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Plots.R
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Plots.R
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######################### SCRIPT PLOTTING RISK & LOGITRISK DISTRIBUTIONS ###########
#library(ggpubr)
#install.packages("gridExtra")
#library(gridExtra)
####col.names of dataset
dataset=RiskData
names(dataset)[names(dataset) == "TRT01A"] <- "Treatment"
dataset$Treatment<-recode(dataset$Treatment,"1='Dimethyl fumarate';2='Galtiramer acetate'; 3='Natalizumab';4='Placebo'")
names(dataset)[names(dataset) == "logitRiskLASSO"] <- "LogitRiskLASSO"
names(dataset)[names(dataset) == "logitRiskPreSpecified"] <- "LogitRiskPreSpecified"
names(dataset)[names(dataset) == "RiskPreSpecified"] <- "RiskPreSpecified"
##### A. The density of the risk score in the whole dataset
#a <- ggplot(dataset, aes(x = LogitRisk))
# y axis scale = ..density.. (default behaviour)
#a + geom_density(fill = "lightgray") +
# geom_vline(aes(xintercept = mean(LogitRisk)),
# linetype = "dashed", size = 0.6,color = "#FC4E07")
#################################################LASSO model########################################
#################################################################################################
# A. The distribution in the whole dataset
#logitrisk
summary(dataset$LogitRiskLASSO) ### mean=-0.5611, median=-0.5991
LogitRiskLASSO<-ggdensity(dataset, x = "LogitRiskLASSO",
fill = "#0073C2FF", color = "#0073C2FF",
add = "mean", rug = TRUE)
#risk
summary(dataset$RiskLASSO)
RiskDistLASSO<-ggdensity(dataset, x = "RiskLASSO",
fill = "#0073C2FF", color = "#0073C2FF",
add = "mean", rug = TRUE, xlim=c(0,0.75))
##### B. The distribution per arm for each study
##data per study
S<-dataset[which(dataset$STUDYID==1),]
K<-dataset[which(dataset$STUDYID==2),]
L<-dataset[which(dataset$STUDYID==3),]
#####FOR LOGIT
a<-ggdensity(S, x = "LogitRiskLASSO",
add = "mean", rug = TRUE, xlim=c(-4,4),
color = "Treatment", fill = "Treatment",
palette = c("blue", "red"), xlab = "Logit Risk score for DEFINE study")
b<-ggdensity(K, x = "LogitRiskLASSO",
add = "mean", rug = TRUE,xlim=c(-4,4),
color = "Treatment", fill = "Treatment",
palette = c("blue", "yellow","red"), xlab = "Logit Risk score for CONFIRM study")
c<-ggdensity(L, x = "LogitRiskLASSO",
add = "mean", rug = TRUE,xlim=c(-4,4),
color = "Treatment", fill = "Treatment",
palette = c("grey", "red"), xlab = "Logit Risk score for AFFIRM study")
RandomizationLogitRiskLASSO<-ggarrange(a,b,c,
labels = c("A", "B", "C"),
ncol = 2, nrow = 2)
###FOR RISK
a<-ggdensity(S, x = "RiskLASSO",
add = "mean", rug = TRUE, xlim=c(0,1),
color = "Treatment", fill = "Treatment",
palette = c("blue", "red"), xlab = "Risk score for DEFINE study")
b<-ggdensity(K, x = "RiskLASSO",
add = "mean", rug = TRUE,xlim=c(0,1),
color = "Treatment", fill = "Treatment",
palette = c("blue", "yellow","red"), xlab = "Risk score for CONFIRM study")
c<-ggdensity(L, x = "RiskLASSO",
add = "mean", rug = TRUE,xlim=c(0,1),
color = "Treatment", fill = "Treatment",
palette = c("grey", "red"), xlab = "Risk score for AFFIRM study")
RandomizationRiskLASSO<-ggarrange(a, b, c,
labels = c("A", "B", "C"),
ncol = 2, nrow = 2)
#C. The distributionin those with true relapse and true non-relapse in the entire dataset
dataset$RELAPSE2year<-as.factor(dataset$RELAPSE2year)
#logitRisk
PrognosticLogitRiskLASSO<-ggdensity(dataset, x = "LogitRiskLASSO",
add = "mean", rug = TRUE,
color = "RELAPSE2year", fill = "RELAPSE2year",
palette = c("black", "grey"), xlab = "Logit Risk score as a prognostic factor")
#Risk
PrognosticRiskLASSO<-ggdensity(dataset, x = "RiskLASSO",
add = "mean", rug = TRUE,
color = "RELAPSE2year", fill = "RELAPSE2year",
palette = c("black", "grey"), xlim=c(0,0.75),xlab = "Risk score as a prognostic factor")
##Risk as prognostic factor
summary(dataset$RiskLASSO[dataset$RELAPSE2year==1])
summary(dataset$RiskLASSO[dataset$RELAPSE2year==0])
t.test(dataset$RiskLASSO[dataset$RELAPSE2year==1])
t.test(dataset$RiskLASSO[dataset$RELAPSE2year==0])
#D. The distribution in those with true relapse and true non-relapse for each arm in each study
##logit risk
S$RELAPSE2year<-as.factor(S$RELAPSE2year)
d<-ggdensity(S, x = "LogitRiskLASSO",merge=T,
add = "mean", rug = TRUE,xlim=c(-2,2),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow"), xlab = "Logit Risk score in DEFINE study")
t.test(S$LogitRiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
t.test(S$LogitRiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
t.test(S$LogitRiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==0])
t.test(S$LogitRiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==1])
