"))
expect_equal(tmp4[["text"]][, "Label"],
c("LSL: 94.95", "USL: 105.04", "30.2"))
expect_equal(signif(tmp5[["text"]][, "Month"], 5),
c(100.00, 100.00, 96.306))
expect_equal(signif(tmp5[["text"]][, "Moisture"], 5),
c(0.40000, 4.6000, 0.00000))
expect_equal(tmp5[["text"]][, "Label"],
c("LSL: 0.5% (w/w)", "USL: 4.5% (w/w)", "96.3"))
expect_equal(tmp5[["text"]][, "Colour"], c("black", "black", "forestgreen"))
expect_equal(tmp5[["hlines"]][, "Moisture"], c(0.5, 4.5))
expect_equal(tmp5[["hlines"]][, "Item"], c("LSL", "USL"))
expect_equal(tmp5[["hlines"]][, "Colour"], c("black", "black"))
expect_equal(tmp5[["hlines"]][, "Type"], c("dotted", "dotted"))
expect_equal(signif(tmp5[["vlines"]][, "Month"], 5), 96.306)
expect_equal(tmp5[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp5[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp5[["vlines"]][, "Type"], "dotdash")
expect_equal(signif(tmp6[["text"]][, "Month"], 5), c(70.000, 60.761))
expect_equal(tmp6[["text"]][, "Moisture"], c(1.4, 1.0))
expect_equal(tmp6[["text"]][, "Label"], c("LSL: 1.5% (w/w)", "60.8"))
expect_equal(tmp6[["hlines"]][, "Moisture"], 1.5)
expect_equal(tmp6[["hlines"]][, "Item"], "LSL")
expect_equal(tmp6[["hlines"]][, "Colour"], "black")
expect_equal(tmp6[["hlines"]][, "Type"], "dotted")
expect_equal(signif(tmp6[["vlines"]][, "Month"], 5), 60.761)
expect_equal(tmp6[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp6[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp6[["vlines"]][, "Type"], "dotdash")
expect_equal(signif(tmp7[["text"]][, "Month"], 5), c(70.000, 60.761))
expect_equal(tmp7[["text"]][, "Moisture"], c(1.4, 1.0))
expect_equal(tmp7[["text"]][, "Label"], c("LSL: 1.5% (w/w)", "60.8"))
expect_equal(tmp7[["hlines"]][, "Moisture"], 1.5)
expect_equal(tmp7[["hlines"]][, "Item"], "LSL")
expect_equal(tmp7[["hlines"]][, "Colour"], "black")
expect_equal(tmp7[["hlines"]][, "Type"], "dotted")
expect_equal(signif(tmp7[["vlines"]][, "Month"], 5), 60.761)
expect_equal(tmp7[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp7[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp7[["vlines"]][, "Type"], "dotdash")
})
test_that("plot_expirest_osle_succeeds_with_transformations", {
re1 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 2, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("log", "log"),
shift = c(1, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re2 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 2, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("sqrt", "sqrt"),
shift = c(0, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re3 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 2, srch_range = c(0, 5000),
alpha = 0.05, alpha_pool = 0.25, xform = c("sq", "sq"),
shift = c(0, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re4 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re5 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "no"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re6 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re7 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
re8 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "no"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
re9 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
# <-><-><-><->
tmp1 <-
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = "%",
y_range = c(-0.01, 0.5), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp2 <-
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = "%",
y_range = c(-0.01, 0.5), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp3 <-
plot_expirest_osle(
model = re3, show_grouping = "yes", response_vbl_unit = "%",
y_range = c(-0.01, 0.5), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line")
suppressWarnings(tmp4 <-
plot_expirest_osle(
model = re4, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"))
suppressWarnings(tmp5 <-
plot_expirest_osle(
model = re5, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "ribbon"))
suppressWarnings(tmp6 <-
plot_expirest_osle(
model = re5, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "ribbon"))
suppressWarnings(tmp7 <-
plot_expirest_osle(
model = re7, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "lean", ci_app = "line"))
suppressWarnings(tmp8 <-
plot_expirest_osle(
model = re8, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "lean", ci_app = "ribbon"))
suppressWarnings(tmp9 <-
plot_expirest_osle(
