R/calculate_outcome.R
In jonathanelee1993/clinicalresponsepackage: Seizure and Epileptic Medication Response Package
#' Calculate outcome
#'
#' This function allow you to calculate a patient's outcome (i.e. it creates the OUTCOME_DATA_CLINICAL
#' file and the MED_SEIZURE_OUTCOME_BAR_TABLE files, as well as creates bar graphs for seizure score,
#' med score, and outcome for each period of 30 days)
#' @keywords outcome
#' @export
#' @import ggplot2
#' @import openxlsx
#' @examples
#' calculate_outcome()
calculate_outcome <- function() {
print("Input the identifier that signify the patient we are doing calculations for")
print("Example: FILA")
patient <- readline(prompt="Enter here: ")
# Directory for the clinic visit source file: G:\MySQL Database\Demographics
print("Input the directory that you wish to draw the CLINIC_VISIT_SOURCE file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
cvs <- "CLINIC_VISIT_SOURCE.xlsx"
cvs <- read.xlsx(cvs,sheet=1,detectDates=TRUE)
print("Type 'yes' if the DEMOGRAPHICS_SOURCE file can be found in the same folder as the CLINIC_VISIT_SOURCE table. Type 'no' if it is in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to draw the DEMOGRAPHICS_SOURCE file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
demo <- "DEMOGRAPHICS_SOURCE.xlsx"
demo <- read.xlsx(demo,sheet=1,detectDates=TRUE)
print("Type 'yes' if this patient's SEIZURE_DATA_CLINICAL file can be found in the same folder as the DEMOGRAPHICS_SOURCE table. Type 'no' if it is in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to draw this patient's SEIZURE_DATA_CLINICAL file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
s.clinical <- "SEIZURE_DATA_CLINICAL.xlsx"
s.clinical <- gsub(" ","",paste(patient,"_",s.clinical))
s.clinical <- read.xlsx(s.clinical,sheet=1,detectDates=TRUE)
print("Type 'yes' if this patient's MED_DATA_CLINICAL file can be found in the same folder as this patient's SEIZURE_DATA_CLINICAL table. Type 'no' if it is in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to draw this patient's MED_DATA_CLINICAL file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
m.clinical <- "MED_DATA_CLINICAL.xlsx"
m.clinical <- gsub(" ","",paste(patient,"_",m.clinical))
m.clinical <- read.xlsx(m.clinical,sheet=1,detectDates=TRUE)
mrnumber <- unique(s.clinical$MRNUMBER)
name <- unique(demo[demo$MRNUMBER==mrnumber,colnames(demo)=="FIRST"])
cvs <- cvs[!is.na(cvs$MRNUMBER),]
cvs <- unique(cvs[cvs$MRNUMBER==mrnumber,colnames(cvs)=="MRNUMBER" | colnames(cvs)=="DATE"])
cvs$DATE <- as.Date(cvs$DATE)
## Create and save FILA_OUTCOME_DATA_CLINICAL.xlsx
outcome <- data.frame(MRNUMBER=integer(),DATE=as.Date(as.character()),DAY_TYPE=integer(),OUTCOME_DAY=integer(),OUTCOME_30_DAYS=integer())
outcome[1:dim(s.clinical)[1],] <- c(s.clinical[,colnames(s.clinical)=="MRNUMBER" | colnames(s.clinical)=="DATE" | colnames(s.clinical)=="DAY_TYPE"],NA,NA)
outcome[,4] <- (s.clinical$SEIZURE_RESPONSE_DAY+m.clinical$MED_RESPONSE_DAY)/2
outcome[,5] <- (s.clinical$SEIZURE_RESPONSE_30_DAYS+m.clinical$MED_RESPONSE_30_DAYS)/2
print("Type 'yes' if you wish to save the OUTCOME_DATA_CLINICAL file in the same folder as this patient's MED_DATA_CLINICAL table. Type 'no' if you would like for it to be in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to save this patient's OUTCOME_DATA_CLINICAL file in")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
