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tests/testthat/test-3c_costing_resource_use_functions.R
In packDAMipd: Decision Analysis Modelling Package with Parameters Estimation Ability from Individual Patient Level Data
###############################################################################
context("testing costing resource use")
test_that("testing costing resource use", {
costs_file <- system.file("extdata", "costs_resource_use.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
# Someone admitted to in patient hospital for 1 day (nhs hospital)
# another day not in NHS hospital
# unit_cost_data shows inpatient hospital admission cost £20
# another patient admitted to in patient hospital for 2 days first time,
# then 2 days another time- so total 4 times -£80
part_data <- ind_part_data[1, ]
res <- costing_resource_use(part_data, "hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"), "day", unit_cost_data,
"Inpatient hospital admissions",
"UnitCost", "UnitUsed", NULL, NULL)
expect_equal(res$totcost_hospital_admission_1, 20, tolerance = 1e-3)
res <- costing_resource_use(
ind_part_data[2, ], "hospital_admission_1",
list("length_1", "length_2"), list("nhs_1", "nhs_2"), "day",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed", NULL, NULL)
expect_equal(res$totcost_hospital_admission_1, 80, tolerance = 1e-3)
expect_error(costing_resource_use(
ind_part_data[2, ], "hospital_admission_1", list("length_1", "length_2"),
list("nhs_1"), "day", unit_cost_data, "Inpatient hospital admissions",
"UnitCost", "UnitUsed", NULL, NULL))
datafile <- system.file("extdata", "resource_use_hc_2_codes.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
# Someone admitted to in patient hospital for 1 day (nhs hospital)
# another day not in NHS hospital
# unit_cost_data shows inpatient hospital admission cost £20
# another patient admitted to in patient hospital for 2 days first time,
# then 2 days another time- so total 4 times -£80
# testing if we use all codes
res <- costing_resource_use(
ind_part_data[1, ],
"hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"),
"day",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed",
list(c("yes", "no"), c(1, 2)), list(c("yes", "no"), c(1, 2))
)
expect_equal(res$totcost_hospital_admission_1, 20, tolerance = 1e-3)
res <- costing_resource_use(
ind_part_data[1, ],
"daycare",
list("number"),
list("nhs_visit"),
"visit",
unit_cost_data, "Day care admission", "UnitCost",
"UnitUsed",
NULL, list(c("yes", "no"), c(1, 2))
)
expect_equal(res$totcost_daycare, 45, tolerance = 1e-3)
expect_error(costing_resource_use(
ind_part_data[1, ],
"daycare",
list("number"),
list("visit"),
"visit",
unit_cost_data, "Day care admission", "UnitCost",
"UnitUsed",
NULL, list(c("yes", "no"), c(1, 2))
))
res <- costing_resource_use(
ind_part_data[1, ],
"other_contact",
list("number_of_contacts"),
NULL, "visit",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
)
expect_equal(res$totcost_other_contact, 39.23, tolerance = 1e-3)
res <- costing_resource_use(
ind_part_data[2, ],
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
)
# 3 contacts of practice nurse- unit is per hour.
expect_equal(res$totcost_other_contact, 126, tolerance = 1e-3)
# data should not be null
expect_error(costing_resource_use(
NULL,
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
# name should not be null
expect_error(costing_resource_use(
ind_part_data[2, ],
NULL,
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
# unit cost column should not be null
expect_error(costing_resource_use(
ind_part_data[2, ],
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, NULL,
"UnitUsed",
NULL, NULL
))
# name of resource use not in patient data
datafile <- system.file("extdata", "resource_use_hc_2_noname.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
expect_error(costing_resource_use(
ind_part_data[2, ],
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use_nounitcostcol.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
expect_error(costing_resource_use(
ind_part_data[2, ],
"hospital_admission_1",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use_nonameres.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
expect_error(costing_resource_use(
ind_part_data[2, ],
"hospital_admission_1",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use_nohos.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
expect_error(costing_resource_use(
ind_part_data[2, ],
"hospital_admission_1",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2_unitlength.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
# unit length is in individual data
res <- costing_resource_use(
ind_part_data,
"hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"),
"unit_length",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed",
NULL, NULL
)
expect_equal(res$totcost_hospital_admission_1, c(20, 80, NA, NA, NA))
#units of resource use expressed and calculated are different
costs_file <- system.file("extdata",
"costs_resource_use_unitexpressed_notright.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2_unitlength.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
# unit length is in individual data
expect_error(costing_resource_use(
ind_part_data,
"hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"),
"unit_length",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed",
NULL, NULL
))
})
###############################################################################
context("testing extracting unit cost matching hrg code")
