tests/testthat/test-class-PKNCAdose.R
In billdenney/pknca: Perform Pharmacokinetic Non-Compartmental Analysis
test_that("PKNCAdose", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.conc.analyte <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2)
tmp.conc.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nstudies=2)
tmp.conc.analyte.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2, nstudies=2)
tmp.dose <- generate.dose(tmp.conc)
rownames(tmp.dose) <- NULL
tmp.dose.analyte <- generate.dose(tmp.conc.analyte)
tmp.dose.study <- generate.dose(tmp.conc.study)
tmp.dose.analyte.study <- generate.dose(tmp.conc.analyte.study)
# Data exists
expect_error(PKNCAdose(data.frame()),
regexp="data must have at least one row.",
info="PKNCAconc requires data")
# Variables present
expect_error(PKNCAdose(tmp.dose, formula=dosea~time|treatment+ID),
regexp="The left side formula must be a variable in the data, empty, or '.'.",
info="All formula parameters must be in the data (LHS)")
expect_error(PKNCAdose(tmp.dose, formula=dose~timea|treatment+ID),
regexp="The right side formula must be a variable in the data or '.'.",
info="All formula parameters must be in the data (RHS)")
expect_error(PKNCAdose(tmp.dose, formula=dose~time|treatmenta+ID),
regexp="All of the variables in the groups must be in the data",
info="All formula parameters must be in the data (groups)")
expect_error(PKNCAdose(tmp.dose, formula=dosea~time|treatment/ID),
regexp="formula for PKNCAdose may not include a slash",
info="The formula string must not contain any slashes")
# Number of variables
expect_error(PKNCAdose(tmp.dose, formula=dose+ID~time|treatment+ID),
regexp="The left side of the formula must have zero or one variable",
info="The right number of parameters in the formula (LHS)")
expect_error(PKNCAdose(tmp.dose, formula=dose~time+ID|treatment+ID),
regexp="The right side of the formula \\(excluding groups\\) must have exactly one variable",
info="The right number of parameters in the formula (RHS)")
expect_error(PKNCAdose(tmp.dose, formula=~time+ID|treatment+ID),
regexp="The right side of the formula \\(excluding groups\\) must have exactly one variable",
info="The right number of parameters in the formula (RHS)")
# Accept "." on either side of the ~
expect_equal(
PKNCAdose(tmp.dose, formula=.~time|treatment+ID),
structure(
list(
data =
cbind(
tmp.dose,
data.frame(
exclude = NA_character_,
route = "extravascular",
duration = 0,
stringsAsFactors = FALSE
)
),
formula = . ~ time | treatment + ID,
columns =
list(
dose = character(),
time = "time",
groups =
list(
group_vars = c("treatment", "ID"),
group_analyte = character()
),
exclude = "exclude",
route = "route",
duration = "duration"
),
units = list()
),
class = c("PKNCAdose", "list")
),
info="PKNCAdose accepts . on the left side of the formula"
)
expect_equal(
PKNCAdose(tmp.dose, formula = dose~.|treatment+ID),
structure(
list(
data =
cbind(
tmp.dose,
data.frame(
exclude = NA_character_,
route = "extravascular",
duration = 0,
stringsAsFactors = FALSE
)
),
formula = dose ~ . | treatment + ID,
columns =
list(
dose = "dose",
time = character(),
groups =
list(
group_vars = c("treatment", "ID"),
group_analyte = character()
),
exclude = "exclude",
route = "route",
duration = "duration"
),
units = list()
),
class = c("PKNCAdose", "list")
),
info = "PKNCAdose accepts . on the right side of the formula"
)
tmp.dose.na <- tmp.dose
tmp.dose.na$time[1] <- NA
expect_error(PKNCAdose(tmp.dose.na, formula=dose~time|treatment+ID),
regexp="Some but not all values are missing for the independent variable",
info="Dose time must either all or none be NA.")
