report_docs/basecase-QFN_TSPOT-noHIVneg.md

In n8thangreen/IDEAdectree: The IDEA study clinical data health economics analysis with decision trees

title: "Basecase cost-effectiveness comparison" author: "Nathan Green" date: "4 February 2016" output: word_document: keep_md: yes

# source("../../../analysis scripts/IDEA/alt-YAML_Binomial_dectrees/indiv-dectree-sampling.R")

library(IDEAdectree)
library(BCEA)
library(ggplot2)

# load("C:/Users/ngreen1/Dropbox/TB/IDEA/R/packages/IDEAdectree/data/TBdata_clinical_cleaned.RData")
load("../data/TBdata_clinical_cleaned.RData")
load("../data/COSTdistns_allerror.RData")
load("../data/senspec_env.RData")
load("../data/drug_dose-cost.RData")

## sensitivities and specificities from IDEA lab data
attach(senspec.env)

dat <- list()

yearindays <- 365
WTP <- c(20000, 30000)/yearindays

dat1 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT",
                           SPEC = TSPOT.noIndet.spec.mean, SENS = TSPOT.noIndet.sens.mean, 
                           SPECvar = TSPOT.noIndet.spec.var, SENSvar = TSPOT.noIndet.sens.var)
dat2 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT",
                           SPEC = TSPOT.HIV.noIndet.spec.mean, SENS = TSPOT.HIV.noIndet.sens.mean, 
                           SPECvar = TSPOT.HIV.noIndet.spec.var, SENSvar = TSPOT.HIV.noIndet.sens.var)
dat3 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT",
                           SPEC = TSPOT.HIVneg.noIndet.spec.mean, SENS = TSPOT.HIVneg.noIndet.sens.mean, 
                           SPECvar = TSPOT.HIVneg.noIndet.spec.var, SENSvar = TSPOT.HIVneg.noIndet.sens.var)

dat$e <- cbind(dat1$e, dat2$e[,2], dat3$e[,2])
dat$c <- cbind(dat1$c, dat2$c[,2], dat3$c[,2])

intlabels <- c("Current",
               "Enhanced TSPOT: All, no Indets", "Enhanced TSPOT: All, with Indets",
               "Enhanced TSPOT: HIV, no Indets", "Enhanced TSPOT: HIV, with Indets")

m <- bcea(e=dat$e, c=-dat$c, ref=1, interventions = intlabels)

contour2(m, wtp=WTP, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))+#, xlim=c(-5,5), ylim=c(-200,200)) +
  ggtitle("") #+ geom_abline(intercept = 0, slope = WTP)

## Warning in x * wtp: longer object length is not a multiple of shorter
## object length

## Warning in y[3] <- x1 * wtp: number of items to replace is not a multiple
## of replacement length

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels = intlabels, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, LEVELS=0.5, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.ceac(dat1, dat2, dat3, dat4, intlabels = intlabels)

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## in years (not days)
m <- bcea(e=dat$e/365, c=-dat$c, ref=1, interventions = intlabels)
contour2(m, wtp=20000, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))

ceac.plot(m)

dat1 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT",
                           SPEC = TSPOT.Indet.spec.mean, SENS = TSPOT.Indet.sens.mean, 
                           SPECvar = TSPOT.Indet.spec.var, SENSvar = TSPOT.Indet.sens.var)
dat2 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT",
                           SPEC = TSPOT.HIV.Indet.spec.mean, SENS = TSPOT.HIV.Indet.sens.mean, 
                           SPECvar = TSPOT.HIV.Indet.spec.var, SENSvar = TSPOT.HIV.Indet.sens.var)
dat3 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT",
                           SPEC = TSPOT.HIVneg.Indet.spec.mean, SENS = TSPOT.HIVneg.Indet.sens.mean, 
                           SPECvar = TSPOT.HIVneg.Indet.spec.var, SENSvar = TSPOT.HIVneg.Indet.sens.var)