print(paste("Saving data clinical outcome table as",gsub(" ","",paste(patient,"_OUTCOME_DATA_CLINICAL.xlsx")),"in directory",getwd()))
xlsx <- "OUTCOME_DATA_CLINICAL.xlsx"
xlsx <- gsub(" ","",paste(patient,"_",xlsx))
xlsx::write.xlsx2(outcome,file=xlsx,showNA=FALSE,row.names=FALSE)
bar_table_dates <- cvs$DATE[which(cvs$DATE %in% outcome$DATE)]
mrn <- cvs$MRNUMBER[1:length(bar_table_dates)]
bar_table_dates <- cbind.data.frame(mrn,bar_table_dates)
seizure_bar_table <- data.frame(MRNUMBER=integer(),START_DATE=as.Date(as.character()),END_DATE=as.Date(as.character()),SEIZURE_FREE=integer(),SEIZURE_0_TO_50=integer(),SEIZURE_50_TO_100=integer(),SEIZURE_GREATER_THAN_100=integer())
seizure_bar_table[1:dim(bar_table_dates)[1],] <- NA
seizure_bar_table$MRNUMBER <- mrn
seizure_bar_table$START_DATE <- bar_table_dates$bar_table_dates
seizure_bar_table$END_DATE[1:dim(seizure_bar_table)[1]-1] <- bar_table_dates$bar_table_dates[2:dim(seizure_bar_table)[1]]-1
seizure_bar_table$END_DATE[dim(seizure_bar_table)[1]] <- max(outcome$DATE)
med_bar_table <- data.frame(MED_FREE=integer(),MED_0_TO_50=integer(),MED_50_TO_100=integer(),MED_GREATER_THAN_100=integer())
med_bar_table[1:dim(bar_table_dates)[1],] <- NA
outcome_bar_table <- data.frame(OUTCOME_FREE=integer(),OUTCOME_0_TO_50=integer(),OUTCOME_50_TO_100=integer(),OUTCOME_GREATER_THAN_100=integer())
outcome_bar_table[1:dim(bar_table_dates)[1],] <- NA
dates <- data.frame(TABLEDATES=as.Date(as.character()))
dates[1:(length(seizure_bar_table$START_DATE)+1),] <- NA
dates[1:length(seizure_bar_table$START_DATE),] <- seizure_bar_table$START_DATE
dates[dim(dates)[1],] <- seizure_bar_table$END_DATE[length(seizure_bar_table$END_DATE)]+1
for (j in 2:length(dates$TABLEDATES)) {
## Create table of values used to create FILA_SEIZURE_BAR_GRAPH.jpeg
s.totalnumdays <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j],])
s.totalfreedays <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY==0,])/s.totalnumdays
s.total0to50days <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY>0 & s.clinical$SEIZURE_RESPONSE_DAY<=50,])/s.totalnumdays
s.total50to100days <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY>50 & s.clinical$SEIZURE_RESPONSE_DAY<=100,])/s.totalnumdays
s.totalgreater100days <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY>100,])/s.totalnumdays
seizure_bar_table$SEIZURE_FREE[j-1] <- round(s.totalfreedays*100,2)
seizure_bar_table$SEIZURE_0_TO_50[j-1] <- round(s.total0to50days*100,2)
seizure_bar_table$SEIZURE_50_TO_100[j-1] <- round(s.total50to100days*100,2)
seizure_bar_table$SEIZURE_GREATER_THAN_100[j-1] <- round(s.totalgreater100days*100,2)
## Create table of values used to create FILA_MED_BAR_GRAPH.jpeg
m.totalnumdays <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j],])
m.totalfreedays <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY==0,])/m.totalnumdays
m.total0to50days <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY>0 & m.clinical$MED_RESPONSE_DAY<=50,])/m.totalnumdays
m.total50to100days <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY>50 & m.clinical$MED_RESPONSE_DAY<=100,])/m.totalnumdays
m.totalgreater100days <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY>100,])/m.totalnumdays
med_bar_table$MED_FREE[j-1] <- round(m.totalfreedays*100,2)
med_bar_table$MED_0_TO_50[j-1] <- round(m.total0to50days*100,2)
med_bar_table$MED_50_TO_100[j-1] <- round(m.total50to100days*100,2)