test_that("testing extracting unit cost matching hrg code", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019.csv",
package = "packDAMipd")
result <- get_cost_ip_dc_hrg("AA22C", ref_cost_data_file, "Currency_Code",
"National_Average_Unit_Cost")
expect_equal(result, 5053, tol = 1e-1)
expect_error(get_cost_ip_dc_hrg(NULL, ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", "EL"))
expect_error(get_cost_ip_dc_hrg("AA22C", NULL, "Currency_Code",
"National_Average_Unit_Cost", "EL"))
expect_error(get_cost_ip_dc_hrg("AA22C", ref_cost_data_file, NULL,
"National_Average_Unit_Cost", "EL"))
expect_error(get_cost_ip_dc_hrg("AA22C", ref_cost_data_file,
"Currency_Code",
NULL, "EL"))
result <- get_cost_ip_dc_hrg("AA22C", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", NULL)
expect_equal(result, 5053, tol = 1e-1)
expect_error(get_cost_ip_dc_hrg("AA", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", "EL"))
})
###############################################################################
context("testing extracting unit cost matching description")
test_that("testing extracting unit cost matching description", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019.csv",
package = "packDAMipd")
result <- get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "EL")
expect_equal(result, 3530, tol = 1e-1)
expect_error(get_cost_ip_dc_description(NULL, ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"EL"))
expect_error(get_cost_ip_dc_description("Cerebrovascular Accident", NULL,
"Currency_Description",
"National_Average_Unit_Cost",
"EL"))
expect_error(get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file, NULL,
"National_Average_Unit_Cost",
"EL"))
expect_error(get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file,
"Currency_Description",
NULL, "EL"))
result <- get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", NULL)
expect_equal(result, 3530, tol = 1e-1)
expect_error(get_cost_ip_dc_description("hello",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"EL"))
})
# # ###############################################################################
context("testing costing inpatient admission")
test_that("testing costing inpatient admission", {
costs_file <- system.file("extdata", "patient_adm_cost_EL.xlsx",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
expect_error(costing_inpatient_daycase_admission(NULL,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = NULL,
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "admission"))
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
NULL,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = NULL,
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = NULL,
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = NULL))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "ad"))
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = NULL,
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 3530, tol = 1e-2)
datafile <- system.file("extdata", "resource_use_hc_ip_nocol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_nonumuse.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_nocols.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_error.xlsx",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file, sheet = "EL")
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file, sheet = "EL")
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = NULL,
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_numuse_wrong.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_numuse_missing.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 3530, tol = 1e-2)
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
datafile <- system.file("extdata", "resource_use_hc_ip_el_missing.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_noelcol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
})
###############################################################################
context("testing extracting unit cost for A&E matching code")
test_that("testing extracting unit cost for A&E matching code", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
re <- get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", "Service_Code")
expect_equal(re, 452, tol = 1e-2)
ref_cost_data_file <- system.file("extdata",
"NHS_costs_2019_AandE.xlsx",
package = "packDAMipd")
re <- get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code", sheet = "AE")
expect_equal(re, 452, tol = 1e-2)
expect_error(get_cost_AandE_code("VB02Z", "T00A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code", sheet = "AE"))
expect_error(get_cost_AandE_code(NULL, "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", NA, ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", NULL,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
NA, "National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code", NA, "Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", NULL))
})
###############################################################################
context("testing extracting unit cost matching description")
test_that("testing extracting unit cost matching description", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
re <- get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "Service_Code")
expect_equal(re, 265.33, tol = 1e-2)
ref_cost_data_file <- system.file("extdata",
"NHS_costs_2019_AandE.xlsx",
package = "packDAMipd")
re <- get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "Service_Code",
sheet = "AE")
expect_equal(re, 265.33, tol = 1e-2)
expect_error(get_cost_AandE_description("Emergency Medicine", "T00A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "Service_Code",
