This document demonstrates running the screening, diagnosis and treatment decision tree model.
First, we need to attach the packages we’ll need. treeSimR is written by us too so this will need to be installed from GitHub.
library(treeSimR)
library(LTBIscreeningproject)
library(dplyr)
library(data.tree)
library(purrr)Load in data
data("intervention_constants", package = "LTBIscreeningproject")
data("cost_effectivness_params", package = "LTBIscreeningproject")
data("scenario_parameters", package = "LTBIscreeningproject")
load("model_input_cohort.RData")According to the parameter values we specified in interv we first need to prepare the cohort data set to only include those individuals we’re interested in analysing.
Only use a single year cohort
cohort <- dplyr::filter(IMPUTED_sample,
issdt_year == interv$year_cohort)EWNI stay long enough to be screened
cohort <- dplyr::filter(cohort,
date_exit_uk1_issdt.years >= interv$min_screen_length_of_stay)Only keep those inidiviuals that are screened before some other event
if (interv$screen_with_delay) {
cohort <- dplyr::filter(cohort,
screen == 1)
}Do we include student in the screening programme?
if (interv$no_students) {
cohort <- dplyr::filter(cohort,
visatype2 != "Students")}Include individuals from ‘higher’ incidence countries only
cohort <- dplyr::filter(cohort,
who_prev_cat_Pareek2011 %in% interv$incidence_grps_screen)Count numbers of TB cases
n.exit_tb <-
cohort %>%
dplyr::filter(exituk_tb) %>%
dplyr::count()
n.uk_tb <-
cohort %>%
dplyr::filter(uk_tb) %>%
dplyr::count()
num_all_tb_cost <-
if (interv$ENDPOINT_cost == "exit uk") {
n.uk_tb
} else if (interv$ENDPOINT_cost == "death") {
n.uk_tb + n.exit_tb}
num_all_tb_QALY <-
if (interv$ENDPOINT_QALY == "exit uk") {
n.uk_tb
} else if (interv$ENDPOINT_QALY == "death") {
n.uk_tb + n.exit_tb}saveRDS(cohort, file = "cohort.Rds")Load input files. We have defined the decision tree using YAML syntax. We have a separate trees for cost and health. They have the same structure and probabilities but different values on the branches. We also create our own class.
osNode.cost.fileName <- system.file("data", "LTBI_dtree-cost-symptoms.yaml",
package = "LTBIscreeningproject")
osNode.health.fileName <- system.file("data", "LTBI_dtree-QALYloss-symptoms.yaml",
package = "LTBIscreeningproject")
costeff.cost <- treeSimR::costeffectiveness_tree(yaml_tree = osNode.cost.fileName)
osNode.cost <- costeff.cost$osNode
costeff.health <- treeSimR::costeffectiveness_tree(yaml_tree = osNode.health.fileName)
osNode.health <- costeff.health$osNode#> Warning in treeSimR::costeffectiveness_tree(yaml_tree = "LTBI_dtree-cost-symptoms.yaml"): Check type of attributes. Should they be numeric rather than character?
#> $osNode
#> levelName distn max min p scale shape type
#> 1 LTBI screening cost unif 0.00 0.00 1.00000 NA NA logical
#> 2 ¦--(0,50] unif 0.00 0.00 0.00000 chance
#> 3 ¦ ¦--LTBI unif 0.00 0.00 0.03000 chance
#> 4 ¦ ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 5 ¦ ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 6 ¦ ¦ ¦--1-Sensitivity unif 0.00 0.00 0.16000 terminal
#> 7 ¦ ¦ °--Sensitivity unif 0.00 0.00 0.84000 chance
#> 8 ¦ ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 9 ¦ ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 10 ¦ ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 11 ¦ ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 12 ¦ ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 13 ¦ ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 14 ¦ ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 15 ¦ ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 16 ¦ ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 17 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 18 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 19 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 20 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 21 ¦ ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 22 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 23 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 24 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 25 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 26 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 27 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 28 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 29 ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 30 ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 31 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 32 ¦ °--non-LTBI unif 0.00 0.00 0.97000 chance
#> 33 ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 34 ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 35 ¦ ¦--Specificity unif 0.00 0.00 0.99000 terminal
#> 36 ¦ °--1-Specificity unif 0.00 0.00 0.01000 chance
#> 37 ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 38 ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 39 ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 40 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 41 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 42 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 43 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 44 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 45 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 46 ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 47 ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 48 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 49 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 50 ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 51 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 52 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 53 ¦--(50,150] unif 0.00 0.00 0.04000 chance
#> 54 ¦ ¦--LTBI unif 0.00 0.00 0.03000 chance
#> 55 ¦ ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 56 ¦ ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 57 ¦ ¦ ¦--1-Sensitivity unif 0.00 0.00 0.16000 terminal
#> 58 ¦ ¦ °--Sensitivity unif 0.00 0.00 0.84000 chance
#> 59 ¦ ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 60 ¦ ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 61 ¦ ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 62 ¦ ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 63 ¦ ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 64 ¦ ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 65 ¦ ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 66 ¦ ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 67 ¦ ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 68 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 69 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 70 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 71 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 72 ¦ ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 73 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 74 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 75 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 76 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 77 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 78 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 79 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 80 ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 81 ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 82 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 83 ¦ °--non-LTBI unif 0.00 0.00 0.97000 chance
#> 84 ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 85 ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 86 ¦ ¦--Specificity unif 0.00 0.00 0.99000 terminal
#> 87 ¦ °--1-Specificity unif 0.00 0.00 0.01000 chance
#> 88 ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 89 ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 90 ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 91 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 92 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 93 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 94 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 95 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 96 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 97 ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 98 ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 99 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 100 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 101 ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 102 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 103 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 104 ¦--(150,250] unif 0.00 0.00 0.16000 chance
#> 105 ¦ ¦--LTBI unif 0.00 0.00 0.03000 chance
#> 106 ¦ ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 107 ¦ ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 108 ¦ ¦ ¦--1-Sensitivity unif 0.00 0.00 0.16000 terminal
#> 109 ¦ ¦ °--Sensitivity unif 0.00 0.00 0.84000 chance