summary(S$LogitRiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
summary(S$LogitRiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
summary(S$LogitRiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==0])
summary(S$LogitRiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==1])
K$RELAPSE2year<-as.factor(K$RELAPSE2year)
e<-ggdensity(K, x = "LogitRiskLASSO",merge=T,
add = "mean", rug = TRUE,xlim=c(-2,2),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow", "red"), xlab = "Logit Risk score in CONFIRM study")
t.test(K$LogitRiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
t.test(K$LogitRiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
t.test(K$LogitRiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
t.test(K$LogitRiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
t.test(K$LogitRiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==0])
t.test(K$LogitRiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==1])
summary(K$LogitRiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
summary(K$LogitRiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
summary(K$LogitRiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
summary(K$LogitRiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
summary(K$LogitRiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==0])
summary(K$LogitRiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==1])
L$RELAPSE2year<-as.factor(L$RELAPSE2year)
f<-ggdensity(L, x = "LogitRiskLASSO",merge=T,
add = "mean", rug = TRUE, xlim=c(-2,2),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow"), xlab = "Logit Risk score in AFFIRM study")
t.test(L$LogitRiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
t.test(L$LogitRiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
t.test(L$LogitRiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==0])
t.test(L$LogitRiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==1])
summary(L$LogitRiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
summary(L$LogitRiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
summary(L$LogitRiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==0])
summary(L$LogitRiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==1])
EffectModLogitRiskLASSO<-ggarrange(d,e,f, labels = c("A","B","C"))
###Risk
S$RELAPSE2year<-as.factor(S$RELAPSE2year)
d<-ggdensity(S, x = "RiskLASSO",merge=T,
add = "mean", rug = TRUE,xlim=c(0,1),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue","red"), xlab = "Risk score in DEFINE study")
t.test(S$RiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
t.test(S$RiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
t.test(S$RiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==0])
t.test(S$RiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==1])
summary(S$RiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
summary(S$RiskLASSO[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
summary(S$RiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==0])
summary(S$RiskLASSO[S$Treatment=="Placebo" & S$RELAPSE2year==1])
K$RELAPSE2year<-as.factor(K$RELAPSE2year)
e<-ggdensity(K, x = "RiskLASSO",merge=T,
add = "mean", rug = TRUE,xlim=c(0,1),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow", "red"), xlab = "Risk score in CONFIRM study")
t.test(K$RiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
t.test(K$RiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
t.test(K$RiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
t.test(K$RiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
t.test(K$RiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==0])
t.test(K$RiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==1])
summary(K$RiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
summary(K$RiskLASSO[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
summary(K$RiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
summary(K$RiskLASSO[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
summary(K$RiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==0])
summary(K$RiskLASSO[K$Treatment=="Placebo" & K$RELAPSE2year==1])
L$RELAPSE2year<-as.factor(L$RELAPSE2year)
f<-ggdensity(L, x = "RiskLASSO",merge=T,
add = "mean", rug = TRUE, xlim=c(0,1),
color = "RELAPSE2year", fill = "Treatment",
palette = c("gray", "red"), xlab = "Risk score in AFFIRM study")
t.test(L$RiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
t.test(L$RiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
t.test(L$RiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==0])
t.test(L$RiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==1])
summary(L$RiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