# Keys must be unique
bad.dose.analyte <- unique(tmp.conc.analyte[,c("treatment", "ID", "analyte")])
bad.dose.analyte$dose <- 1
bad.dose.analyte$time <- 0
expect_error(
PKNCAdose(bad.dose.analyte, formula=dose~time|treatment+ID),
regexp="Rows that are not unique per group and time"
)
expect_equal(
PKNCAdose(
tmp.dose,
formula=dose~time|treatment+ID
),
PKNCAdose(
dplyr::as_tibble(tmp.dose),
formula=dose~time|treatment+ID
),
info="tibble and data.frame classes both work and create identical objects"
)
})
test_that("PKNCAdose without a data.frame as input", {
tmp <- structure(list(), class="foo")
captured_message <- tryCatch(as.data.frame(tmp), error=function(e) e$message)
expect_error(PKNCAdose(tmp, formula=.~time|treatment+ID),
regexp=captured_message,
fixed=TRUE,
info="PKNCAdose tries to make arbitrary data into a data.frame")
})
test_that("PKNCAdose model.frame", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp_conc_single <- generate.conc(nsub=1, ntreat=1, time.points=0:24)
tmp.conc.analyte <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2)
tmp.conc.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nstudies=2)
tmp.conc.analyte.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2, nstudies=2)
tmp.dose <- generate.dose(tmp.conc)
tmp_dose_single <- generate.dose(tmp_conc_single)
mydose1 <- PKNCAdose(formula=dose~time|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose1),
rep(1:2, each=5),
info="getDepVar.PKNCAdose works with two-sided formula")
expect_equal(getIndepVar.PKNCAdose(mydose1),
rep(0, 10),
info="getIndepVar.PKNCAdose works with two-sided formula")
expect_equal(model.frame.PKNCAdose(mydose1),
data.frame("getDepVar.PKNCAdose(formula)"=rep(1:2, each=5),
"getIndepVar.PKNCAdose(formula)"=0,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with two-sided formula")
mydose2 <- PKNCAdose(formula=~time|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose2),
rep(NA_integer_, 10),
info="getDepVar.PKNCAdose works with one-sided formula")
expect_equal(getIndepVar.PKNCAdose(mydose2),
rep(0, 10),
info="getIndepVar.PKNCAdose works with one-sided formula")
expect_equal(model.frame.PKNCAdose(mydose2),
data.frame("getDepVar.PKNCAdose(formula)"=NA_integer_,
"getIndepVar.PKNCAdose(formula)"=0,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with one-sided formula")
mydose3 <- PKNCAdose(formula=.~time|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose3),
rep(NA_integer_, 10),
info="getDepVar.PKNCAdose works with one-sided formula ('.' on LHS)")
expect_equal(getIndepVar.PKNCAdose(mydose3),
rep(0, 10),
info="getIndepVar.PKNCAdose works with one-sided formula ('.' on LHS)")
expect_equal(model.frame.PKNCAdose(mydose3),
data.frame("getDepVar.PKNCAdose(formula)"=NA_integer_,
"getIndepVar.PKNCAdose(formula)"=0,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with one-sided formula ('.' on LHS)")
mydose4 <- PKNCAdose(formula=dose~.|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose4),
rep(1:2, each=5),
info="getDepVar.PKNCAdose works with one-sided formula ('.' on RHS)")
expect_equal(getIndepVar.PKNCAdose(mydose4),
rep(NA_integer_, 10),
info="getIndepVar.PKNCAdose works with one-sided formula ('.' on RHS)")
expect_equal(model.frame.PKNCAdose(mydose4),
data.frame("getDepVar.PKNCAdose(formula)"=rep(1:2, each=5),
"getIndepVar.PKNCAdose(formula)"=NA_integer_,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with one-sided formula ('.' on RHS)")
# You can't give multiple rows per group if you don't give time.
expect_error(PKNCAdose(formula=dose~.|treatment+ID, data=rbind(tmp.dose, tmp.dose)),
regexp="Rows that are not unique per group and time.*found within dosing data",
info="Dosing must have unique values with time and group")
expect_equal(
group_vars.PKNCAdose(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)),
c("treatment", "ID")
)
expect_equal(
group_vars.PKNCAdose(PKNCAdose(tmp_dose_single, formula=dose~time)),
character(0),
info="Ungrouped data works with group_vars"
)
})
test_that("print.PKNCAdose", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
mydose <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)
tmp.conc.nogroup <- generate.conc(nsub=1, ntreat=1, time.points=0:24)
tmp.dose.nogroup <- generate.dose(tmp.conc.nogroup)
mydose.nogroup <- PKNCAdose(tmp.dose.nogroup, formula=dose~time)
expect_output(print(mydose),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is not specified.
