###################################################
# tables.R
#
# Author: Helena Edlund
# Created on: 2017-07-26
# Last modified on:
# Purpose: Produce all project related tables contained in the report
# Dependencies: environmentPrep.R
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####################################################################################
#
# Exposure summary tables by covariates
#
####################################################################################
covList <- c("SEXM","RENAL","HEPATICL","RACEL","ETHNIC","ARAL","ECOG")
# Summarize categorical groups
CovSummary <- mySummary(covList, summarizeCat, exposureData)
CovSummary$Characteristic <- as.character(CovSummary$Characteristic)
# Add exposure
for(i in 1:length(covList)){
temp1 <-
ddply(exposureData, covList[i],
plyr::summarise,
AUC24h = paste0(signif(median(AUC24hss), digits=4)," [",
signif(quantile(AUC24hss, p = 0.025), digits=4), "-",
signif(quantile(AUC24hss, p = 0.975), digits=4), "]"),
Cmax = paste0(signif(median(Cmaxss), digits=4)," [",
signif(quantile(Cmaxss, p = 0.025), digits=4), "-",
signif(quantile(Cmaxss, p = 0.975), digits=4), "]"))
temp1$Characteristic <- covList[i]
names(temp1)[1] <- "Category"
if(i == 1){
temp2 <- temp1
} else {
temp2 <- rbind(temp2, temp1)
}
}
temp2$Category <- as.character(temp2$Category)
temp2$Category[is.na(temp2$Category)] <- "Missing"
# Merge
ExposureByCategory <-
dplyr::left_join(CovSummary, temp2, by=c("Characteristic", "Category"))
ExposureByCategory <-
ExposureByCategory[,!(colnames(ExposureByCategory)=="Percent")]
write.csv(ExposureByCategory,
file = paste(resCovModelDir, paste0("exposureByCatTab_", deliveryDate,".csv"), sep = "/"),
row.names = F)
# --------------------------------
# Organ impairment listings
# --------------------------------
# remove duplicated IDs, take the PK values without ARA
ids <- exposureData[duplicated(exposureData$NMSEQSID),"NMSEQSID"]
forListings <-
exposureData[!(exposureData$NMSEQSID %in% ids & exposureData$ARAL=="Yes"), ]
colsToIncludeRenal <-
c("OSTUDYID","NMSEQSID","OSID",
"RENAL","BCRCL","BEGFR",
"HEPATIC","BAST","BALT","BBILI",
"AUC24hss","Cmaxss")
colHeadersRenal <-
c("Study","ID","OSID",
"RenalImpairment","CrCL","eGFR",
"HepaticImpairment","AST","ALT","Bilirubin",
"PredictedAUC24hss","PredictedCmaxss")
colsToIncludeHepatic <-
c("OSTUDYID","NMSEQSID","OSID",
"HEPATIC","BAST","BALT","BBILI",
"RENAL","BCRCL","BEGFR",
"AUC24hss","Cmaxss")
colHeadersHepatic <-
c("Study","ID","OSID",
"HepaticImpairment","AST","ALT","Bilirubin",
"RenalImpairment","CrCL","eGFR",
"PredictedAUC24hss","PredictedCmaxss")
# ------------ Renal tab ------------------
forListingsRenal <-
forListings[forListings$RENAL != "Normal",]
## round to 4 significant digits
forListingsRenal$BCRCL <- signif(forListingsRenal$BCRCL, digits=4)
forListingsRenal$BEGFR <- signif(forListingsRenal$BEGFR, digits=4)
forListingsRenal$BBILI <- signif(forListingsRenal$BBILI, digits=4)
forListingsRenal <- forListingsRenal[ , colsToIncludeRenal]
names(forListingsRenal) <- colHeadersRenal
# Sort by study, impariment status and ID
forListingsRenal <-
forListingsRenal[order(forListingsRenal$Study,forListingsRenal$RenalImpairment,forListingsRenal$ID),]
write.csv(forListingsRenal, file = paste(resCovModelDir, "renalImparimentListing.csv",sep="/"),
quote = F, row.names = F)
# ------------ Hepatic tab ------------------
forListingsHepatic <-
forListings[forListings$HEPATIC != "Normal" & !is.na(forListings$HEPATIC),]
## round to 4 significant digits
forListingsHepatic$BCRCL <- signif(forListingsHepatic$BCRCL, digits=4)
forListingsHepatic$BEGFR <- signif(forListingsHepatic$BEGFR, digits=4)
forListingsHepatic$BBILI <- signif(forListingsHepatic$BBILI, digits=4)
forListingsHepatic<- forListingsHepatic[,colsToIncludeHepatic]
names(forListingsHepatic) <- colHeadersHepatic
# Sort by study, impariment status and ID
forListingsHepatic <-
forListingsHepatic[order(forListingsHepatic$Study,forListingsHepatic$HepaticImpairment, forListingsHepatic$ID),]
write.csv(forListingsHepatic, file = paste(resCovModelDir, "hepaticImparimentListing.csv",sep="/"),
quote = F, row.names = F)
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