Nothing
tests/testthat/test-3c_costing_medication_patches_functions.R
In packDAMipd: Decision Analysis Modelling Package with Parameters Estimation Ability from Individual Patient Level Data
###############################################################################
context("testing microcosting patches")
test_that("testing microcosting patches", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_brandmissing_ipd.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 <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "jg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg/b"))
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = NULL,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = NA,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
# no cols with drug names
conv_file <- system.file("extdata", "Med_calc_nodrugcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
# no column for form in conversion table
conv_file <- system.file("extdata", "Med_calc_noformcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
# no unit column in conversion table
conv_file <- system.file("extdata", "Med_calc_nounitcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
#no conversion factor column in conversion table
conv_file <- system.file("extdata", "Med_calc_noconvfactorcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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(microcosting_patches_wide(ind_part_data = NULL,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = NULL,
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = NULL,
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = NULL,
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = NULL,
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = NULL,
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
# no brand information
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)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NULL,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NA,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NULL,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NA)
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NULL,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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_nobrandcol.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)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nosizecol.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)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_errorbrand.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
## 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 <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = "patch_unit_str",
no_taken = "patch_no_taken",
freq_taken = "patch_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/hr", "mcg/day")),
list_of_code_brand = list(c(1, 2, 3),
c("BuTrans", "Fencino", "Butec")),
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(
ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_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/hr", "mcg/day")),
list_of_code_brand =
list(c(1, 2, 3), c("BuTrans",
"Fencino", "Butec")),
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nodosage.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_unitdiff.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_nopatchname.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(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nounitcost.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
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_unit_notright.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
conv_file <- system.file("extdata", "Med_calc_testNA.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1286, 2880), tolerance = 1e-1)
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 <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, NA),
tolerance = 1e-3)
})
###############################################################################
###############################################################################
context("testing microcosting patches when data being long format")
test_that("testing microcosting patches when data being long format", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
names <- colnames(ind_part_data)
ending <- length(names)
ind_part_data_long <- tidyr::gather(ind_part_data, measurement, value,
names[2]:names[ending], factor_key = TRUE)
the_columns <- c("measurement", "value")
#using the package price when the brand name of the medication is known
res <- microcosting_patches_long(the_columns,
ind_part_data_long = ind_part_data_long,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
index <- which(res$measurement == "totmed_period_patches")[1]
expect_equal(as.numeric(res$value[index]), 1304.571,
tolerance = 1e-3)
expect_error(microcosting_patches_long(the_columns,
ind_part_data_long = NULL,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
})
###############################################################################
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###############################################################################
context("testing microcosting patches")
test_that("testing microcosting patches", {
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_brandmissing_ipd.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
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 <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "jg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mg/b"))
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = NULL,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = NA,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
# no cols with drug names
conv_file <- system.file("extdata", "Med_calc_nodrugcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
# no column for form in conversion table
conv_file <- system.file("extdata", "Med_calc_noformcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
# no unit column in conversion table
conv_file <- system.file("extdata", "Med_calc_nounitcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
#no conversion factor column in conversion table
conv_file <- system.file("extdata", "Med_calc_noconvfactorcol.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NA,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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(microcosting_patches_wide(ind_part_data = NULL,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = NULL,
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = NULL,
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = NULL,
freq_taken = "patch_frequency",
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = NULL,
timeperiod = "4 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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = NULL,
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 = "mcg/hr"))
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = NULL,
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
# no brand information
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)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NULL,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NA,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
eqdose_cov_tab = table,
basis_strength_unit = NULL)
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NULL,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = NULL,
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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_nobrandcol.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)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nosizecol.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)
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_errorbrand.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
## 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 <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = "patch_unit_str",
no_taken = "patch_no_taken",
freq_taken = "patch_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/hr", "mcg/day")),
list_of_code_brand = list(c(1, 2, 3),
c("BuTrans", "Fencino", "Butec")),
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, 2922.240),
tolerance = 1e-3)
expect_error(microcosting_patches_wide(
ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_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/hr", "mcg/day")),
list_of_code_brand =
list(c(1, 2, 3), c("BuTrans",
"Fencino", "Butec")),
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nodosage.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_unitdiff.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_nopatchname.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(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
med_costs_file <- system.file("extdata",
"medicaton_costs_all_nounitcost.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
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
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_unit_notright.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
expect_error(microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
conv_file <- system.file("extdata", "Med_calc_testNA.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1286, 2880), tolerance = 1e-1)
med_costs_file <- system.file("extdata", "medicaton_costs_all.xlsx",
package = "packDAMipd")
data_file <- system.file("extdata", "medication_all.xlsx",
package = "packDAMipd")
ind_part_data <- load_trial_data(data_file)
med_costs <- load_trial_data(med_costs_file)
conv_file <- system.file("extdata", "Med_calc.xlsx",
package = "packDAMipd")
table <- load_trial_data(conv_file)
#using the package price when the brand name of the medication is known
res <- microcosting_patches_wide(ind_part_data = ind_part_data,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 months",
unit_cost_data = med_costs,
unit_cost_column = "UnitCost",
cost_calculated_per = "Basis",
strength_column = "Strength",
list_of_code_names = NULL,
list_of_code_freq = NULL,
list_of_code_dose_unit = NULL,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
expect_equal(res$totmed_period_patches, c(1304.571, NA),
tolerance = 1e-3)
})
###############################################################################
###############################################################################
context("testing microcosting patches when data being long format")
test_that("testing microcosting patches when data being long format", {
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)
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")
#using the package price when the brand name of the medication is known
res <- microcosting_patches_long(the_columns,
ind_part_data_long = ind_part_data_long,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr")
index <- which(res$measurement == "totmed_period_patches")[1]
expect_equal(as.numeric(res$value[index]), 1304.571,
tolerance = 1e-3)
expect_error(microcosting_patches_long(the_columns,
ind_part_data_long = NULL,
name_med = "patch_name",
brand_med = "patch_brand",
dose_med = "patch_strength",
unit_med = NULL,
no_taken = "patch_no_taken",
freq_taken = "patch_frequency",
timeperiod = "4 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,
list_of_code_brand = NULL,
eqdose_cov_tab = table,
basis_strength_unit = "mcg/hr"))
})
###############################################################################
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