model = re9, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "lean", ci_app = "ribbon"))
# <-><-><-><->
expect_length(tmp1, 7)
expect_s3_class(tmp1$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp1[["text"]][, "Month"], 5), c(30.000, 22.993))
expect_equal(tmp1[["text"]][, "Related"], c(0.31, 0.35))
expect_length(tmp2, 7)
expect_s3_class(tmp2$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp2[["text"]][, "Month"], 5), c(30.000, 20.582))
expect_equal(tmp2[["text"]][, "Related"], c(0.31, 0.35))
expect_length(tmp3, 7)
expect_s3_class(tmp3$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp3[["text"]][, "Month"], 5), c(20.000, 14.709))
expect_equal(tmp3[["text"]][, "Related"], c(0.31, 0.35))
expect_length(tmp4, 7)
expect_s3_class(tmp4$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp4[["text"]][, "Month"], 5), c(50.000, 50.000, 43.224))
expect_equal(tmp4[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp5, 7)
expect_s3_class(tmp5$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp5[["text"]][, "Month"], 5), c(60.000, 60.000, 51.516))
expect_equal(tmp5[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp6, 7)
expect_s3_class(tmp6$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp6[["text"]][, "Month"], 5), c(60.000, 60.000, 51.516))
expect_equal(tmp6[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp7, 7)
expect_s3_class(tmp7$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp7[["text"]][, "Month"], 5), c(60.000, 60.000, 55.908))
expect_equal(tmp7[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp8, 7)
expect_s3_class(tmp8$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp8[["text"]][, "Month"], 5), c(60.000, 60.000, 50.735))
expect_equal(tmp8[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp9, 7)
expect_s3_class(tmp9$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp9[["text"]][, "Month"], 5),
c(120.000, 120.000, 117.04))
expect_equal(tmp9[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
})
test_that("plot_expirest_osle_fails", {
t_dat <- exp1[exp1$Batch %in% c("b2", "b5", "b7"), ]
usl <- 105
lsl <- 95
# <-><-><-><->
re1 <-
expirest_osle(
data = t_dat, response_vbl = "Potency", time_vbl = "Month",
batch_vbl = "Batch", rl = 98, rl_sf = 3, sl = c(95, 105),
sl_sf = c(3, 4), srch_range = c(0, 500), alpha = 0.05,
alpha_pool = 0.25, xform = c("no", "no"), shift = c(0, 0),
sf_option = "loose", ivl = "confidence", ivl_type = "one.sided",
ivl_side = "lower")
ree <- re1
class(ree) <- "expirest"
re2 <- suppressWarnings(
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", rl = 3, rl_sf = 2, sl = c(1.5, 3.5),
sl_sf = c(2, 2), srch_range = c(0, 50), alpha = 0.05,
alpha_pool = 0.25, xform = c("no", "no"), shift = c(0, 0),
sf_option = "loose", ivl = "confidence", ivl_type = "one.sided",
ivl_side = "lower")
)
# <-><-><-><->
expect_error(
plot_expirest_osle(
model = ree, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"model must be an object of class expirest_osle")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = 1,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"response_vbl_unit must be a string")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = "range", x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"y_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = 107, x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"y_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = "range", mtbs = "verified",
plot_option = "full", ci_app = "line"),
"x_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = 36, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"x_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "incorrect",
plot_option = "incorrect", ci_app = "line"),
"specify mtbs either as \"verified\", \"cics\", \"dics\", ")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "incorrect", ci_app = "line"),
"specify plot_option either as \"full\" or \"lean\"")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "points"),
"specify ci_app either as \"line\" or \"ribbon\"")
expect_error(
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"Expiry determination was not successful")
})
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context("Plot illustrating the ordinary shelf life estimation (osle)")
test_that("plot_expirest_osle_succeeds", {
re1 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 1, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("no", "no"),
