tests/testthat/test-3c_costing_opioid_liquids_averageMED_functions.R
In sheejamk/packDAMipd: Decision Analysis Modelling Package with Parameters Estimation Ability from Individual Patient Level Data
#####################################################################
context("testing costing liquids")
test_that("testing costing liquids", {
med_costs_file <- system.file("extdata", "medicaton_costs_all_brandcolname_error.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_brand_empty.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = NULL,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.1, 17.9), tolerance = 1e-3)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = NA,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.1, 17.9), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all_nobrandcol.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = NULL,
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = NULL,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.1, 17.9), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_emptyrow.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name is given
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.2, NA), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name is given
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.2, 26.8), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_brand_empty.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.16, 26.79), tolerance = 1e-3)
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = NULL,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = NULL,
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = NULL,
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = NULL,
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = NULL,
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = NULL,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = NULL,
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = NULL,
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = NULL,
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(56.16, 26.79), tolerance = 1e-3)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NA)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.2, 26.79), tolerance = 1e-3)
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/hr"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_codes.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = "bottle_unit",
bottle_lasts = "liq_lasts",
bottle_lasts_unit = "lasts_unit",
preparation_dose = "liq_strength",
preparation_unit = "str_unit",
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names =
list(c(1, 2), c("Morphine", "Oxycodone")),
list_of_code_brand =
list(c(1, 2), c("Oramorph", "Oxycodone")),
list_of_code_bottle_size_unit =
list(c(1, 2), c("ml", "l")),
list_of_code_bottle_lasts_unit =
list(c(1, 2, 3), c("days", "weeks", "months")),
list_preparation_dose_unit =
list(c(1, 2), c("mg/ml", "g/ml")),
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(54.106, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_codes.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = "bottle_unit",
bottle_lasts = "liq_lasts",
bottle_lasts_unit = "lasts_unit",
preparation_dose = "liq_strength",
preparation_unit = "str_unit",
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names =
list(c(1, 2), c("Morphine", "Oxycodone")),
list_of_code_brand =
list(c(1, 2), c("Oramorph", "Oxycodone")),
list_of_code_bottle_size_unit =
list(c(1, 2), c("ml", "l")),
list_of_code_bottle_lasts_unit =
list(c(1, 2, 3), c("days", "weeks", "months")),
list_preparation_dose_unit =
list(c(1, 2), c("mg/ml", "g/ml")),
eqdose_covtab = NULL,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.106, 17.857), tolerance = 1e-3)
data_file <- system.file("extdata",
"medication_liq_codes_namenotsameasdose.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = "bottle_unit",
bottle_lasts = "liq_lasts",
bottle_lasts_unit = "lasts_unit",
preparation_dose = "liq_strength",
preparation_unit = "str_unit",
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names =
list(c(1, 2), c("Morphine", "Oxycodone")),
list_of_code_brand =
list(c(1, 2), c("Oramorph", "Oxycodone")),
list_of_code_bottle_size_unit =
list(c(1), c("ml")),
list_of_code_bottle_lasts_unit =
list(c(1, 2, 3), c("days", "weeks", "months")),
list_preparation_dose_unit =
list(c(1), c("mg/ml")),
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <-
system.file("extdata", "medicaton_costs_all_errorbrand.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <-
system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_liqlastsbeforeday.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(1204.106, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_nonamecol.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the med
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata",
"medication_costs_all_brand_nounitcostcol.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata",
