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Created ROSALI screening version

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Corentin Choisy
2025-02-13 15:24:10 +01:00
parent 7712f8396f
commit f04322a9db
8 changed files with 3751 additions and 49 deletions
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90
RProject/Scripts/Analysis/aggregation.R
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@ -147,19 +147,35 @@ replicate_pcm_analysis<- function(df=NULL,treatment='TT',irtmodel='PCM2',method=
#### Create data.frame
#results <- c(sapply(c(2,4),function(x) paste0(x,c('A','B','C'))),sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
#results2 <- c(sapply(seq(10,20,2),function(x) paste0(x,c('A','B','C','D','E'))))
#results <- c(sapply(c(50,100,300),function(x) paste0(results,'_',x)))
#results2 <- c(sapply(c(50,100,300),function(x) paste0(results2,'_',x)))
#results <- c(results,results2)
results <- c(sapply(c(2,4),function(x) paste0(x,c('A','B','C'))),sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
results2 <- c(sapply(seq(10,20,2),function(x) paste0(x,c('A','B','C','D','E'))))
results <- c(sapply(c(50,100,300),function(x) paste0(results,'_',x)))
results <- c(sapply(c("050",100,300),function(x) paste0(results,'_',x)))
results2 <- c(sapply(c(50,100,300),function(x) paste0(results2,'_',x)))
results2 <- c(sapply(c("050",100,300),function(x) paste0(results2,'_',x)))
results <- sort(results)
results2 <- sort(results2)
results <- c(results,results2)
results <- c(sapply(1:16,function(x) c(results[x],results[x+16],results[x+32])),
sapply(1:30,function(x) c(results[x+48],results[x+30+48],results[x+60+48]))
)
results <- gsub('050',"50",results)
# results <- c(sapply(1:16,function(x) c(results[x],results[x+16],results[x+32])),
# sapply(1:30,function(x) c(results[x+48],results[x+30+48],results[x+60+48]))
# )
#### Compiler function
compile_simulation <- function(scenario) {
@ -302,21 +318,21 @@ res.dat[is.nan(res.dat)] <- NA
#### Create data.frame
results <- c(sapply(c(2,4),function(x) paste0(x,c('A','B','C'))),sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
results <- c(sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
results2 <- c(sapply(seq(10,20,2),function(x) paste0(x,c('A','B','C','D','E'))))
results <- c(sapply(c(50,100,300),function(x) paste0(results,'_',x)))
results <- c(sapply(c("050",100,300),function(x) paste0(results,'_',x)))
results2 <- c(sapply(c(50,100,300),function(x) paste0(results2,'_',x)))
results2 <- c(sapply(c("050",100,300),function(x) paste0(results2,'_',x)))
results <- sort(results)
results2 <- sort(results2)
results <- c(results,results2)
results <- c(sapply(1:16,function(x) c(results[x],results[x+16],results[x+32])),
sapply(1:30,function(x) c(results[x+48],results[x+30+48],results[x+60+48]))
)
results <- results[19:length(results)]
results <- gsub('050',"50",results)
#### Compiler function
@ -425,19 +441,23 @@ res.dat.dif$bias <- res.dat.dif$eff.size-res.dat.dif$m.beta
#### Create data.frame
results <- c(sapply(c(2,4),function(x) paste0(x,c('A','B','C'))),sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
results2 <- c(sapply(seq(10,20,2),function(x) paste0(x,c('A','B','C','D','E'))))
results <- c(sapply(c(50,100,300),function(x) paste0(results,'_',x)))
results <- c(sapply(c("050",100,300),function(x) paste0(results,'_',x)))
results2 <- c(sapply(c(50,100,300),function(x) paste0(results2,'_',x)))
results2 <- c(sapply(c("050",100,300),function(x) paste0(results2,'_',x)))
results <- sort(results)
results2 <- sort(results2)
results <- c(results,results2)
results <- c(sapply(1:16,function(x) c(results[x],results[x+16],results[x+32])),
sapply(1:30,function(x) c(results[x+48],results[x+30+48],results[x+60+48]))
)
results <- gsub('050',"50",results)
#### Compiler function
@ -719,19 +739,36 @@ res.dat.dif.rosali$bias <- res.dat.dif.rosali$eff.size-res.dat.dif.rosali$m.beta