First 6 rows of dosing data:
treatment ID dose time exclude route duration
Trt 1 1 1 0 <NA> extravascular 0
Trt 1 2 1 0 <NA> extravascular 0
Trt 1 3 1 0 <NA> extravascular 0
Trt 1 4 1 0 <NA> extravascular 0
Trt 1 5 1 0 <NA> extravascular 0
Trt 2 1 2 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works")
expect_output(print(mydose.nogroup),
regexp="Formula for dosing:
dose ~ time
Nominal time column is not specified.
Data for dosing:
treatment ID dose time exclude route duration
Trt 1 1 1 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works with no groups")
expect_output(print(mydose, n=-5),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is not specified.
First 5 rows of dosing data:
treatment ID dose time exclude route duration
Trt 1 1 1 0 <NA> extravascular 0
Trt 1 2 1 0 <NA> extravascular 0
Trt 1 3 1 0 <NA> extravascular 0
Trt 1 4 1 0 <NA> extravascular 0
Trt 1 5 1 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works")
expect_output(print(mydose, summarize=TRUE),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is not specified.
Number unique entries in each group:
treatment ID
2 5",
fixed=TRUE,
info="Summary print.PKNCAdose works")
expect_output(
print(mydose.nogroup, summarize=TRUE),
regexp="No groups"
)
})
test_that("PKNCAdose with exclusions", {
tmp.conc <- generate.conc(nsub=2, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
tmp.dose$excl <- NA_character_
mydose <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, exclude="excl")
expect_equal(
mydose,
structure(
list(
data =
cbind(
tmp.dose,
data.frame(
route = "extravascular",
duration = 0,
stringsAsFactors = FALSE
)
),
formula = dose~time|treatment+ID,
columns =
list(
dose = "dose",
time = "time",
groups =
list(
group_vars = c("treatment", "ID"),
group_analyte = character()
),
exclude = "excl",
route = "route",
duration = "duration"
),
units = list()
),
class=c("PKNCAdose", "list")
)
)
})
test_that("PKNCAdose route and duration", {
tmp.conc <- generate.conc(nsub=2, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
expect_equal(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID),
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, route="extravascular"),
info="route is assumed as extravascular")
expect_equal(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID),
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0),
info="duration is assumed as 0")
expect_equal(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID),
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="extravascular"),
info="route and duration are correctly assumed")
dose.iv <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="intravascular")
dose.ev <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="extravascular")
expect_equal(dose.iv,
{
tmp <- dose.ev
tmp$data$route <- "intravascular"
tmp
},
info="Intravascular route works")
expect_error(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="foo"),
regexp="route must have values of either 'extravascular' or 'intravascular'. Please set to one of those values and retry.",
info="route must be an accepted value")
tmp.dose.iv <- tmp.dose
tmp.dose.iv$route <- "intravascular"
# Note that the column names are in a different order when specified
# in the input data.frame or not.
expect_equal(
{
tmp <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="intravascular")
tmp$data <- tmp$data[,sort(names(tmp$data))]
tmp
},
{
tmp <- PKNCAdose(tmp.dose.iv, formula=dose~time|treatment+ID, duration=0, route="route")
tmp$data <- tmp$data[,sort(names(tmp$data))]
tmp
},
ignore_attr=TRUE
)
})
test_that("time.nominal within PKNCAdose", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
tmp.dose$nom_time <- tmp.dose$time
rownames(tmp.dose) <- NULL
expect_equal(
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID,
time.nominal="nom_time"),
structure(list(
data=
cbind(
tmp.dose,
data.frame(
exclude=NA_character_,
route="extravascular",
duration=0,
stringsAsFactors=FALSE
)
),
formula = dose ~ time | treatment + ID,
columns =
list(
dose = "dose",
time = "time",
groups = list(group_vars = c("treatment", "ID"), group_analyte = character()),
exclude = "exclude",
route = "route",
duration = "duration",
time.nominal = "nom_time"
),
units = list()
),
class = c("PKNCAdose", "list")),
info="PKNCAdose accepts time.nominal"
)
expect_error(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID,