dat$e <- cbind(dat1$e, dat2$e[,2], dat3$e[,2])
dat$c <- cbind(dat1$c, dat2$c[,2], dat3$c[,2])

intlabels <- c("Current",
               "Enhanced TSPOT: All, no Indets", "Enhanced TSPOT: All, with Indets",
               "Enhanced TSPOT: HIV, no Indets", "Enhanced TSPOT: HIV, with Indets")

m <- bcea(e=dat$e, c=-dat$c, ref=1, interventions = intlabels)

contour2(m, wtp=WTP, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))+#, xlim=c(-5,5), ylim=c(-200,200)) +
  ggtitle("") #+ geom_abline(intercept = 0, slope = WTP)

## Warning in x * wtp: longer object length is not a multiple of shorter
## object length

## Warning in y[3] <- x1 * wtp: number of items to replace is not a multiple
## of replacement length

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels = intlabels, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, LEVELS=0.5, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.ceac(dat1, dat2, dat3, dat4, intlabels = intlabels)

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## in years (not days)
m <- bcea(e=dat$e/365, c=-dat$c, ref=1, interventions = intlabels)
contour2(m, wtp=20000, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))

ceac.plot(m)

dat1 <- IDEAdectree.simple(data=data, name.ruleout = "QFN",
                           SPEC = QFN.noIndet.spec.mean, SENS = QFN.noIndet.sens.mean, 
                           SPECvar = QFN.noIndet.spec.var, SENSvar = QFN.noIndet.sens.var)
dat2 <- IDEAdectree.simple(data=data, name.ruleout = "QFN",
                           SPEC = QFN.Indet.spec.mean, SENS = QFN.Indet.sens.mean, 
                           SPECvar = QFN.Indet.spec.var, SENSvar = QFN.Indet.sens.var)
dat3 <- IDEAdectree.simple(data=data, name.ruleout = "QFN",
                           SPEC = QFN.HIV.noIndet.spec.mean, SENS = QFN.HIV.noIndet.sens.mean, 
                           SPECvar = QFN.HIV.noIndet.spec.var, SENSvar = QFN.HIV.noIndet.sens.var)
dat4 <- IDEAdectree.simple(data=data, name.ruleout = "QFN",
                           SPEC = QFN.HIV.Indet.spec.mean, SENS = QFN.HIV.Indet.sens.mean, 
                           SPECvar = QFN.HIV.Indet.spec.var, SENSvar = QFN.HIV.Indet.sens.var)

dat$e <- cbind(dat1$e, dat2$e[,2], dat3$e[,2], dat4$e[,2])
dat$c <- cbind(dat1$c, dat2$c[,2], dat3$c[,2], dat4$c[,2])

intlabels <- c("Current",
               "Enhanced QFN: All, no Indets", "Enhanced QFN: All, with Indets",
               "Enhanced QFN: HIV, no Indets", "Enhanced QFN: HIV, with Indets")

m <- bcea(e=dat$e, c=-dat$c, ref=1, interventions = intlabels)

contour2(m, wtp=WTP, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))+#, xlim=c(-5,5), ylim=c(-200,200)) +
  ggtitle("") #+ geom_abline(intercept = 0, slope = WTP)

## Warning in x * wtp: longer object length is not a multiple of shorter
## object length

## Warning in y[3] <- x1 * wtp: number of items to replace is not a multiple
## of replacement length

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, LEVELS=0.5, wtpNEG = "Y")

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## [[1]]
## NULL
## 
## [[2]]
## NULL

my.plot.ceac(dat1, dat2, dat3, dat4, intlabels)

## Warning in if (is.na(dat4)) {: the condition has length > 1 and only the
## first element will be used

## in years (not days)
m <- bcea(e=dat$e/365, c=-dat$c, ref=1, interventions = intlabels)
contour2(m, wtp=20000, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))

ceac.plot(m)

detach(senspec.env)

n8thangreen/IDEAdectree documentation built on Feb. 10, 2020, 11:35 a.m.