#### Create data.frame
#results <- c(sapply(c(2,4),function(x) paste0(x,c('A','B','C'))),sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
#results2 <- c(sapply(seq(10,20,2),function(x) paste0(x,c('A','B','C','D','E'))))
#results <- c(sapply(c(50,100,300),function(x) paste0(results,'_',x)))
#results2 <- c(sapply(c(50,100,300),function(x) paste0(results2,'_',x)))
#results <- c(results,results2)
#results <- c(sapply(1:16,function(x) c(results[x],results[x+16],results[x+32])),
# sapply(1:30,function(x) c(results[x+48],results[x+30+48],results[x+60+48]))
#)
results <- c(sapply(c(2,4),function(x) paste0(x,c('A','B','C'))),sapply(c(6,8),function(x) paste0(x,c('A','B','C','D','E'))))
results2 <- c(sapply(seq(10,20,2),function(x) paste0(x,c('A','B','C','D','E'))))
results <- c(sapply(c(50,100,300),function(x) paste0(results,'_',x)))
results <- c(sapply(c("050",100,300),function(x) paste0(results,'_',x)))
results2 <- c(sapply(c(50,100,300),function(x) paste0(results2,'_',x)))
results2 <- c(sapply(c("050",100,300),function(x) paste0(results2,'_',x)))
results <- sort(results)
results2 <- sort(results2)
results <- c(results,results2)
results <- c(sapply(1:16,function(x) c(results[x],results[x+16],results[x+32])),
sapply(1:30,function(x) c(results[x+48],results[x+30+48],results[x+60+48]))
)
results <- gsub('050',"50",results)
#### Compiler function
@ -985,6 +1022,7 @@ res.dat.dif.resali[substr(res.dat.dif.resali$scenario,1,2)%in%seq(10,16,2),'nb.d
res.dat.dif.resali[substr(res.dat.dif.resali$scenario,1,2)%in%seq(18,20,2),'nb.dif'] <- 3
res.dat.dif.resali[res.dat.dif.resali$N==50,"dif.size"] <- res.dat.dif.resali[which(res.dat.dif.resali$N==50)+1,"dif.size"]
res.dat.dif.resali[res.dat.dif.resali$scenario.type=="B",]$eff.size <- 0.2
res.dat.dif.resali[res.dat.dif.resali$scenario=="20E" & res.dat.dif.resali$N==50,]$dif.size <- -0.5
res.dat.dif.resali[res.dat.dif.resali$scenario.type=="C" & res.dat.dif.resali$dif.size==0,]$eff.size <- 0.4
res.dat.dif.resali[res.dat.dif.resali$scenario.type=="C" & res.dat.dif.resali$dif.size!=0,]$eff.size <- 0.2
res.dat.dif.resali[res.dat.dif.resali$scenario.type=="D" & res.dat.dif.resali$dif.size!=0,]$eff.size <- 0.4
@ -1203,7 +1241,8 @@ res.dat.article.rosali.2$bias <- -1*res.dat.article.rosali.2$bias
res.dat.article.rosali.2.nodif <- res.dat.article.rosali.2[res.dat.article.rosali.2$nb.dif==0,]
# STRATEGY 3 - RESIDIF
res.dat.dif.resali[1,"N"] <- 50
res.dat.dif.resali$dif.size <- res.dat.dif.rosali$dif.size
res.dat.article.residif <- res.dat.dif.resali[,c("N","J","eff.size","nb.dif","dif.size",
"m.beta","bias","true.value.in.ci.p","h0.rejected.p",
"theoretical.power")]
@ -1219,7 +1258,7 @@ res.dat.article.residif[res.dat.article.residif$nb.dif==0,"true.gamma"] <- NA
res.dat.article.residif[is.na(res.dat.article.residif)] <- " "
res.dat.article.residif$bias <- -1*res.dat.article.residif$bias
res.dat.article.residif <- reshape(res.dat.article.residif,
direction = "wide", idvar = c("J","true.beta","nb.dif",'true.gamma'),timevar = "N" )
direction = "wide", idvar = c("J","true.beta","nb.dif",'true.gamma'),timevar = "N")
res.dat.article.residif.dif <- res.dat.article.residif[res.dat.article.residif$nb.dif>0,]
write.csv(res.dat.article.residif.dif,"/home/corentin/Documents/These/Valorisation/Articles/Simulations 1/Tables/res_RESIDIF_DIF.csv")
res.dat.article.residif.nodif <- res.dat.article.residif[res.dat.article.residif$nb.dif==0,]
@ -1240,6 +1279,7 @@ res.dat.article.residif.2[res.dat.article.residif.2$nb.dif==0,"true.gamma"] <- N
res.dat.article.residif.2[is.na(res.dat.article.residif.2)] <- " "
res.dat.article.residif.2$bias <- -1*res.dat.article.residif.2$bias
res.dat.article.residif.2.nodif <- res.dat.article.residif.2[res.dat.article.residif.2$nb.dif==0,]
res.dat.article.residif.dif
# STRATEGY 4 - PERFECT-DIF