time.nominal="foo"),
regexp="time.nominal, if given, must be a column name in the input data",
info="PKNCAdose time.nominal must be a column in the data")
# Test printing
dose_with_nom_time <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID,
time.nominal="nom_time")
expect_output(print(dose_with_nom_time),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is: nom_time
First 6 rows of dosing data:
treatment ID dose time nom_time exclude route duration
Trt 1 1 1 0 0 <NA> extravascular 0
Trt 1 2 1 0 0 <NA> extravascular 0
Trt 1 3 1 0 0 <NA> extravascular 0
Trt 1 4 1 0 0 <NA> extravascular 0
Trt 1 5 1 0 0 <NA> extravascular 0
Trt 2 1 2 0 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works")
})
test_that("setDuration", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
tmp.dose$nom_time <- tmp.dose$time
rownames(tmp.dose) <- NULL
mydose <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)
expect_message(
expect_equal(
setDuration(mydose),
mydose,
info="No changes with no arguments"
),
class = "pknca_foundcolumn_duration"
)
expect_error(setDuration(mydose, duration="foo", rate="bar"),
regexp="Both duration and rate cannot be given at the same time",
fixed=TRUE,
info="Cannot give both duration and rate")
expect_message(expect_error(
setDuration(mydose, duration="foobar"),
regexp="duration must be numeric without missing (NA) or infinite values, and all values must be >= 0",
fixed=TRUE,
info="Cannot give both duration as non-numeric"),
class = "pknca_foundcolumn_duration"
)
duration_example <- suppressMessages(setDuration(mydose, rate=2))
expect_true(all(mydose$data$duration == 0))
expect_equal(
duration_example$data$duration,
duration_example$data$dose/2
)
expect_equal(duration_example$columns$duration, "duration")
})
test_that("Test uniqueness after excluding rows (#298)", {
repeated_with_exclusion <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c(NA, "duplicate")
)
expect_error(
PKNCAdose(repeated_with_exclusion, formula=dose~time|id),
regexp="Rows that are not unique per group and time.*dosing"
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion, formula=dose~time|id, exclude = "exclude"),
class = "PKNCAdose"
)
repeated_with_exclusion_firstrow <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c("duplicate", NA)
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_firstrow, formula=dose~time|id, exclude = "exclude"),
class = "PKNCAdose"
)
repeated_with_exclusion_nogroup <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c("duplicate", NA)
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_firstrow, formula=dose~., exclude = "exclude"),
class = "PKNCAdose"
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_firstrow, formula=dose~.|id, exclude = "exclude"),
class = "PKNCAdose"
)
repeated_with_exclusion_row2 <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c(NA, "duplicate")
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_row2, formula=dose~.|id, exclude = "exclude"),
class = "PKNCAdose"
)
})
test_that("PKNCAdose units (#336)", {
d <- data.frame(dose = 1, time = 0, doseu_x = "A")
# No units
o_dose <- PKNCAdose(data = d, dose~time)
expect_equal(o_dose$units, list())
expect_null(o_dose$columns$doseu)
# Each unit column individually
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_x")
expect_equal(o_dose$units, list())
expect_equal(o_dose$columns$doseu, structure("doseu_x", unit_type = "column"))
# Each unit as a value, not a column
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_y")
expect_equal(o_dose$units, list(doseu = structure("doseu_y", unit_type = "value")))
expect_null(o_dose$columns$doseu)
# Preferred units
expect_error(
PKNCAdose(data = d, dose~time, doseu_pref = "doseu_z"),
regexp = "Preferred units may not be set unless original units are set: doseu_pref"
)
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_y", doseu_pref = "doseu_z")
expect_equal(
o_dose$units,
list(
doseu = structure("doseu_y", unit_type = "value"),
doseu_pref = structure("doseu_z", unit_type = "value")
)
)
expect_null(o_dose$columns$doseu)
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_x", doseu_pref = "doseu_z")
expect_equal(o_dose$units, list(doseu_pref = structure("doseu_z", unit_type = "value")))
expect_equal(
o_dose$columns$doseu,
structure("doseu_x", unit_type = "column")
)
})
billdenney/pknca documentation built on June 11, 2025, 1:49 a.m.