#> 110 ¦ ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 111 ¦ ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 112 ¦ ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 113 ¦ ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 114 ¦ ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 115 ¦ ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 116 ¦ ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 117 ¦ ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 118 ¦ ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 119 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 120 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 121 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 122 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 123 ¦ ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 124 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 125 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 126 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 127 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 128 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 129 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 130 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 131 ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 132 ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 133 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 134 ¦ °--non-LTBI unif 0.00 0.00 0.97000 chance
#> 135 ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 136 ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 137 ¦ ¦--Specificity unif 0.00 0.00 0.99000 terminal
#> 138 ¦ °--1-Specificity unif 0.00 0.00 0.01000 chance
#> 139 ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 140 ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 141 ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 142 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 143 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 144 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 145 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 146 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 147 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 148 ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 149 ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 150 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 151 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 152 ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 153 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 154 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 155 ¦--(250,350] unif 0.00 0.00 0.60000 chance
#> 156 ¦ ¦--LTBI unif 0.00 0.00 0.03000 chance
#> 157 ¦ ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 158 ¦ ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 159 ¦ ¦ ¦--1-Sensitivity unif 0.00 0.00 0.16000 terminal
#> 160 ¦ ¦ °--Sensitivity unif 0.00 0.00 0.84000 chance
#> 161 ¦ ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 162 ¦ ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 163 ¦ ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 164 ¦ ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 165 ¦ ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 166 ¦ ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 167 ¦ ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 168 ¦ ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 169 ¦ ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 170 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 171 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 172 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 173 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 174 ¦ ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 175 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 176 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 177 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 178 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 179 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 180 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 181 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 182 ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 183 ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 184 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 185 ¦ °--non-LTBI unif 0.00 0.00 0.97000 chance
#> 186 ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 187 ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 188 ¦ ¦--Specificity unif 0.00 0.00 0.99000 terminal
#> 189 ¦ °--1-Specificity unif 0.00 0.00 0.01000 chance
#> 190 ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 191 ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 192 ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 193 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 194 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 195 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 196 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 197 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 198 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 199 ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 200 ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 201 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 202 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 203 ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 204 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 205 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 206 °--(350,1e+05] unif 0.00 0.00 0.20000 chance
#> 207 ¦--LTBI unif 0.00 0.00 0.03000 chance
#> 208 ¦ ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 209 ¦ °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 210 ¦ ¦--1-Sensitivity unif 0.00 0.00 0.16000 terminal
#> 211 ¦ °--Sensitivity unif 0.00 0.00 0.84000 chance
#> 212 ¦ ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 213 ¦ °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 214 ¦ ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 215 ¦ ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 216 ¦ ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 217 ¦ ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 218 ¦ ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 219 ¦ ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 220 ¦ ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 221 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 222 ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 223 ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 224 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 225 ¦ °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 226 ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 227 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 228 ¦ ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 229 ¦ ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 230 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 231 ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 232 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 chance
#> 233 ¦ ¦ ¦--Effective unif 0.00 0.00 0.90000 terminal
#> 234 ¦ ¦ °--Not Effective unif 0.00 0.00 0.10000 terminal
#> 235 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 236 °--non-LTBI unif 0.00 0.00 0.97000 chance
#> 237 ¦--Not Agree to Screen unif 0.00 0.00 0.40000 terminal
#> 238 °--Agree to Screen unif 106.00 50.00 0.60000 chance
#> 239 ¦--Specificity unif 0.00 0.00 0.99000 terminal
#> 240 °--1-Specificity unif 0.00 0.00 0.01000 chance
#> 241 ¦--Not Start Treatment unif 0.00 0.00 0.30000 terminal
#> 242 °--Start Treatment unif 0.00 0.00 0.70000 chance
#> 243 ¦--Symptoms Hepatotoxicity gamma NA NA 0.00245 87.889 6.679 chance
#> 244 ¦ ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 245 ¦ ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 246 ¦ ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 247 ¦ °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 248 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 249 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 250 °--Not Symptoms Hepatotoxicity unif 0.00 0.00 0.99755 chance
#> 251 ¦--Symptoms Nausea gamma NA NA 0.14300 13 5 chance
#> 252 ¦ ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 253 ¦ °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#> 254 °--Not Symptoms Nausea unif 0.00 0.00 0.85700 chance
#> 255 ¦--Complete Treatment unif 842.45 511.69 0.80000 terminal
#> 256 °--Not Complete Treatment unif 140.41 85.24 0.20000 terminal
#>
#> $data
#> $data$data_prob
#> [1] NA
#>
#> $data$data_val
#> [1] NA
#>
#>
#> attr(,"details")
#> [1] ""
#> attr(,"class")
#> [1] "costeffectiveness_object" "list"Create look-up tables using the cohort data to give proportion in each incidence in country of origin and the probability of LTBI for each of these.