shift = c(0, 0), sf_option = "loose", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re2 <-
expirest_osle(
data = exp4, response_vbl = "Conc", time_vbl = "Month",
batch_vbl = "Batch", sl = c(95.0, 105.0), sl_sf = c(3, 4),
srch_range = c(0, 500), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "no"), shift = c(0, 0), sf_option = "loose",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re3 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(1, 2),
srch_range = c(0, 500), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "no"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
re4 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = 1.5, sl_sf = 2, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("no", "no"),
shift = c(0, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "lower")
# <-><-><-><->
tmp1 <-
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = "%",
x_range = NULL, y_range = c(-0.01, 0.5), mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp2 <-
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = " mg/kg",
x_range = c(-1, 29), y_range = c(92, 107), mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp3 <-
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = NULL,
x_range = c(-1, 29), y_range = c(92, 107), mtbs = "verified",
plot_option = "full", ci_app = "ribbon")
suppressWarnings(tmp4 <-
plot_expirest_osle(
model = re2, show_grouping = "no", response_vbl_unit = NULL,
x_range = c(-1, 29), y_range = c(92, 107), mtbs = "verified",
plot_option = "full", ci_app = "ribbon"))
suppressWarnings(tmp5 <-
plot_expirest_osle(
model = re3, show_grouping = "no", response_vbl_unit = "% (w/w)",
x_range = NULL, y_range = c(0.2, 5.2), mtbs = "verified",
plot_option = "full", ci_app = "line"))
suppressWarnings(tmp6 <-
plot_expirest_osle(
model = re4, show_grouping = "no", response_vbl_unit = "% (w/w)",
x_range = NULL, y_range = c(0.2, 5.2), mtbs = "verified",
plot_option = "full", ci_app = "line"))
suppressWarnings(tmp7 <-
plot_expirest_osle(
model = re4, show_grouping = "no", response_vbl_unit = "% (w/w)",
x_range = NULL, y_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"))
# <-><-><-><->
expect_length(tmp1, 7)
expect_s3_class(tmp1$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp1[["text"]][, "Month"], 5), c(20.000, 19.018))
expect_equal(tmp1[["text"]][, "Related"], c(0.35, 0.39))
expect_equal(tmp1[["text"]][, "Label"], c("USL: 0.34%", "19.0"))
expect_equal(tmp1[["text"]][, "Colour"], c("black", "forestgreen"))
expect_equal(tmp1[["hlines"]][1, "Related"], 0.34)
expect_equal(tmp1[["hlines"]][1, "Item"], "USL")
expect_equal(tmp1[["hlines"]][1, "Colour"], "black")
expect_equal(tmp1[["hlines"]][1, "Type"], "dotted")
expect_equal(signif(tmp1[["vlines"]][, "Month"], 5), 19.018)
expect_equal(tmp1[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp1[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp1[["vlines"]][, "Type"], "dotdash")
expect_length(tmp2, 7)
expect_s3_class(tmp2$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp2[["text"]][, "Month"], 5), c(29.000, 29.000, 23.698))
expect_equal(tmp2[["text"]][, "Conc"], c(94.45, 105.54, 92.45))
expect_equal(tmp2[["text"]][, "Label"],
c("LSL: 94.95 mg/kg", "USL: 105.04 mg/kg", "23.7"))
expect_equal(tmp2[["text"]][, "Colour"], c("black", "black", "forestgreen"))
expect_equal(tmp2[["hlines"]][, "Conc"], c(94.95, 105.04))
expect_equal(tmp2[["hlines"]][, "Item"], c("LSL", "USL"))
expect_equal(tmp2[["hlines"]][, "Colour"], c("black", "black"))
expect_equal(tmp2[["hlines"]][, "Type"], c("dotted", "dotted"))
expect_equal(signif(tmp2[["vlines"]][, "Month"], 5), 23.698)
expect_equal(tmp2[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp2[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp2[["vlines"]][, "Type"], "dotdash")
expect_equal(tmp3[["text"]][, "Label"],
c("LSL: 94.95", "USL: 105.04", "23.7"))
expect_equal(tmp4[["text"]][, "Label"],
c("LSL: 94.95", "USL: 105.04", "30.2"))
expect_equal(signif(tmp5[["text"]][, "Month"], 5),
c(100.00, 100.00, 96.306))
expect_equal(signif(tmp5[["text"]][, "Moisture"], 5),
c(0.40000, 4.6000, 0.00000))
expect_equal(tmp5[["text"]][, "Label"],
c("LSL: 0.5% (w/w)", "USL: 4.5% (w/w)", "96.3"))
expect_equal(tmp5[["text"]][, "Colour"], c("black", "black", "forestgreen"))
expect_equal(tmp5[["hlines"]][, "Moisture"], c(0.5, 4.5))