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test_that("PKNCAdose", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.conc.analyte <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2)
tmp.conc.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nstudies=2)
tmp.conc.analyte.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2, nstudies=2)
tmp.dose <- generate.dose(tmp.conc)
rownames(tmp.dose) <- NULL
tmp.dose.analyte <- generate.dose(tmp.conc.analyte)
tmp.dose.study <- generate.dose(tmp.conc.study)
tmp.dose.analyte.study <- generate.dose(tmp.conc.analyte.study)
# Data exists
expect_error(PKNCAdose(data.frame()),
regexp="data must have at least one row.",
info="PKNCAconc requires data")
# Variables present
expect_error(PKNCAdose(tmp.dose, formula=dosea~time|treatment+ID),
regexp="The left side formula must be a variable in the data, empty, or '.'.",
info="All formula parameters must be in the data (LHS)")
expect_error(PKNCAdose(tmp.dose, formula=dose~timea|treatment+ID),
regexp="The right side formula must be a variable in the data or '.'.",
info="All formula parameters must be in the data (RHS)")
expect_error(PKNCAdose(tmp.dose, formula=dose~time|treatmenta+ID),
regexp="All of the variables in the groups must be in the data",
info="All formula parameters must be in the data (groups)")
expect_error(PKNCAdose(tmp.dose, formula=dosea~time|treatment/ID),
regexp="formula for PKNCAdose may not include a slash",
info="The formula string must not contain any slashes")
# Number of variables
expect_error(PKNCAdose(tmp.dose, formula=dose+ID~time|treatment+ID),
regexp="The left side of the formula must have zero or one variable",
info="The right number of parameters in the formula (LHS)")
expect_error(PKNCAdose(tmp.dose, formula=dose~time+ID|treatment+ID),
regexp="The right side of the formula \\(excluding groups\\) must have exactly one variable",
info="The right number of parameters in the formula (RHS)")
expect_error(PKNCAdose(tmp.dose, formula=~time+ID|treatment+ID),
regexp="The right side of the formula \\(excluding groups\\) must have exactly one variable",
info="The right number of parameters in the formula (RHS)")
# Accept "." on either side of the ~
expect_equal(
PKNCAdose(tmp.dose, formula=.~time|treatment+ID),
structure(
list(
data =
cbind(
tmp.dose,
data.frame(
exclude = NA_character_,
route = "extravascular",
duration = 0,
stringsAsFactors = FALSE
)
),
formula = . ~ time | treatment + ID,
columns =
list(
dose = character(),
time = "time",
groups =
list(
group_vars = c("treatment", "ID"),
group_analyte = character()
),
exclude = "exclude",
route = "route",
duration = "duration"
),
units = list()
),
class = c("PKNCAdose", "list")
),
info="PKNCAdose accepts . on the left side of the formula"
)
expect_equal(
PKNCAdose(tmp.dose, formula = dose~.|treatment+ID),
structure(
list(
data =
cbind(
tmp.dose,
data.frame(
exclude = NA_character_,
route = "extravascular",
duration = 0,
stringsAsFactors = FALSE
)
),
formula = dose ~ . | treatment + ID,
columns =
list(
dose = "dose",
time = character(),
groups =
list(
group_vars = c("treatment", "ID"),
group_analyte = character()
),
exclude = "exclude",
route = "route",
duration = "duration"
),
units = list()
),
class = c("PKNCAdose", "list")
),
info = "PKNCAdose accepts . on the right side of the formula"
)
tmp.dose.na <- tmp.dose
tmp.dose.na$time[1] <- NA
expect_error(PKNCAdose(tmp.dose.na, formula=dose~time|treatment+ID),
regexp="Some but not all values are missing for the independent variable",
info="Dose time must either all or none be NA.")