who_levels <- c("(0,50]", "(50,150]", "(150,250]", "(250,350]", "(350,1e+05]")
p_incid_grp <- miscUtilities::prop_table(cohort$who_prev_cat_Pareek2011)
pLatentTB.who <- data.frame(who_prev_cat_Pareek2011 = names(p_incid_grp),
LTBI = c(0.03, 0.13, 0.2, 0.3, 0.3))Then insert these probabilities in to the decision tree
for (i in seq_along(who_levels)) {
osNode.cost$Set(p = p_incid_grp[i],
filterFun = function(x) x$name == who_levels[i])
osNode.health$Set(p = p_incid_grp[i],
filterFun = function(x) x$name == who_levels[i])
}
for (i in who_levels) {
pLTBI <- subset(pLatentTB.who,
who_prev_cat_Pareek2011 == i,
select = LTBI)
osNode.cost$Set(p = pLTBI,
filterFun = function(x) x$pathString == miscUtilities::pastef("LTBI screening cost", i, "LTBI"))
osNode.health$Set(p = pLTBI,
filterFun = function(x) x$pathString == miscUtilities::pastef("LTBI screening QALY loss", i, "LTBI"))
osNode.cost$Set(p = 1 - pLTBI,
filterFun = function(x) x$pathString == miscUtilities::pastef("LTBI screening cost", i, "non-LTBI"))
osNode.health$Set(p = 1 - pLTBI,
filterFun = function(x) x$pathString == miscUtilities::pastef("LTBI screening QALY loss", i, "non-LTBI"))
}Now we can run the decision tree model using the scenario parameter values, active TB cases, and cost and health decision tree objects.
A single scenario:
decision_tree_cluster(parameters = scenario_parameters[[1]],
N.mc = interv$N.mc,
n.uk_tb = 10, #as.numeric(n.uk_tb),
n.exit_tb = 10, #as.numeric(n.exit_tb),
cost_dectree = "osNode_cost_2009.Rds",
health_dectree = "osNode_health_2009.Rds")
#> $mc_cost
#> [1] 37.27940 36.37491 37.06578 36.67532 36.26612 36.40452 36.22418 36.55427 36.97845 37.68561
#>
#> $mc_health
#> [1] 4.806743e-06 5.340375e-06 5.137309e-06 5.309466e-06 4.995974e-06 4.651200e-06 5.618218e-06 5.200578e-06 5.229864e-06 4.938510e-06
#>
#> $n_tb_screen_all
#> sim status n
#> 1 1 disease-free 4
#> 2 1 tb 16
#> 3 2 disease-free 2
#> 4 2 tb 18
#> 5 3 disease-free 4
#> 6 3 tb 16
#> 7 4 disease-free 1
#> 8 4 tb 19
#> 9 5 disease-free 5
#> 10 5 tb 15
#> 11 6 disease-free 5
#> 12 6 tb 15
#> 13 7 disease-free 5
#> 14 7 tb 15
#> 15 8 disease-free 4
#> 16 8 tb 16
#> 17 9 disease-free 3
#> 18 9 tb 17
#> 19 10 disease-free 2
#> 20 10 tb 18
#>
#> $n_tb_screen_uk
#> sim status n
#> 1 1 disease-free 1
#> 2 1 tb 9
#> 3 2 disease-free 4
#> 4 2 tb 6
#> 5 3 disease-free 2
#> 6 3 tb 8
#> 7 4 disease-free 0
#> 8 4 tb 10
#> 9 5 disease-free 0
#> 10 5 tb 10
#> 11 6 disease-free 1
#> 12 6 tb 9
#> 13 7 disease-free 1
#> 14 7 tb 9
#> 15 8 disease-free 0
#> 16 8 tb 10
#> 17 9 disease-free 4
#> 18 9 tb 6
#> 19 10 disease-free 0
#> 20 10 tb 10
#>