sheet = "AE"))
expect_error(get_cost_AandE_description(NULL, "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", NULL,
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
NULL,
"Currency_Description",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
NULL,
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
NULL,
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
NULL))
})
############################################################################
context("testing extracting unit cost matching description")
test_that("testing extracting unit cost matching description", {
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_ae_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
result <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(result$totcost_AE_Admission[1], 672, tol = 1e-2)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = NULL,
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = NULL,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
result <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(result$totcost_AE_Admission[1], 672, tol = 1e-2)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = NULL,
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = NULL,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = NULL,
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = NULL,
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = NULL,
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "ss"))
result <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(result$totcost_AE_Admission[1], 754, tol = 1e-2)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "dd",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "dd", descrip_ae = NULL,
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_notypecol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_nonumusecol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
costs_file <- system.file("extdata",
"NHS_costs_2019_AandE_nocode.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_ae_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
datafile <- system.file("extdata",
"resource_use_ae_ip_lengthtypecodediff.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_extranumuse.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_lessnumuse.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 671, tol = 1e-2)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 754, tol = 1e-2)
datafile <- system.file("extdata", "resource_use_ae_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 671, tol = 1e-2)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 754, tol = 1e-2)
})
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###############################################################################
context("testing costing resource use")
test_that("testing costing resource use", {
costs_file <- system.file("extdata", "costs_resource_use.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
# Someone admitted to in patient hospital for 1 day (nhs hospital)
# another day not in NHS hospital
# unit_cost_data shows inpatient hospital admission cost £20
# another patient admitted to in patient hospital for 2 days first time,
# then 2 days another time- so total 4 times -£80
part_data <- ind_part_data[1, ]
res <- costing_resource_use(part_data, "hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"), "day", unit_cost_data,
"Inpatient hospital admissions",
"UnitCost", "UnitUsed", NULL, NULL)
expect_equal(res$totcost_hospital_admission_1, 20, tolerance = 1e-3)
res <- costing_resource_use(
ind_part_data[2, ], "hospital_admission_1",
list("length_1", "length_2"), list("nhs_1", "nhs_2"), "day",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed", NULL, NULL)
expect_equal(res$totcost_hospital_admission_1, 80, tolerance = 1e-3)
expect_error(costing_resource_use(
ind_part_data[2, ], "hospital_admission_1", list("length_1", "length_2"),
list("nhs_1"), "day", unit_cost_data, "Inpatient hospital admissions",
"UnitCost", "UnitUsed", NULL, NULL))
datafile <- system.file("extdata", "resource_use_hc_2_codes.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
# Someone admitted to in patient hospital for 1 day (nhs hospital)
# another day not in NHS hospital
# unit_cost_data shows inpatient hospital admission cost £20
# another patient admitted to in patient hospital for 2 days first time,
# then 2 days another time- so total 4 times -£80
# testing if we use all codes
res <- costing_resource_use(
ind_part_data[1, ],
"hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"),
"day",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed",
list(c("yes", "no"), c(1, 2)), list(c("yes", "no"), c(1, 2))
)
expect_equal(res$totcost_hospital_admission_1, 20, tolerance = 1e-3)
res <- costing_resource_use(
ind_part_data[1, ],
"daycare",
list("number"),
list("nhs_visit"),
"visit",
unit_cost_data, "Day care admission", "UnitCost",
"UnitUsed",
NULL, list(c("yes", "no"), c(1, 2))
)
expect_equal(res$totcost_daycare, 45, tolerance = 1e-3)
expect_error(costing_resource_use(
ind_part_data[1, ],
"daycare",
list("number"),
list("visit"),
"visit",
unit_cost_data, "Day care admission", "UnitCost",
"UnitUsed",
NULL, list(c("yes", "no"), c(1, 2))
))
res <- costing_resource_use(
ind_part_data[1, ],
"other_contact",
list("number_of_contacts"),
NULL, "visit",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
)
expect_equal(res$totcost_other_contact, 39.23, tolerance = 1e-3)
res <- costing_resource_use(
ind_part_data[2, ],
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
)