# Keys must be unique
bad.dose.analyte <- unique(tmp.conc.analyte[,c("treatment", "ID", "analyte")])
bad.dose.analyte$dose <- 1
bad.dose.analyte$time <- 0
expect_error(
PKNCAdose(bad.dose.analyte, formula=dose~time|treatment+ID),
regexp="Rows that are not unique per group and time"
)
expect_equal(
PKNCAdose(
tmp.dose,
formula=dose~time|treatment+ID
),
PKNCAdose(
dplyr::as_tibble(tmp.dose),
formula=dose~time|treatment+ID
),
info="tibble and data.frame classes both work and create identical objects"
)
})
test_that("PKNCAdose without a data.frame as input", {
tmp <- structure(list(), class="foo")
captured_message <- tryCatch(as.data.frame(tmp), error=function(e) e$message)
expect_error(PKNCAdose(tmp, formula=.~time|treatment+ID),
regexp=captured_message,
fixed=TRUE,
info="PKNCAdose tries to make arbitrary data into a data.frame")
})
test_that("PKNCAdose model.frame", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp_conc_single <- generate.conc(nsub=1, ntreat=1, time.points=0:24)
tmp.conc.analyte <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2)
tmp.conc.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nstudies=2)
tmp.conc.analyte.study <- generate.conc(nsub=5, ntreat=2, time.points=0:24,
nanalytes=2, nstudies=2)
tmp.dose <- generate.dose(tmp.conc)
tmp_dose_single <- generate.dose(tmp_conc_single)
mydose1 <- PKNCAdose(formula=dose~time|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose1),
rep(1:2, each=5),
info="getDepVar.PKNCAdose works with two-sided formula")
expect_equal(getIndepVar.PKNCAdose(mydose1),
rep(0, 10),
info="getIndepVar.PKNCAdose works with two-sided formula")
expect_equal(model.frame.PKNCAdose(mydose1),
data.frame("getDepVar.PKNCAdose(formula)"=rep(1:2, each=5),
"getIndepVar.PKNCAdose(formula)"=0,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with two-sided formula")
mydose2 <- PKNCAdose(formula=~time|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose2),
rep(NA_integer_, 10),
info="getDepVar.PKNCAdose works with one-sided formula")
expect_equal(getIndepVar.PKNCAdose(mydose2),
rep(0, 10),
info="getIndepVar.PKNCAdose works with one-sided formula")
expect_equal(model.frame.PKNCAdose(mydose2),
data.frame("getDepVar.PKNCAdose(formula)"=NA_integer_,
"getIndepVar.PKNCAdose(formula)"=0,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with one-sided formula")
mydose3 <- PKNCAdose(formula=.~time|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose3),
rep(NA_integer_, 10),
info="getDepVar.PKNCAdose works with one-sided formula ('.' on LHS)")
expect_equal(getIndepVar.PKNCAdose(mydose3),
rep(0, 10),
info="getIndepVar.PKNCAdose works with one-sided formula ('.' on LHS)")
expect_equal(model.frame.PKNCAdose(mydose3),
data.frame("getDepVar.PKNCAdose(formula)"=NA_integer_,
"getIndepVar.PKNCAdose(formula)"=0,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with one-sided formula ('.' on LHS)")
mydose4 <- PKNCAdose(formula=dose~.|treatment+ID, data=tmp.dose)
expect_equal(getDepVar.PKNCAdose(mydose4),
rep(1:2, each=5),
info="getDepVar.PKNCAdose works with one-sided formula ('.' on RHS)")
expect_equal(getIndepVar.PKNCAdose(mydose4),
rep(NA_integer_, 10),
info="getIndepVar.PKNCAdose works with one-sided formula ('.' on RHS)")
expect_equal(model.frame.PKNCAdose(mydose4),
data.frame("getDepVar.PKNCAdose(formula)"=rep(1:2, each=5),
"getIndepVar.PKNCAdose(formula)"=NA_integer_,
treatment=rep(c("Trt 1", "Trt 2"), each=5),
ID=rep(1:5, 2),
stringsAsFactors=FALSE),
ignore_attr=TRUE,
info="model.frame.PKNCAdose works with one-sided formula ('.' on RHS)")
# You can't give multiple rows per group if you don't give time.
expect_error(PKNCAdose(formula=dose~.|treatment+ID, data=rbind(tmp.dose, tmp.dose)),
regexp="Rows that are not unique per group and time.*found within dosing data",
info="Dosing must have unique values with time and group")
expect_equal(
group_vars.PKNCAdose(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)),
c("treatment", "ID")
)
expect_equal(
group_vars.PKNCAdose(PKNCAdose(tmp_dose_single, formula=dose~time)),
character(0),
info="Ungrouped data works with group_vars"
)
})
test_that("print.PKNCAdose", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
mydose <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)
tmp.conc.nogroup <- generate.conc(nsub=1, ntreat=1, time.points=0:24)
tmp.dose.nogroup <- generate.dose(tmp.conc.nogroup)
mydose.nogroup <- PKNCAdose(tmp.dose.nogroup, formula=dose~time)
expect_output(print(mydose),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is not specified.
