tests/testthat/test-3c_costing_opioid_tablets_averageMED_functions.R
In sheejamk/packDAMipd: Decision Analysis Modelling Package with Parameters Estimation Ability from Individual Patient Level Data
#######################################################################
context("testing costing opioid tablets using average MED tablets")
test_that("testing costing opioid tablets using average MED tablets", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_brandNull.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_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_str",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one 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_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(10.1, 0), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_strengthnotgiven.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_str",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_true(sum(is.na(res$totmed_period_tablets_mg)) ==
length(res$totmed_period_tablets_mg))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_test.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(40.1, 8), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_unitnotseparate.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_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one 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_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(40.1, 8), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_test_error.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_2.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(10.14, 0), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.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_tabletunitwrong.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.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 medication is known
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(617.50, 0), tolerance = 1e-2)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = NULL,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = NULL,
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_no_tabname.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 medication is known
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.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 medication is known
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA)
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "NA"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_brandcolname_error.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_sizecol_error.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA))
#no brand name given in ipd data or we dont care about it for tablets
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nounitcost.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
data_file <- system.file("extdata", "medication_namemissing.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_namecol_nameerror.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_formcol_nameerror.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
## Information is coded in the data file
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_with_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_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "4 months",
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("Buprenorphine", "Fentanyl")),
list_of_code_freq =
list(c(1, 2, 3),
c("once a day", "twice a day", "once a week")),
list_of_code_dose_unit =
list(c(1, 2), c("mcg", "mg")),
list_of_code_brand = list(c(1, 2),
c("Buprenorphine",
"Temgesic")),
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(1217, 96), tolerance = 1e-1)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "4 months",
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("Buprenorphine", "Fentanyl")),
list_of_code_freq =
list(c(1, 2, 3),
c("once a day", "twice a day",
"once a week")),
list_of_code_dose_unit =
list(c(1, 2), c("mcg", "mg")),
list_of_code_brand = list(c(1, 2),
c("Buprenorphine", "Temgesic")),
eqdose_cov_tab = NULL,
basis_strength_unit = "mg")
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "4 months",
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("Buprenorphine", "Fentanyl")),
list_of_code_freq =
list(c(1, 2, 3),
c("once a day", "twice a day", "once a week")),
list_of_code_dose_unit =
list(c(1, 2), c("mcg", "mg")),
list_of_code_brand = list(c(1, 2),
c("Buprenorphine", "Temgesic")),
eqdose_cov_tab = NA,
basis_strength_unit = "mg")
})
###############################################################################
data_file <- system.file("extdata", "med_tablets_timepoints.csv",