# 3 contacts of practice nurse- unit is per hour.
expect_equal(res$totcost_other_contact, 126, tolerance = 1e-3)
# data should not be null
expect_error(costing_resource_use(
NULL,
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
# name should not be null
expect_error(costing_resource_use(
ind_part_data[2, ],
NULL,
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
# unit cost column should not be null
expect_error(costing_resource_use(
ind_part_data[2, ],
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, NULL,
"UnitUsed",
NULL, NULL
))
# name of resource use not in patient data
datafile <- system.file("extdata", "resource_use_hc_2_noname.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
expect_error(costing_resource_use(
ind_part_data[2, ],
"other_contact",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use_nounitcostcol.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
expect_error(costing_resource_use(
ind_part_data[2, ],
"hospital_admission_1",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use_nonameres.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
expect_error(costing_resource_use(
ind_part_data[2, ],
"hospital_admission_1",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use_nohos.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
expect_error(costing_resource_use(
ind_part_data[2, ],
"hospital_admission_1",
list("number_of_contacts"),
NULL, "hour",
unit_cost_data, NULL, "UnitCost",
"UnitUsed",
NULL, NULL
))
costs_file <- system.file("extdata", "costs_resource_use.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2_unitlength.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
# unit length is in individual data
res <- costing_resource_use(
ind_part_data,
"hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"),
"unit_length",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed",
NULL, NULL
)
expect_equal(res$totcost_hospital_admission_1, c(20, 80, NA, NA, NA))
#units of resource use expressed and calculated are different
costs_file <- system.file("extdata",
"costs_resource_use_unitexpressed_notright.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_2_unitlength.csv",
package = "packDAMipd")
ind_part_data <- load_trial_data(datafile)
unit_cost_data <- load_trial_data(costs_file)
# unit length is in individual data
expect_error(costing_resource_use(
ind_part_data,
"hospital_admission_1",
list("length_1", "length_2"),
list("nhs_1", "nhs_2"),
"unit_length",
unit_cost_data, "Inpatient hospital admissions", "UnitCost",
"UnitUsed",
NULL, NULL
))
})
###############################################################################
context("testing extracting unit cost matching hrg code")
test_that("testing extracting unit cost matching hrg code", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019.csv",
package = "packDAMipd")
result <- get_cost_ip_dc_hrg("AA22C", ref_cost_data_file, "Currency_Code",
"National_Average_Unit_Cost")
expect_equal(result, 5053, tol = 1e-1)
expect_error(get_cost_ip_dc_hrg(NULL, ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", "EL"))
expect_error(get_cost_ip_dc_hrg("AA22C", NULL, "Currency_Code",
"National_Average_Unit_Cost", "EL"))
expect_error(get_cost_ip_dc_hrg("AA22C", ref_cost_data_file, NULL,
"National_Average_Unit_Cost", "EL"))
expect_error(get_cost_ip_dc_hrg("AA22C", ref_cost_data_file,
"Currency_Code",
NULL, "EL"))
result <- get_cost_ip_dc_hrg("AA22C", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", NULL)
expect_equal(result, 5053, tol = 1e-1)
expect_error(get_cost_ip_dc_hrg("AA", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", "EL"))
})
###############################################################################
context("testing extracting unit cost matching description")
test_that("testing extracting unit cost matching description", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019.csv",
package = "packDAMipd")
result <- get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "EL")
expect_equal(result, 3530, tol = 1e-1)
expect_error(get_cost_ip_dc_description(NULL, ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"EL"))
expect_error(get_cost_ip_dc_description("Cerebrovascular Accident", NULL,
"Currency_Description",
"National_Average_Unit_Cost",
"EL"))
expect_error(get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file, NULL,
"National_Average_Unit_Cost",
"EL"))
expect_error(get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file,
"Currency_Description",
NULL, "EL"))
result <- get_cost_ip_dc_description("Cerebrovascular Accident",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", NULL)
expect_equal(result, 3530, tol = 1e-1)
expect_error(get_cost_ip_dc_description("hello",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"EL"))
})
# # ###############################################################################
context("testing costing inpatient admission")
test_that("testing costing inpatient admission", {
costs_file <- system.file("extdata", "patient_adm_cost_EL.xlsx",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
expect_error(costing_inpatient_daycase_admission(NULL,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = NULL,
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "admission"))
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
NULL,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = NULL,
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col = NULL,
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = NULL))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = NULL,
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "ad"))
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = NULL,
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 3530, tol = 1e-2)
datafile <- system.file("extdata", "resource_use_hc_ip_nocol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_nonumuse.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_nocols.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_error.xlsx",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file, sheet = "EL")
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col =
"Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_hc_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file, sheet = "EL")
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = NULL,
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_numuse_wrong.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_numuse_missing.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 3530, tol = 1e-2)
result <- costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = "number_use",