First 6 rows of dosing data:
treatment ID dose time exclude route duration
Trt 1 1 1 0 <NA> extravascular 0
Trt 1 2 1 0 <NA> extravascular 0
Trt 1 3 1 0 <NA> extravascular 0
Trt 1 4 1 0 <NA> extravascular 0
Trt 1 5 1 0 <NA> extravascular 0
Trt 2 1 2 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works")
expect_output(print(mydose.nogroup),
regexp="Formula for dosing:
dose ~ time
Nominal time column is not specified.
Data for dosing:
treatment ID dose time exclude route duration
Trt 1 1 1 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works with no groups")
expect_output(print(mydose, n=-5),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is not specified.
First 5 rows of dosing data:
treatment ID dose time exclude route duration
Trt 1 1 1 0 <NA> extravascular 0
Trt 1 2 1 0 <NA> extravascular 0
Trt 1 3 1 0 <NA> extravascular 0
Trt 1 4 1 0 <NA> extravascular 0
Trt 1 5 1 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works")
expect_output(print(mydose, summarize=TRUE),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is not specified.
Number unique entries in each group:
treatment ID
2 5",
fixed=TRUE,
info="Summary print.PKNCAdose works")
expect_output(
print(mydose.nogroup, summarize=TRUE),
regexp="No groups"
)
})
test_that("PKNCAdose with exclusions", {
tmp.conc <- generate.conc(nsub=2, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
tmp.dose$excl <- NA_character_
mydose <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, exclude="excl")
expect_equal(
mydose,
structure(
list(
data =
cbind(
tmp.dose,
data.frame(
route = "extravascular",
duration = 0,
stringsAsFactors = FALSE
)
),
formula = dose~time|treatment+ID,
columns =
list(
dose = "dose",
time = "time",
groups =
list(
group_vars = c("treatment", "ID"),
group_analyte = character()
),
exclude = "excl",
route = "route",
duration = "duration"
),
units = list()
),
class=c("PKNCAdose", "list")
)
)
})
test_that("PKNCAdose route and duration", {
tmp.conc <- generate.conc(nsub=2, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
expect_equal(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID),
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, route="extravascular"),
info="route is assumed as extravascular")
expect_equal(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID),
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0),
info="duration is assumed as 0")
expect_equal(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID),
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="extravascular"),
info="route and duration are correctly assumed")
dose.iv <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="intravascular")
dose.ev <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="extravascular")
expect_equal(dose.iv,
{
tmp <- dose.ev
tmp$data$route <- "intravascular"
tmp
},
info="Intravascular route works")
expect_error(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="foo"),
regexp="route must have values of either 'extravascular' or 'intravascular'. Please set to one of those values and retry.",
info="route must be an accepted value")
tmp.dose.iv <- tmp.dose
tmp.dose.iv$route <- "intravascular"
# Note that the column names are in a different order when specified
# in the input data.frame or not.
expect_equal(
{
tmp <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID, duration=0, route="intravascular")
tmp$data <- tmp$data[,sort(names(tmp$data))]
tmp
},
{
tmp <- PKNCAdose(tmp.dose.iv, formula=dose~time|treatment+ID, duration=0, route="route")
tmp$data <- tmp$data[,sort(names(tmp$data))]
tmp
},
ignore_attr=TRUE
)
})
test_that("time.nominal within PKNCAdose", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
tmp.dose$nom_time <- tmp.dose$time
rownames(tmp.dose) <- NULL
expect_equal(
PKNCAdose(tmp.dose, formula=dose~time|treatment+ID,
time.nominal="nom_time"),
structure(list(
data=
cbind(
tmp.dose,
data.frame(
exclude=NA_character_,
route="extravascular",
duration=0,
stringsAsFactors=FALSE
)
),
formula = dose ~ time | treatment + ID,
columns =
list(
dose = "dose",
time = "time",
groups = list(group_vars = c("treatment", "ID"), group_analyte = character()),
exclude = "exclude",
route = "route",
duration = "duration",
time.nominal = "nom_time"
),
units = list()
),
class = c("PKNCAdose", "list")),
info="PKNCAdose accepts time.nominal"
)
expect_error(PKNCAdose(tmp.dose, formula=dose~time|treatment+ID,
time.nominal="foo"),