package = "packDAMipd")
med_tablets_timepoints <- load_trial_data(data_file)
opioids_tablets_timepoints <- med_tablets_timepoints[med_tablets_timepoints$tabdrugname != 97, ]
list_code_names <- list(seq(1:21), c("Buprenorphine", "Co-codamol (strength not given)", "Codeine phosphate", "Co-dydramol (strength not given)", "Dihydrocodeine", "Fentanyl", "Hydromorphone", "Meptazinol", "Morphine", "Oxycodone", "Pethidin", "Tapentadol", "Tramadol", "Methadone", "Co-codamol 8/500", "Co-codamol 15/500", "Co-codamol 30/500", "Co-dydramol 7.46/500", "Co-dydramol 10/500", "Co-dydramol 20/500", "Co-dydramol 30/500"))
list_code_freq <- list(seq(1:20), c("Once a day", "Twice a day",
"Three times a day", "Four times a day",
"Five times a day", "Six times a day",
"Seven times a day", "Eight times a day",
"Nine times a day", "Ten times a day",
"Once every 2 days", "Once every 3 days",
"Once every 4 days", "Once every 5 days",
"Once every 6 days", "Once a week",
"Twice a week", "Thrice a week",
"Four times a week", "Not stated"))
list_code_dose_unit <- list(seq(1:2), c("mcg", "mg"))
med_costs_file <- system.file("extdata",
"Medications_unit_costs_all.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
equiv_dose_calc <- load_trial_data(system.file("extdata",
"Med_calc.xlsx",
package = "packDAMipd"))
index <- which(colnames(opioids_tablets_timepoints) == "tabdrugnameother")
colnames(opioids_tablets_timepoints)[index] <- "tabdrugother"
# Morphine brand MST is replaced with MST Continus
indices <- which(opioids_tablets_timepoints$tabdrugname == 9 &
opioids_tablets_timepoints$tabbrandname == "MST")
opioids_tablets_timepoints$tabbrandname[indices] <- "MST Continus"
# co-codamol no brand mame called Ef-fervescent replaced with ""
indices <- which(opioids_tablets_timepoints$tabdrugname == 17 &
opioids_tablets_timepoints$tabbrandname == "EF-Fervescent")
opioids_tablets_timepoints$tabbrandname[indices] <- ""
# Morphine brand mame called Zomproh replaced with "Zomorph"
indices <- which(opioids_tablets_timepoints$tabdrugname == 9
& opioids_tablets_timepoints$tabbrandname == "Zomproh")
opioids_tablets_timepoints$tabbrandname[indices] <- "Zomorph"
# Tramadol brand mame called "Mabron Slow Release" replaced with "Mabron"
indices <- which(opioids_tablets_timepoints$tabdrugname == 13 &
opioids_tablets_timepoints$tabbrandname == "Mabron Slow Release")
opioids_tablets_timepoints$tabbrandname[indices] <- "Mabron"
# Tramadol brand mame called "Marbon" replaced with "Mabron"
indices <- which(opioids_tablets_timepoints$tabdrugname == 13 &
opioids_tablets_timepoints$tabbrandname == "Marbon")
opioids_tablets_timepoints$tabbrandname[indices] <- "Mabron"
# Oxycodone brand name called "Longtech" replaced with "Longtec"
indices <- which(opioids_tablets_timepoints$tabdrugname == 10 &
opioids_tablets_timepoints$tabbrandname == "Longtech")
opioids_tablets_timepoints$tabbrandname[indices] <- "Longtec"
opioids_tablets_timepoints[["tab_actual"]] <- ""
for (i in 1:nrow(opioids_tablets_timepoints)) {
m <- opioids_tablets_timepoints$tabdrugname[i]
if (m == 97) {
opioids_tablets_timepoints$tab_actual[i] <- opioids_tablets_timepoints$tabdrugother[i]
} else {
opioids_tablets_timepoints$tab_actual[i] <- list_code_names[[2]][m]
}
}
tmp <- opioids_tablets_timepoints[1:2, ]
tmp1 <- costing_opioid_tablets_averageMED_wide(tmp, "tab_actual",
"tabbrandname", "tabmedicationstrength", "tabmedicationunit",
"tabletscount", "tabletsfrequency",
"1 day", med_costs,
"PackageRate", "Basis", "Strength",
list_of_code_names = NULL,
list_of_code_freq = list_code_freq,
list_of_code_dose_unit =
list_code_dose_unit,
list_of_code_brand = NULL,
eqdose_cov_tab = equiv_dose_calc)
expect_equal(tmp1$totmed_equiv_period_tablets, c(12.5, 12.5))
###############################################################################
context("testing costing opioid tablets using average MED tablets when data being long format")
test_that("testing costing opioid tablets using average MED tablets when data being long format", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.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)
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_tablets_averageMED_long(the_columns,
ind_part_data_long = ind_part_data_long,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
index <- which(res$measurement == "totmed_period_tablets_mg")[1]
expect_equal(as.numeric(res$value[index]), 617.50, tolerance = 1e-3)
expect_error(costing_opioid_tablets_averageMED_long(the_columns,
ind_part_data_long = NULL,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
})
sheejamk/packDAMipd documentation built on March 29, 2024, 7:41 p.m.