"medication_costs_all_bottlevol_notmatching.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata",
"medication_costs_all_notcostedperbottle.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(54.106, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_strength_unitdiff.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_bottlevol_unitdiff.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(50004, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc_unit_notright.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata", "medicaton_costs_all_preparation_unitwrong.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/ml"))
})
###############################################################################
data_file <- system.file("extdata", "med_liquids_timepoints.csv",
package = "packDAMipd")
med_liquids_timepoints <- load_trial_data(data_file)
opioids_liquids_timepoints <- med_liquids_timepoints[med_liquids_timepoints$liquiddrugname != 97, ]
list_code_names <- list(seq(1:3), c("Morphine", "Oxycodone", "Methadone"))
list_code_dose_unit <- list(seq(1:1), "mg/ml")
opioids_liquids_timepoints[["liquidfrequency_actual"]] <-
paste( opioids_liquids_timepoints$liquidfrequency, "day", sep = "")
opioids_liquids_timepoints[["liquidpreparation"]] <-
paste( opioids_liquids_timepoints$liquidmedicationstrengthmass, "mg", "/", opioids_liquids_timepoints$liquidmedicationstrengthvol, "ml", sep = "")
opioids_liquids_timepoints[["liquidbottlesize_actual"]] <- ""
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 1 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "100 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 2 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "200 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 3 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "300 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 4 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "400 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 5 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "500 ml"
# opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 6 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "30 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 7 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "120 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 8 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "150 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 9 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "250 ml"
med_unit_costs <- load_trial_data(system.file("extdata", "Medications_unit_costs_all.xlsx", package = "packDAMipd"))
equiv_dose_calc <- load_trial_data(system.file("extdata", "Med_calc.xlsx", package = "packDAMipd"))
colindex <- which(colnames(opioids_liquids_timepoints) == "liquiddrugnameother")
colnames(opioids_liquids_timepoints)[colindex] <- "liquiddrugother"
opioids_liquids_timepoints[["liquid_actual"]] <- ""
for (i in 1:nrow(opioids_liquids_timepoints)) {
m = opioids_liquids_timepoints$liquiddrugname[i]
if (m == 97) {
opioids_liquids_timepoints$liquid_actual[i] = opioids_liquids_timepoints$liquiddrugother[i]
} else {
opioids_liquids_timepoints$liquid_actual[i] = list_code_names[[2]][m]
}
}
tmp <- opioids_liquids_timepoints[1,]
tmp <- packDAMipd::costing_opioid_liquids_averageMED_wide(
ind_part_data = tmp,
name_med = "liquid_actual",
brand_med = "liquidbrandname",
bottle_size = "liquidbottlesize_actual",
bottle_size_unit = NULL,
bottle_lasts = "liquidfrequency_actual",
bottle_lasts_unit = NULL,
preparation_dose = "liquidpreparation",
timeperiod = "1 day",
unit_cost_data = med_unit_costs,
unit_cost_column = "PackageRate",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = equiv_dose_calc,
basis_strength_unit = NULL)
expect_equal(tmp$totmed_per_equiv_period_liquid, 25, tolerance = 1e-2)
###############################################################################
context("testing costing liquids when data being long format")
test_that("testing costing liquids when data being long format", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
names <- colnames(ind_part_data)
ending <- length(names)
ind_part_data_long <- tidyr::gather(ind_part_data, measurement, value,
names[2]:names[ending], factor_key = TRUE)
the_columns <- c("measurement", "value")
res <- costing_opioid_liquids_averageMED_long(the_columns,
ind_part_data_long = ind_part_data_long,
name_med = "liq_name",
brand_med = NULL,
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
index <- which(res$measurement == "totmed_per_equiv_period_liquid")[1]
expect_equal(as.numeric(res$value[index]), 56.2, tolerance = 1e-3)
expect_error(costing_opioid_liquids_averageMED_long(the_columns,
ind_part_data_long = NULL,
name_med = "liq_name",
brand_med = NULL,
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
})
sheejamk/packDAMipd documentation built on March 29, 2024, 7:41 p.m.