regexp="time.nominal, if given, must be a column name in the input data",
info="PKNCAdose time.nominal must be a column in the data")
# Test printing
dose_with_nom_time <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID,
time.nominal="nom_time")
expect_output(print(dose_with_nom_time),
regexp="Formula for dosing:
dose ~ time | treatment + ID
Nominal time column is: nom_time
First 6 rows of dosing data:
treatment ID dose time nom_time exclude route duration
Trt 1 1 1 0 0 <NA> extravascular 0
Trt 1 2 1 0 0 <NA> extravascular 0
Trt 1 3 1 0 0 <NA> extravascular 0
Trt 1 4 1 0 0 <NA> extravascular 0
Trt 1 5 1 0 0 <NA> extravascular 0
Trt 2 1 2 0 0 <NA> extravascular 0",
fixed=TRUE,
info="Generic print.PKNCAdose works")
})
test_that("setDuration", {
tmp.conc <- generate.conc(nsub=5, ntreat=2, time.points=0:24)
tmp.dose <- generate.dose(tmp.conc)
tmp.dose$nom_time <- tmp.dose$time
rownames(tmp.dose) <- NULL
mydose <- PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)
expect_message(
expect_equal(
setDuration(mydose),
mydose,
info="No changes with no arguments"
),
class = "pknca_foundcolumn_duration"
)
expect_error(setDuration(mydose, duration="foo", rate="bar"),
regexp="Both duration and rate cannot be given at the same time",
fixed=TRUE,
info="Cannot give both duration and rate")
expect_message(expect_error(
setDuration(mydose, duration="foobar"),
regexp="duration must be numeric without missing (NA) or infinite values, and all values must be >= 0",
fixed=TRUE,
info="Cannot give both duration as non-numeric"),
class = "pknca_foundcolumn_duration"
)
duration_example <- suppressMessages(setDuration(mydose, rate=2))
expect_true(all(mydose$data$duration == 0))
expect_equal(
duration_example$data$duration,
duration_example$data$dose/2
)
expect_equal(duration_example$columns$duration, "duration")
})
test_that("Test uniqueness after excluding rows (#298)", {
repeated_with_exclusion <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c(NA, "duplicate")
)
expect_error(
PKNCAdose(repeated_with_exclusion, formula=dose~time|id),
regexp="Rows that are not unique per group and time.*dosing"
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion, formula=dose~time|id, exclude = "exclude"),
class = "PKNCAdose"
)
repeated_with_exclusion_firstrow <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c("duplicate", NA)
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_firstrow, formula=dose~time|id, exclude = "exclude"),
class = "PKNCAdose"
)
repeated_with_exclusion_nogroup <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c("duplicate", NA)
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_firstrow, formula=dose~., exclude = "exclude"),
class = "PKNCAdose"
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_firstrow, formula=dose~.|id, exclude = "exclude"),
class = "PKNCAdose"
)
repeated_with_exclusion_row2 <-
data.frame(
dose = 1,
time = c(0, 0),
id = 1,
exclude = c(NA, "duplicate")
)
expect_s3_class(
PKNCAdose(repeated_with_exclusion_row2, formula=dose~.|id, exclude = "exclude"),
class = "PKNCAdose"
)
})
test_that("PKNCAdose units (#336)", {
d <- data.frame(dose = 1, time = 0, doseu_x = "A")
# No units
o_dose <- PKNCAdose(data = d, dose~time)
expect_equal(o_dose$units, list())
expect_null(o_dose$columns$doseu)
# Each unit column individually
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_x")
expect_equal(o_dose$units, list())
expect_equal(o_dose$columns$doseu, structure("doseu_x", unit_type = "column"))
# Each unit as a value, not a column
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_y")
expect_equal(o_dose$units, list(doseu = structure("doseu_y", unit_type = "value")))
expect_null(o_dose$columns$doseu)
# Preferred units
expect_error(
PKNCAdose(data = d, dose~time, doseu_pref = "doseu_z"),
regexp = "Preferred units may not be set unless original units are set: doseu_pref"
)
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_y", doseu_pref = "doseu_z")
expect_equal(
o_dose$units,
list(
doseu = structure("doseu_y", unit_type = "value"),
doseu_pref = structure("doseu_z", unit_type = "value")
)
)
expect_null(o_dose$columns$doseu)
o_dose <- PKNCAdose(data = d, dose~time, doseu = "doseu_x", doseu_pref = "doseu_z")
expect_equal(o_dose$units, list(doseu_pref = structure("doseu_z", unit_type = "value")))
expect_equal(
o_dose$columns$doseu,
structure("doseu_x", unit_type = "column")
)
})
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