knitr::opts_chunk$set( fig.path = "basecase-QFN_TSPOT-HIVneg_files/" )
# source("../../../analysis scripts/IDEA/alt-YAML_Binomial_dectrees/indiv-dectree-sampling.R")
library(IDEAdectree) library(BCEA) library(ggplot2) # load("C:/Users/ngreen1/Dropbox/TB/IDEA/R/packages/IDEAdectree/data/TBdata_clinical_cleaned.RData") load("../data/TBdata_clinical_cleaned.RData") load("../data/COSTdistns_allerror.RData") load("../data/senspec_env.RData") load("../data/drug_dose-cost.RData") ## sensitivities and specificities from IDEA lab data attach(senspec.env) dat <- list() yearindays <- 365 WTP <- c(20000, 30000)/yearindays
dat1 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT", SPEC = TSPOT.noIndet.spec.mean, SENS = TSPOT.noIndet.sens.mean, SPECvar = TSPOT.noIndet.spec.var, SENSvar = TSPOT.noIndet.sens.var) dat2 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT", SPEC = TSPOT.HIV.noIndet.spec.mean, SENS = TSPOT.HIV.noIndet.sens.mean, SPECvar = TSPOT.HIV.noIndet.spec.var, SENSvar = TSPOT.HIV.noIndet.sens.var) dat3 <- IDEAdectree.simple(data=data, name.ruleout = "TSPOT", SPEC = TSPOT.HIVneg.noIndet.spec.mean, SENS = TSPOT.HIVneg.noIndet.sens.mean, SPECvar = TSPOT.HIVneg.noIndet.spec.var, SENSvar = TSPOT.HIVneg.noIndet.sens.var) dat$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$c, ref=1, interventions = intlabels) contour2(m, wtp=WTP, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))+#, xlim=c(-5,5), ylim=c(-200,200)) + ggtitle("") #+ geom_abline(intercept = 0, slope = WTP) my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels = intlabels, wtpNEG = "Y") my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, wtpNEG = "Y") my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, LEVELS=0.5, wtpNEG = "Y") my.plot.ceac(dat1, dat2, dat3, dat4, intlabels = intlabels) ## in years (not days) m <- bcea(e=dat$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$c, ref=1, interventions = intlabels) contour2(m, wtp=WTP, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))+#, xlim=c(-5,5), ylim=c(-200,200)) + ggtitle("") #+ geom_abline(intercept = 0, slope = WTP) my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels = intlabels, wtpNEG = "Y") my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, wtpNEG = "Y") my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, LEVELS=0.5, wtpNEG = "Y") my.plot.ceac(dat1, dat2, dat3, dat4, intlabels = intlabels) ## in years (not days) m <- bcea(e=dat$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$c, ref=1, interventions = intlabels) contour2(m, wtp=WTP, graph = "ggplot2", ICER.size=2, pos=c(0.1,0.9))+#, xlim=c(-5,5), ylim=c(-200,200)) + ggtitle("") #+ geom_abline(intercept = 0, slope = WTP) my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, wtpNEG = "Y") my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, wtpNEG = "Y") my.plot.bcea(dat1, dat2, dat3, dat4, WTP, intlabels, contour=TRUE, LEVELS=0.5, wtpNEG = "Y") my.plot.ceac(dat1, dat2, dat3, dat4, intlabels) ## in years (not days) m <- bcea(e=dat$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)
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