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#####################################################################
context("testing costing liquids")
test_that("testing costing liquids", {
med_costs_file <- system.file("extdata", "medicaton_costs_all_brandcolname_error.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_brand_empty.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = NULL,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.1, 17.9), tolerance = 1e-3)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = NA,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.1, 17.9), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all_nobrandcol.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = NULL,
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = NULL,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.1, 17.9), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_emptyrow.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name is given
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.2, NA), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name is given
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.2, 26.8), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_brand_empty.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.16, 26.79), tolerance = 1e-3)
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = NULL,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = NULL,
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = NULL,
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = NULL,
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = NULL,
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = NULL,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = NULL,
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = NULL,
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = NULL,
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(56.16, 26.79), tolerance = 1e-3)
res <- costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NA)
expect_equal(res$totmed_per_equiv_period_liquid, c(56.2, 26.79), tolerance = 1e-3)
expect_error(costing_opioid_liquids_averageMED_wide(ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/hr"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_codes.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = "bottle_unit",
bottle_lasts = "liq_lasts",
bottle_lasts_unit = "lasts_unit",
preparation_dose = "liq_strength",
preparation_unit = "str_unit",
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names =
list(c(1, 2), c("Morphine", "Oxycodone")),
list_of_code_brand =
list(c(1, 2), c("Oramorph", "Oxycodone")),
list_of_code_bottle_size_unit =
list(c(1, 2), c("ml", "l")),
list_of_code_bottle_lasts_unit =
list(c(1, 2, 3), c("days", "weeks", "months")),
list_preparation_dose_unit =
list(c(1, 2), c("mg/ml", "g/ml")),
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(54.106, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_codes.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = "bottle_unit",
bottle_lasts = "liq_lasts",
bottle_lasts_unit = "lasts_unit",
preparation_dose = "liq_strength",
preparation_unit = "str_unit",
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names =
list(c(1, 2), c("Morphine", "Oxycodone")),
list_of_code_brand =
list(c(1, 2), c("Oramorph", "Oxycodone")),
list_of_code_bottle_size_unit =
list(c(1, 2), c("ml", "l")),
list_of_code_bottle_lasts_unit =
list(c(1, 2, 3), c("days", "weeks", "months")),
list_preparation_dose_unit =
list(c(1, 2), c("mg/ml", "g/ml")),
eqdose_covtab = NULL,
basis_strength_unit = NULL)
expect_equal(res$totmed_per_equiv_period_liquid, c(54.106, 17.857), tolerance = 1e-3)
data_file <- system.file("extdata",
"medication_liq_codes_namenotsameasdose.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = "bottle_unit",
bottle_lasts = "liq_lasts",
bottle_lasts_unit = "lasts_unit",
preparation_dose = "liq_strength",
preparation_unit = "str_unit",
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names =
list(c(1, 2), c("Morphine", "Oxycodone")),
list_of_code_brand =
list(c(1, 2), c("Oramorph", "Oxycodone")),
list_of_code_bottle_size_unit =
list(c(1), c("ml")),
list_of_code_bottle_lasts_unit =
list(c(1, 2, 3), c("days", "weeks", "months")),
list_preparation_dose_unit =
list(c(1), c("mg/ml")),
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <-
system.file("extdata", "medicaton_costs_all_errorbrand.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <-
system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_liqlastsbeforeday.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(1204.106, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_nonamecol.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the med
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata",
"medication_costs_all_brand_nounitcostcol.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata",
"medication_costs_all_bottlevol_notmatching.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata",
"medication_costs_all_notcostedperbottle.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(54.106, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_strength_unitdiff.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq_bottlevol_unitdiff.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
res <- costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = NULL,
basis_strength_unit = "mg/ml")