summary(L$RiskLASSO[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
summary(L$RiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==0])
summary(L$RiskLASSO[L$Treatment=="Placebo" & L$RELAPSE2year==1])
EffectModRiskLASSO<-ggarrange(d,e,f,labels = c("A","B","C"))
################################################# PreSpecified model ########################################
#################################################################################################
# A. The distribution in the whole dataset
#logitrisk
summary(dataset$LogitRiskPreSpecified) ### mean=-0.5611, median=-0.5991
LogitRiskLASSOPreSpecified<-ggdensity(dataset, x = "LogitRiskPreSpecified",
fill = "#0073C2FF", color = "#0073C2FF",
add = "mean", rug = TRUE)
#risk
summary(dataset$RiskPreSpecified)
RiskDistPreSpecified<-ggdensity(dataset, x = "RiskPreSpecified",
fill = "#0073C2FF", color = "#0073C2FF",
add = "mean", rug = TRUE, xlim=c(0,0.75))
##### B. The distribution per arm for each study
##data per study
S<-dataset[which(dataset$STUDYID==1),]
K<-dataset[which(dataset$STUDYID==2),]
L<-dataset[which(dataset$STUDYID==3),]
#####FOR LOGIT
a<-ggdensity(S, x = "LogitRiskPreSpecified",
add = "mean", rug = TRUE, xlim=c(-4,4),
color = "Treatment", fill = "Treatment",
palette = c("blue", "red"), xlab = "Logit Risk score for DEFINE study")
b<-ggdensity(K, x = "LogitRiskPreSpecified",
add = "mean", rug = TRUE,xlim=c(-4,4),
color = "Treatment", fill = "Treatment",
palette = c("blue", "yellow","red"), xlab = "Logit Risk score for CONFIRM study")
c<-ggdensity(L, x = "LogitRiskPreSpecified",
add = "mean", rug = TRUE,xlim=c(-4,4),
color = "Treatment", fill = "Treatment",
palette = c("grey", "red"), xlab = "Logit Risk score for AFFIRM study")
RandomizationLogitRiskPreSpecified<-ggarrange(a,b,c,
labels = c("A", "B", "C"),
ncol = 2, nrow = 2)
###FOR RISK
a<-ggdensity(S, x = "RiskPreSpecified",
add = "mean", rug = TRUE, xlim=c(0,1),
color = "Treatment", fill = "Treatment",
palette = c("blue", "red"), xlab = "Risk score for DEFINE study")
b<-ggdensity(K, x = "RiskPreSpecified",
add = "mean", rug = TRUE,xlim=c(0,1),
color = "Treatment", fill = "Treatment",
palette = c("blue", "yellow","red"), xlab = "Risk score for CONFIRM study")
c<-ggdensity(L, x = "RiskPreSpecified",
add = "mean", rug = TRUE,xlim=c(0,1),
color = "Treatment", fill = "Treatment",
palette = c("grey", "red"), xlab = "Risk score for AFFIRM study")
RandomizationRiskPreSpecified<-ggarrange(a, b, c,
labels = c("A", "B", "C"),
ncol = 2, nrow = 2)
#C. The distributionin those with true relapse and true non-relapse in the entire dataset
dataset$RELAPSE2year<-as.factor(dataset$RELAPSE2year)
#logitRisk
PrognosticLogitRiskPreSpecified<-ggdensity(dataset, x = "LogitRiskPreSpecified",
add = "mean", rug = TRUE,
color = "RELAPSE2year", fill = "RELAPSE2year",
palette = c("black", "grey"), xlab = "Logit Risk score as a prognostic factor")
#Risk
PrognosticRiskPreSpecified<-ggdensity(dataset, x = "RiskPreSpecified",
add = "mean", rug = TRUE,
color = "RELAPSE2year", fill = "RELAPSE2year",
palette = c("black", "grey"),xlim=c(0,0.75), xlab = "Risk score as a prognostic factor")
##Risk as prognostic factor
summary(dataset$RiskPreSpecified[dataset$RELAPSE2year==1])
summary(dataset$RiskPreSpecified[dataset$RELAPSE2year==0])
t.test(dataset$RiskPreSpecified[dataset$RELAPSE2year==1])
t.test(dataset$RiskPreSpecified[dataset$RELAPSE2year==0])
#D. The distribution in those with true relapse and true non-relapse for each arm in each study
##logit risk
S$RELAPSE2year<-as.factor(S$RELAPSE2year)
d<-ggdensity(S, x = "LogitRiskPreSpecified",merge=T,
add = "mean", rug = TRUE,xlim=c(-2,2),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow"), xlab = "Logit Risk score in DEFINE study")
t.test(S$LogitRiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
t.test(S$LogitRiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
t.test(S$LogitRiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==0])
t.test(S$LogitRiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==1])
summary(S$LogitRiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
summary(S$LogitRiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
summary(S$LogitRiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==0])
summary(S$LogitRiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==1])
K$RELAPSE2year<-as.factor(K$RELAPSE2year)
e<-ggdensity(K, x = "LogitRiskPreSpecified",merge=T,
add = "mean", rug = TRUE,xlim=c(-2,2),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow", "red"), xlab = "Logit Risk score in CONFIRM study")
t.test(K$LogitRiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