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#######################################################################
context("testing costing opioid tablets using average MED tablets")
test_that("testing costing opioid tablets using average MED tablets", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_brandNull.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_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_str",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one 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_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(10.1, 0), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_strengthnotgiven.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_str",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_true(sum(is.na(res$totmed_period_tablets_mg)) ==
length(res$totmed_period_tablets_mg))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_test.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(40.1, 8), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_unitnotseparate.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_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one 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_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(40.1, 8), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_test_error.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_2.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "one day",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(10.14, 0), tolerance = 1e-2)
med_costs_file <- system.file("extdata", "medicaton_costs_all.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_tabletunitwrong.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.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 medication is known
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(617.50, 0), tolerance = 1e-2)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = NULL,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = NULL,
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all_no_tabname.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 medication is known
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.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 medication is known
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA)
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "NA"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_brandcolname_error.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_sizecol_error.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA))
#no brand name given in ipd data or we dont care about it for tablets
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(617.50, 48), tolerance = 1e-2)
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nounitcost.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
data_file <- system.file("extdata", "medication_namemissing.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_namecol_nameerror.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_formcol_nameerror.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
expect_error(costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = NULL,
dose_med = "tab_strength",
unit_med = NULL,
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
## Information is coded in the data file
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_with_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_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "4 months",
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("Buprenorphine", "Fentanyl")),
list_of_code_freq =
list(c(1, 2, 3),
c("once a day", "twice a day", "once a week")),
list_of_code_dose_unit =
list(c(1, 2), c("mcg", "mg")),
list_of_code_brand = list(c(1, 2),
c("Buprenorphine",
"Temgesic")),
eqdose_cov_tab = table,
basis_strength_unit = "mg")
expect_equal(res$totmed_period_tablets_mg, c(1217, 96), tolerance = 1e-1)
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "4 months",
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("Buprenorphine", "Fentanyl")),
list_of_code_freq =
list(c(1, 2, 3),
c("once a day", "twice a day",
"once a week")),
list_of_code_dose_unit =
list(c(1, 2), c("mcg", "mg")),
list_of_code_brand = list(c(1, 2),
c("Buprenorphine", "Temgesic")),
eqdose_cov_tab = NULL,
basis_strength_unit = "mg")
res <- costing_opioid_tablets_averageMED_wide(ind_part_data = ind_part_data,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "4 months",
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("Buprenorphine", "Fentanyl")),
list_of_code_freq =
list(c(1, 2, 3),
c("once a day", "twice a day", "once a week")),
list_of_code_dose_unit =
list(c(1, 2), c("mcg", "mg")),
list_of_code_brand = list(c(1, 2),
c("Buprenorphine", "Temgesic")),
eqdose_cov_tab = NA,
basis_strength_unit = "mg")
})
###############################################################################
