#######Data acquisition######
#' dataBT
#' This extracts the breath test data
#' @param channel the data base query
#' @keywords Fructose
#' @export
#' @examples #dataBT(channel)
dataBT<-function(channel){
dataBT <- sqlQuery(channel , "SELECT BreathTests.* FROM BreathTests")
}
#### Breath Tests ####
#' dataFructose
#' This extracts the raw fructose data from the database
#' @param dataBT the data frame
#' @keywords Fructose
#' @export
#' @examples #dataFructose(dataBT)
dataFructose<-function(dataBT){
#Creates a vector array of characters
#For fructose assessment:
#Just get the patients who had fructose breath tests:
dataFruc<-dataBT[grepl(".*\\d.*",dataBT$frucH2,perl=T),]
#Exclude columns that create confusion eg with H2 change
dataFruc<-dataBT[!grepl(".*Hydrogen and Methane level.*|.*ppm.*",dataBT$frucH2),]
#Select the columns you are interested in:
dataFruc<-dataFruc%>%select(frucTimePoint,frucH2)
dataFruc<-dataFruc[!is.na(dataFruc$frucTimePoint),]
#
VecArrFrucVal<-unlist(strsplit(dataFruc$frucH2, split="_"))
VecArrFrucTimePoint<-unlist(strsplit(dataFruc$frucTimePoint, split="_"))
Fruc<-as.data.frame(cbind(VecArrFrucVal,VecArrFrucTimePoint),stringsAsFactors=F)
Fruc<-paste(VecArrFrucVal,VecArrFrucTimePoint,sep=":")
#Split then combine
Fruc<-paste(Fruc, collapse = "")
Fruc<-as.data.frame(strsplit(Fruc, "H2"))
names(Fruc)<-c("main")
Fruc$main<-sub(":Time Point \\(min\\)","",Fruc$main)
Fruc$main<-gsub("(\\d+)\\a(\\d+)","\\1,\\2",Fruc$main)
Fruc$main<-gsub("\\a","",Fruc$main)
Fruc$main<-strsplit(Fruc$main, ",",perl=T)
return(Fruc)
#From here you can do individual graphs
}
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