expect_equal(tmp5[["hlines"]][, "Item"], c("LSL", "USL"))
expect_equal(tmp5[["hlines"]][, "Colour"], c("black", "black"))
expect_equal(tmp5[["hlines"]][, "Type"], c("dotted", "dotted"))
expect_equal(signif(tmp5[["vlines"]][, "Month"], 5), 96.306)
expect_equal(tmp5[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp5[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp5[["vlines"]][, "Type"], "dotdash")
expect_equal(signif(tmp6[["text"]][, "Month"], 5), c(70.000, 60.761))
expect_equal(tmp6[["text"]][, "Moisture"], c(1.4, 1.0))
expect_equal(tmp6[["text"]][, "Label"], c("LSL: 1.5% (w/w)", "60.8"))
expect_equal(tmp6[["hlines"]][, "Moisture"], 1.5)
expect_equal(tmp6[["hlines"]][, "Item"], "LSL")
expect_equal(tmp6[["hlines"]][, "Colour"], "black")
expect_equal(tmp6[["hlines"]][, "Type"], "dotted")
expect_equal(signif(tmp6[["vlines"]][, "Month"], 5), 60.761)
expect_equal(tmp6[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp6[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp6[["vlines"]][, "Type"], "dotdash")
expect_equal(signif(tmp7[["text"]][, "Month"], 5), c(70.000, 60.761))
expect_equal(tmp7[["text"]][, "Moisture"], c(1.4, 1.0))
expect_equal(tmp7[["text"]][, "Label"], c("LSL: 1.5% (w/w)", "60.8"))
expect_equal(tmp7[["hlines"]][, "Moisture"], 1.5)
expect_equal(tmp7[["hlines"]][, "Item"], "LSL")
expect_equal(tmp7[["hlines"]][, "Colour"], "black")
expect_equal(tmp7[["hlines"]][, "Type"], "dotted")
expect_equal(signif(tmp7[["vlines"]][, "Month"], 5), 60.761)
expect_equal(tmp7[["vlines"]][, "Item"], "poi.model")
expect_equal(tmp7[["vlines"]][, "Colour"], "forestgreen")
expect_equal(tmp7[["vlines"]][, "Type"], "dotdash")
})
test_that("plot_expirest_osle_succeeds_with_transformations", {
re1 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 2, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("log", "log"),
shift = c(1, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re2 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 2, srch_range = c(0, 500),
alpha = 0.05, alpha_pool = 0.25, xform = c("sqrt", "sqrt"),
shift = c(0, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re3 <-
expirest_osle(
data = exp2, response_vbl = "Related", time_vbl = "Month",
batch_vbl = "Batch", sl = 0.3, sl_sf = 2, srch_range = c(0, 5000),
alpha = 0.05, alpha_pool = 0.25, xform = c("sq", "sq"),
shift = c(0, 0), sf_option = "tight", ivl = "confidence",
ivl_type = "one.sided", ivl_side = "upper")
re4 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re5 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "no"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re6 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "lower")
re7 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
re8 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("sq", "no"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
re9 <-
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", sl = c(0.5, 4.5), sl_sf = c(2, 2),
srch_range = c(0, 5000), alpha = 0.05, alpha_pool = 0.25,
xform = c("no", "sq"), shift = c(0, 0), sf_option = "tight",
ivl = "confidence", ivl_type = "one.sided", ivl_side = "upper")
# <-><-><-><->
tmp1 <-
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = "%",
y_range = c(-0.01, 0.5), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp2 <-
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = "%",
y_range = c(-0.01, 0.5), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line")
tmp3 <-
plot_expirest_osle(
model = re3, show_grouping = "yes", response_vbl_unit = "%",
y_range = c(-0.01, 0.5), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line")
suppressWarnings(tmp4 <-
plot_expirest_osle(
model = re4, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"))
suppressWarnings(tmp5 <-
plot_expirest_osle(
model = re5, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "ribbon"))
suppressWarnings(tmp6 <-
plot_expirest_osle(
model = re5, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "ribbon"))
suppressWarnings(tmp7 <-
plot_expirest_osle(
model = re7, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "lean", ci_app = "line"))
suppressWarnings(tmp8 <-
plot_expirest_osle(
model = re8, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "lean", ci_app = "ribbon"))
suppressWarnings(tmp9 <-
plot_expirest_osle(
model = re9, show_grouping = "no", response_vbl_unit = "% (w/w)",
y_range = c(0.2, 5.2), x_range = NULL, mtbs = "verified",