t.test(K$LogitRiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
t.test(K$LogitRiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
t.test(K$LogitRiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
t.test(K$LogitRiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==0])
t.test(K$LogitRiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==1])
summary(K$LogitRiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
summary(K$LogitRiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
summary(K$LogitRiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
summary(K$LogitRiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
summary(K$LogitRiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==0])
summary(K$LogitRiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==1])
L$RELAPSE2year<-as.factor(L$RELAPSE2year)
f<-ggdensity(L, x = "LogitRiskPreSpecified",merge=T,
add = "mean", rug = TRUE, xlim=c(-2,2),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow"), xlab = "Logit Risk score in AFFIRM study")
t.test(L$LogitRiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
t.test(L$LogitRiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
t.test(L$LogitRiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==0])
t.test(L$LogitRiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==1])
summary(L$LogitRiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
summary(L$LogitRiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
summary(L$LogitRiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==0])
summary(L$LogitRiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==1])
EffectModLogitRiskPreSpecified<-ggarrange(d,e,f, labels = c("A","B","C"))
###Risk
S$RELAPSE2year<-as.factor(S$RELAPSE2year)
d<-ggdensity(S, x = "RiskPreSpecified",merge=T,
add = "mean", rug = TRUE,xlim=c(0,1),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue","red"), xlab = "Risk score in DEFINE study")
t.test(S$RiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
t.test(S$RiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
t.test(S$RiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==0])
t.test(S$RiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==1])
summary(S$RiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==0])
summary(S$RiskPreSpecified[S$Treatment=="Dimethyl fumarate" & S$RELAPSE2year==1])
summary(S$RiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==0])
summary(S$RiskPreSpecified[S$Treatment=="Placebo" & S$RELAPSE2year==1])
K$RELAPSE2year<-as.factor(K$RELAPSE2year)
e<-ggdensity(K, x = "RiskPreSpecified",merge=T,
add = "mean", rug = TRUE,xlim=c(0,1),
color = "RELAPSE2year", fill = "Treatment",
palette = c("blue", "yellow", "red"), xlab = "Risk score in CONFIRM study")
t.test(K$RiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
t.test(K$RiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
t.test(K$RiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
t.test(K$RiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
t.test(K$RiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==0])
t.test(K$RiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==1])
summary(K$RiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==0])
summary(K$RiskPreSpecified[K$Treatment=="Dimethyl fumarate" & K$RELAPSE2year==1])
summary(K$RiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==0])
summary(K$RiskPreSpecified[K$Treatment=="Galtiramer acetate" & K$RELAPSE2year==1])
summary(K$RiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==0])
summary(K$RiskPreSpecified[K$Treatment=="Placebo" & K$RELAPSE2year==1])
L$RELAPSE2year<-as.factor(L$RELAPSE2year)
f<-ggdensity(L, x = "RiskPreSpecified",merge=T,
add = "mean", rug = TRUE, xlim=c(0,1),
color = "RELAPSE2year", fill = "Treatment",
palette = c("gray", "red"), xlab = "Risk score in AFFIRM study")
t.test(L$RiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
t.test(L$RiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
t.test(L$RiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==0])
t.test(L$RiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==1])
summary(L$RiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==0])
summary(L$RiskPreSpecified[L$Treatment=="Natalizumab" & L$RELAPSE2year==1])
summary(L$RiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==0])
summary(L$RiskPreSpecified[L$Treatment=="Placebo" & L$RELAPSE2year==1])
EffectModRiskPreSpecified<-ggarrange(d,e,f,labels = c("A","B","C"))
#boxplot(RiskData$RiskLASSO,RiskData$RiskPreSpecified,ylab=c("Baseline Risk score"), names = c("LASSO-Model","PreSpecified-Model"))
#remove no needed items
rm(a)
rm(b)
rm(c)
rm(d)
rm(e)
rm(f)
rm(K)
rm(L)
rm(S)