#> $p_LTBI_to_effectiveTx
#> (350,1e+05]
#> 0.108864
#>
#> $subset_pop
#> LTBI_pre tests positive startTx completeTx cured LTBI_post
#> 1 0.2868171 0.6 0.1488349 0.08930096 0.05358058 0.03122406 0.2555931
#>
#> $call
#> decision_tree_cluster(parameters = scenario_parameters[[1]],
#> N.mc = interv$N.mc, n.uk_tb = 10, n.exit_tb = 10, cost_dectree = "osNode_cost_2009.Rds",
#> health_dectree = "osNode_health_2009.Rds")
#>
#> $N.mc
#> [1] 10Multiple scenarios:
lapply(scenario_parameters[1:3],
decision_tree_cluster,
N.mc = 1,
n.uk_tb = 10, #as.numeric(n.uk_tb),
n.exit_tb = 10, #as.numeric(n.exit_tb),
cost_dectree = "osNode_cost_2009.Rds",
health_dectree = "osNode_health_2009.Rds")
#> $`1`
#> $`1`$mc_cost
#> [1] 36.51917
#>
#> $`1`$mc_health
#> [1] 5.271375e-06
#>
#> $`1`$n_tb_screen_all
#> sim status n
#> 1 1 disease-free 2
#> 2 1 tb 18
#>
#> $`1`$n_tb_screen_uk
#> sim status n
#> 1 1 disease-free 1
#> 2 1 tb 9
#>
#> $`1`$p_LTBI_to_effectiveTx
#> (350,1e+05]
#> 0.108864
#>
#> $`1`$subset_pop
#> LTBI_pre tests positive startTx completeTx cured LTBI_post
#> 1 0.2868171 0.6 0.1488349 0.08930096 0.05358058 0.03122406 0.2555931
#>
#> $`1`$call
#> FUN(parameters = X[[i]], N.mc = 1, n.uk_tb = 10, n.exit_tb = 10,
#> cost_dectree = "osNode_cost_2009.Rds", health_dectree = "osNode_health_2009.Rds")
#>
#> $`1`$N.mc
#> [1] 1
#>
#>
#> $`2`
#> $`2`$mc_cost
#> [1] 44.03829
#>
#> $`2`$mc_health
#> [1] 7.074663e-06
#>
#> $`2`$n_tb_screen_all
#> sim status n
#> 1 1 disease-free 3
#> 2 1 tb 17
#>
#> $`2`$n_tb_screen_uk
#> sim status n
#> 1 1 disease-free 2
#> 2 1 tb 8
#>
#> $`2`$p_LTBI_to_effectiveTx
#> (350,1e+05]
#> 0.145152
#>
#> $`2`$subset_pop
#> LTBI_pre tests positive startTx completeTx cured LTBI_post
#> 1 0.2868171 0.6 0.1488349 0.1190679 0.07144077 0.04163208 0.2451851
#>
#> $`2`$call
#> FUN(parameters = X[[i]], N.mc = 1, n.uk_tb = 10, n.exit_tb = 10,
#> cost_dectree = "osNode_cost_2009.Rds", health_dectree = "osNode_health_2009.Rds")
#>
#> $`2`$N.mc
#> [1] 1
#>
#>
#> $`3`
#> $`3`$mc_cost
#> [1] 52.58395
#>
#> $`3`$mc_health
#> [1] 9.690061e-06
#>
#> $`3`$n_tb_screen_all
#> sim status n
#> 1 1 disease-free 6
#> 2 1 tb 14
#>
#> $`3`$n_tb_screen_uk
#> sim status n
#> 1 1 disease-free 1
#> 2 1 tb 9
#>
#> $`3`$p_LTBI_to_effectiveTx
#> (350,1e+05]
#> 0.18144
#>
#> $`3`$subset_pop
#> LTBI_pre tests positive startTx completeTx cured LTBI_post
#> 1 0.2868171 0.6 0.1488349 0.1488349 0.08930096 0.0520401 0.234777
#>
#> $`3`$call
#> FUN(parameters = X[[i]], N.mc = 1, n.uk_tb = 10, n.exit_tb = 10,
#> cost_dectree = "osNode_cost_2009.Rds", health_dectree = "osNode_health_2009.Rds")
#>
#> $`3`$N.mc
#> [1] 1