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission")
expect_equal(result$totcost_ip_admission[1], 5053, tol = 1e-2)
datafile <- system.file("extdata", "resource_use_hc_ip_el_missing.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
datafile <- system.file("extdata", "resource_use_hc_ip_noelcol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = NULL,
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = "Currency_Description",
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
expect_error(costing_inpatient_daycase_admission(ind_part_data,
hrg_code_ip_admi = "HRGcode",
descrip_ip_admi = "Description",
number_use_ip_admi = NULL,
elective_col = "EL",
unit_cost_data,
hrg_code_col = "Currency_Code",
description_col = NULL,
unit_cost_col =
"National_Average_Unit_Cost",
cost_calculated_in = "admission"))
})
###############################################################################
context("testing extracting unit cost for A&E matching code")
test_that("testing extracting unit cost for A&E matching code", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
re <- get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", "Service_Code")
expect_equal(re, 452, tol = 1e-2)
ref_cost_data_file <- system.file("extdata",
"NHS_costs_2019_AandE.xlsx",
package = "packDAMipd")
re <- get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code", sheet = "AE")
expect_equal(re, 452, tol = 1e-2)
expect_error(get_cost_AandE_code("VB02Z", "T00A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code", sheet = "AE"))
expect_error(get_cost_AandE_code(NULL, "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", NA, ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", NULL,
"Currency_Code",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
NA, "National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code", NA, "Service_Code"))
expect_error(get_cost_AandE_code("VB02Z", "T01A", ref_cost_data_file,
"Currency_Code",
"National_Average_Unit_Cost", NULL))
})
###############################################################################
context("testing extracting unit cost matching description")
test_that("testing extracting unit cost matching description", {
ref_cost_data_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
re <- get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "Service_Code")
expect_equal(re, 265.33, tol = 1e-2)
ref_cost_data_file <- system.file("extdata",
"NHS_costs_2019_AandE.xlsx",
package = "packDAMipd")
re <- get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "Service_Code",
sheet = "AE")
expect_equal(re, 265.33, tol = 1e-2)
expect_error(get_cost_AandE_description("Emergency Medicine", "T00A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost", "Service_Code",
sheet = "AE"))
expect_error(get_cost_AandE_description(NULL, "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", NULL,
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
NULL,
"Currency_Description",
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
NULL,
"National_Average_Unit_Cost",
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
NULL,
"Service_Code"))
expect_error(get_cost_AandE_description("Emergency Medicine", "T01A",
ref_cost_data_file,
"Currency_Description",
"National_Average_Unit_Cost",
NULL))
})
############################################################################
context("testing extracting unit cost matching description")
test_that("testing extracting unit cost matching description", {
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_ae_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
result <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(result$totcost_AE_Admission[1], 672, tol = 1e-2)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = NULL,
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = NULL,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
result <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(result$totcost_AE_Admission[1], 672, tol = 1e-2)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = NULL,
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = NULL,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = NULL,
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = NULL,
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = NULL,
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "ss"))
result <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(result$totcost_AE_Admission[1], 754, tol = 1e-2)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "dd",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "dd", descrip_ae = NULL,
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_notypecol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_nonumusecol.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
costs_file <- system.file("extdata",
"NHS_costs_2019_AandE_nocode.csv",
package = "packDAMipd")
datafile <- system.file("extdata", "resource_use_ae_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
datafile <- system.file("extdata",
"resource_use_ae_ip_lengthtypecodediff.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_extranumuse.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
expect_error(costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance"))
datafile <- system.file("extdata", "resource_use_ae_ip_lessnumuse.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = NULL,
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 671, tol = 1e-2)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = "number_use",
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 754, tol = 1e-2)
datafile <- system.file("extdata", "resource_use_ae_ip.csv",
package = "packDAMipd")
ind_part_data <- packDAMipd::load_trial_data(datafile)
costs_file <- system.file("extdata",
"National_schedule_of_NHS_costs_2019_AandE.csv",
package = "packDAMipd")
unit_cost_data <- packDAMipd::load_trial_data(costs_file)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = "code", descrip_ae = NULL,
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 671, tol = 1e-2)
res <- costing_AandE_admission(ind_part_data = ind_part_data,
code_ae = NULL, descrip_ae = "desc",
number_use_ae = NULL,
type_admit_ae = "type_admit",
unit_cost_data = unit_cost_data,
code_col = "Currency_Code",
type_admit_col = "Service_Code",
description_col = "Currency_Description",
unit_cost_col = "National_Average_Unit_Cost",
cost_calculated_in = "attendance")
expect_equal(res$totcost_AE_Admission[1], 754, tol = 1e-2)
})
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