data_file <- system.file("extdata", "med_tablets_timepoints.csv",
package = "packDAMipd")
med_tablets_timepoints <- load_trial_data(data_file)
opioids_tablets_timepoints <- med_tablets_timepoints[med_tablets_timepoints$tabdrugname != 97, ]
list_code_names <- list(seq(1:21), c("Buprenorphine", "Co-codamol (strength not given)", "Codeine phosphate", "Co-dydramol (strength not given)", "Dihydrocodeine", "Fentanyl", "Hydromorphone", "Meptazinol", "Morphine", "Oxycodone", "Pethidin", "Tapentadol", "Tramadol", "Methadone", "Co-codamol 8/500", "Co-codamol 15/500", "Co-codamol 30/500", "Co-dydramol 7.46/500", "Co-dydramol 10/500", "Co-dydramol 20/500", "Co-dydramol 30/500"))
list_code_freq <- list(seq(1:20), c("Once a day", "Twice a day",
"Three times a day", "Four times a day",
"Five times a day", "Six times a day",
"Seven times a day", "Eight times a day",
"Nine times a day", "Ten times a day",
"Once every 2 days", "Once every 3 days",
"Once every 4 days", "Once every 5 days",
"Once every 6 days", "Once a week",
"Twice a week", "Thrice a week",
"Four times a week", "Not stated"))
list_code_dose_unit <- list(seq(1:2), c("mcg", "mg"))
med_costs_file <- system.file("extdata",
"Medications_unit_costs_all.xlsx",
package = "packDAMipd")
med_costs <- load_trial_data(med_costs_file)
equiv_dose_calc <- load_trial_data(system.file("extdata",
"Med_calc.xlsx",
package = "packDAMipd"))
index <- which(colnames(opioids_tablets_timepoints) == "tabdrugnameother")
colnames(opioids_tablets_timepoints)[index] <- "tabdrugother"
# Morphine brand MST is replaced with MST Continus
indices <- which(opioids_tablets_timepoints$tabdrugname == 9 &
opioids_tablets_timepoints$tabbrandname == "MST")
opioids_tablets_timepoints$tabbrandname[indices] <- "MST Continus"
# co-codamol no brand mame called Ef-fervescent replaced with ""
indices <- which(opioids_tablets_timepoints$tabdrugname == 17 &
opioids_tablets_timepoints$tabbrandname == "EF-Fervescent")
opioids_tablets_timepoints$tabbrandname[indices] <- ""
# Morphine brand mame called Zomproh replaced with "Zomorph"
indices <- which(opioids_tablets_timepoints$tabdrugname == 9
& opioids_tablets_timepoints$tabbrandname == "Zomproh")
opioids_tablets_timepoints$tabbrandname[indices] <- "Zomorph"
# Tramadol brand mame called "Mabron Slow Release" replaced with "Mabron"
indices <- which(opioids_tablets_timepoints$tabdrugname == 13 &
opioids_tablets_timepoints$tabbrandname == "Mabron Slow Release")
opioids_tablets_timepoints$tabbrandname[indices] <- "Mabron"
# Tramadol brand mame called "Marbon" replaced with "Mabron"
indices <- which(opioids_tablets_timepoints$tabdrugname == 13 &
opioids_tablets_timepoints$tabbrandname == "Marbon")
opioids_tablets_timepoints$tabbrandname[indices] <- "Mabron"
# Oxycodone brand name called "Longtech" replaced with "Longtec"
indices <- which(opioids_tablets_timepoints$tabdrugname == 10 &
opioids_tablets_timepoints$tabbrandname == "Longtech")
opioids_tablets_timepoints$tabbrandname[indices] <- "Longtec"
opioids_tablets_timepoints[["tab_actual"]] <- ""
for (i in 1:nrow(opioids_tablets_timepoints)) {
m <- opioids_tablets_timepoints$tabdrugname[i]
if (m == 97) {
opioids_tablets_timepoints$tab_actual[i] <- opioids_tablets_timepoints$tabdrugother[i]
} else {
opioids_tablets_timepoints$tab_actual[i] <- list_code_names[[2]][m]
}
}
tmp <- opioids_tablets_timepoints[1:2, ]
tmp1 <- costing_opioid_tablets_averageMED_wide(tmp, "tab_actual",
"tabbrandname", "tabmedicationstrength", "tabmedicationunit",
"tabletscount", "tabletsfrequency",
"1 day", med_costs,
"PackageRate", "Basis", "Strength",
list_of_code_names = NULL,
list_of_code_freq = list_code_freq,
list_of_code_dose_unit =
list_code_dose_unit,
list_of_code_brand = NULL,
eqdose_cov_tab = equiv_dose_calc)
expect_equal(tmp1$totmed_equiv_period_tablets, c(12.5, 12.5))
###############################################################################
context("testing costing opioid tablets using average MED tablets when data being long format")
test_that("testing costing opioid tablets using average MED tablets when data being long format", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.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)
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_tablets_averageMED_long(the_columns,
ind_part_data_long = ind_part_data_long,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg")
index <- which(res$measurement == "totmed_period_tablets_mg")[1]
expect_equal(as.numeric(res$value[index]), 617.50, tolerance = 1e-3)
expect_error(costing_opioid_tablets_averageMED_long(the_columns,
ind_part_data_long = NULL,
name_med = "tab_name",
brand_med = "tab_brand",
dose_med = "tab_strength",
unit_med = "tab_str_unit",
no_taken = "tab_no_taken",
freq_taken = "tab_frequency",
timeperiod = "2 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg"))
})
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