expect_equal(res$totmed_per_equiv_period_liquid, c(50004, 17.857), tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc_unit_notright.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/ml"))
med_costs_file <- system.file("extdata", "medicaton_costs_all_preparation_unitwrong.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the me
expect_error(costing_opioid_liquids_averageMED_wide(
ind_part_data = ind_part_data,
name_med = "liq_name",
brand_med = "liq_brand",
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_strength",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit =
NULL,
list_of_code_bottle_lasts_unit =
NULL,
list_preparation_dose_unit =
NULL,
eqdose_covtab = table,
basis_strength_unit = "mg/ml"))
})
###############################################################################
data_file <- system.file("extdata", "med_liquids_timepoints.csv",
package = "packDAMipd")
med_liquids_timepoints <- load_trial_data(data_file)
opioids_liquids_timepoints <- med_liquids_timepoints[med_liquids_timepoints$liquiddrugname != 97, ]
list_code_names <- list(seq(1:3), c("Morphine", "Oxycodone", "Methadone"))
list_code_dose_unit <- list(seq(1:1), "mg/ml")
opioids_liquids_timepoints[["liquidfrequency_actual"]] <-
paste( opioids_liquids_timepoints$liquidfrequency, "day", sep = "")
opioids_liquids_timepoints[["liquidpreparation"]] <-
paste( opioids_liquids_timepoints$liquidmedicationstrengthmass, "mg", "/", opioids_liquids_timepoints$liquidmedicationstrengthvol, "ml", sep = "")
opioids_liquids_timepoints[["liquidbottlesize_actual"]] <- ""
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 1 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "100 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 2 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "200 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 3 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "300 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 4 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "400 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 5 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "500 ml"
# opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 6 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "30 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 7 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "120 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 8 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "150 ml"
opioids_liquids_timepoints[opioids_liquids_timepoints$liquidbottlesize == 9 & !is.na(opioids_liquids_timepoints$liquidbottlesize),]$liquidbottlesize_actual <- "250 ml"
med_unit_costs <- load_trial_data(system.file("extdata", "Medications_unit_costs_all.xlsx", package = "packDAMipd"))
equiv_dose_calc <- load_trial_data(system.file("extdata", "Med_calc.xlsx", package = "packDAMipd"))
colindex <- which(colnames(opioids_liquids_timepoints) == "liquiddrugnameother")
colnames(opioids_liquids_timepoints)[colindex] <- "liquiddrugother"
opioids_liquids_timepoints[["liquid_actual"]] <- ""
for (i in 1:nrow(opioids_liquids_timepoints)) {
m = opioids_liquids_timepoints$liquiddrugname[i]
if (m == 97) {
opioids_liquids_timepoints$liquid_actual[i] = opioids_liquids_timepoints$liquiddrugother[i]
} else {
opioids_liquids_timepoints$liquid_actual[i] = list_code_names[[2]][m]
}
}
tmp <- opioids_liquids_timepoints[1,]
tmp <- packDAMipd::costing_opioid_liquids_averageMED_wide(
ind_part_data = tmp,
name_med = "liquid_actual",
brand_med = "liquidbrandname",
bottle_size = "liquidbottlesize_actual",
bottle_size_unit = NULL,
bottle_lasts = "liquidfrequency_actual",
bottle_lasts_unit = NULL,
preparation_dose = "liquidpreparation",
timeperiod = "1 day",
unit_cost_data = med_unit_costs,
unit_cost_column = "PackageRate",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = equiv_dose_calc,
basis_strength_unit = NULL)
expect_equal(tmp$totmed_per_equiv_period_liquid, 25, tolerance = 1e-2)
###############################################################################
context("testing costing liquids when data being long format")
test_that("testing costing liquids when data being long format", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_liq.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
names <- colnames(ind_part_data)
ending <- length(names)
ind_part_data_long <- tidyr::gather(ind_part_data, measurement, value,
names[2]:names[ending], factor_key = TRUE)
the_columns <- c("measurement", "value")
res <- costing_opioid_liquids_averageMED_long(the_columns,
ind_part_data_long = ind_part_data_long,
name_med = "liq_name",
brand_med = NULL,
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL)
index <- which(res$measurement == "totmed_per_equiv_period_liquid")[1]
expect_equal(as.numeric(res$value[index]), 56.2, tolerance = 1e-3)
expect_error(costing_opioid_liquids_averageMED_long(the_columns,
ind_part_data_long = NULL,
name_med = "liq_name",
brand_med = NULL,
bottle_size = "liq_bottle_size",
bottle_size_unit = NULL,
bottle_lasts = "liq_lasts",
bottle_lasts_unit = NULL,
preparation_dose = "liq_pre",
preparation_unit = NULL,
timeperiod = "1 day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_brand = NULL,
list_of_code_bottle_size_unit = NULL,
list_of_code_bottle_lasts_unit = NULL,
list_preparation_dose_unit = NULL,
eqdose_covtab = table,
basis_strength_unit = NULL))
})
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