plot_option = "lean", ci_app = "ribbon"))
# <-><-><-><->
expect_length(tmp1, 7)
expect_s3_class(tmp1$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp1[["text"]][, "Month"], 5), c(30.000, 22.993))
expect_equal(tmp1[["text"]][, "Related"], c(0.31, 0.35))
expect_length(tmp2, 7)
expect_s3_class(tmp2$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp2[["text"]][, "Month"], 5), c(30.000, 20.582))
expect_equal(tmp2[["text"]][, "Related"], c(0.31, 0.35))
expect_length(tmp3, 7)
expect_s3_class(tmp3$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp3[["text"]][, "Month"], 5), c(20.000, 14.709))
expect_equal(tmp3[["text"]][, "Related"], c(0.31, 0.35))
expect_length(tmp4, 7)
expect_s3_class(tmp4$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp4[["text"]][, "Month"], 5), c(50.000, 50.000, 43.224))
expect_equal(tmp4[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp5, 7)
expect_s3_class(tmp5$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp5[["text"]][, "Month"], 5), c(60.000, 60.000, 51.516))
expect_equal(tmp5[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp6, 7)
expect_s3_class(tmp6$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp6[["text"]][, "Month"], 5), c(60.000, 60.000, 51.516))
expect_equal(tmp6[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp7, 7)
expect_s3_class(tmp7$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp7[["text"]][, "Month"], 5), c(60.000, 60.000, 55.908))
expect_equal(tmp7[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp8, 7)
expect_s3_class(tmp8$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp8[["text"]][, "Month"], 5), c(60.000, 60.000, 50.735))
expect_equal(tmp8[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
expect_length(tmp9, 7)
expect_s3_class(tmp9$Graph, c("gg", "ggplot"))
expect_equal(signif(tmp9[["text"]][, "Month"], 5),
c(120.000, 120.000, 117.04))
expect_equal(tmp9[["text"]][, "Moisture"], c(0.4, 4.6, 0.0))
})
test_that("plot_expirest_osle_fails", {
t_dat <- exp1[exp1$Batch %in% c("b2", "b5", "b7"), ]
usl <- 105
lsl <- 95
# <-><-><-><->
re1 <-
expirest_osle(
data = t_dat, response_vbl = "Potency", time_vbl = "Month",
batch_vbl = "Batch", rl = 98, rl_sf = 3, sl = c(95, 105),
sl_sf = c(3, 4), srch_range = c(0, 500), alpha = 0.05,
alpha_pool = 0.25, xform = c("no", "no"), shift = c(0, 0),
sf_option = "loose", ivl = "confidence", ivl_type = "one.sided",
ivl_side = "lower")
ree <- re1
class(ree) <- "expirest"
re2 <- suppressWarnings(
expirest_osle(
data = exp3, response_vbl = "Moisture", time_vbl = "Month",
batch_vbl = "Batch", rl = 3, rl_sf = 2, sl = c(1.5, 3.5),
sl_sf = c(2, 2), srch_range = c(0, 50), alpha = 0.05,
alpha_pool = 0.25, xform = c("no", "no"), shift = c(0, 0),
sf_option = "loose", ivl = "confidence", ivl_type = "one.sided",
ivl_side = "lower")
)
# <-><-><-><->
expect_error(
plot_expirest_osle(
model = ree, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"model must be an object of class expirest_osle")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = 1,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"response_vbl_unit must be a string")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = "range", x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"y_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = 107, x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"y_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = "range", mtbs = "verified",
plot_option = "full", ci_app = "line"),
"x_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = 36, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"x_range must be a vector of length 2")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "incorrect",
plot_option = "incorrect", ci_app = "line"),
"specify mtbs either as \"verified\", \"cics\", \"dics\", ")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "incorrect", ci_app = "line"),
"specify plot_option either as \"full\" or \"lean\"")
expect_error(
plot_expirest_osle(
model = re1, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "points"),
"specify ci_app either as \"line\" or \"ribbon\"")
expect_error(
plot_expirest_osle(
model = re2, show_grouping = "yes", response_vbl_unit = NULL,
y_range = c(93, 107), x_range = NULL, mtbs = "verified",
plot_option = "full", ci_app = "line"),
"Expiry determination was not successful")
})
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