med_bar_table$MED_GREATER_THAN_100[j-1] <- round(m.totalgreater100days*100,2)
## Create table of values used to create FILA_OUTCOME_BAR_GRAPH.jpeg
o.totalnumdays <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j],])
o.totalfreedays <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY==0,])/o.totalnumdays
o.total0to50days <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY>0 & outcome$OUTCOME_DAY<=50,])/o.totalnumdays
o.total50to100days <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY>50 & outcome$OUTCOME_DAY<=100,])/o.totalnumdays
o.totalgreater100days <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY>100,])/o.totalnumdays
outcome_bar_table$OUTCOME_FREE[j-1] <- round(o.totalfreedays*100,2)
outcome_bar_table$OUTCOME_0_TO_50[j-1] <- round(o.total0to50days*100,2)
outcome_bar_table$OUTCOME_50_TO_100[j-1] <- round(o.total50to100days*100,2)
outcome_bar_table$OUTCOME_GREATER_THAN_100[j-1] <- round(o.totalgreater100days*100,2)
}
s.graph <- function(s.bar_graph,t,di) {
if (di==TRUE) {
s.bar_graph$PERIOD <- seq(1:(length(s.bar_graph$PERIOD)))
s.bar_graph$PERIOD <- paste("Month",s.bar_graph$PERIOD)
}
seizure_bar_graph <- ggplot(data=s.bar_graph,aes(x=PERIOD,y=PERCENT,fill=SECTION,colour=SECTION))
seizure_bar_graph <- seizure_bar_graph + geom_bar(stat="identity")
seizure_bar_graph <- seizure_bar_graph + scale_colour_manual(name="",
breaks=c("Seizure Free","Seizures 0-50%","Seizures 50-100%","Seizures Worse"),
values=c("Seizure Free"="black",
"Seizures 0-50%"="black",
"Seizures 50-100%"="black",
"Seizures Worse"="black"))
seizure_bar_graph <- seizure_bar_graph + scale_fill_manual(name="",
breaks=c("Seizure Free","Seizures 0-50%","Seizures 50-100%","Seizures Worse"),
values=c("white","green","yellow","red"))
seizure_bar_graph <- seizure_bar_graph + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,siz=3))
seizure_bar_graph <- seizure_bar_graph + labs(title=paste(gsub(" ","",paste(t,"'s")),"Seizure Response"),
x="Time on Therapy",
y="% of Time Period on Therapy")
seizure_bar_graph <- seizure_bar_graph + theme(axis.title.y=element_text(angle=90,size=6))
return(seizure_bar_graph)
}
m.graph <- function(m.bar_graph,t,di) {
med_bar_graph <- ggplot(data=m.bar_graph,aes(x=PERIOD,y=PERCENT,fill=SECTION,colour=SECTION))
med_bar_graph <- med_bar_graph + geom_bar(stat="identity")
med_bar_graph <- med_bar_graph + scale_colour_manual(name="",
breaks=c("Med Free","Meds 0-50%","Meds 50-100%","Meds Worse"),
values=c("Med Free"="black",
"Meds 0-50%"="black",
"Meds 50-100%"="black",
"Meds Worse"="black"))
med_bar_graph <- med_bar_graph + scale_fill_manual(name="",
breaks=c("Med Free","Meds 0-50%","Meds 50-100%","Meds Worse"),
values=c("white","green","yellow","red"))
med_bar_graph <- med_bar_graph + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,size=4))
med_bar_graph <- med_bar_graph + labs(title=paste(gsub(" ","",paste(t,"'s")),"Med Response"),
x="Time on Therapy",
y="% of Time Period on Therapy")
med_bar_graph <- med_bar_graph + theme(axis.title.y=element_text(angle=90,size=6))
return(med_bar_graph)
}
o.graph <- function(o.bar_graph,t,di) {
outcome_bar_graph <- ggplot(data=o.bar_graph,aes(x=PERIOD,y=PERCENT,fill=SECTION,colour=SECTION))
outcome_bar_graph <- outcome_bar_graph + geom_bar(stat="identity")
outcome_bar_graph <- outcome_bar_graph + scale_colour_manual(name="",
breaks=c("Outcome Free","Outcome 0-50%","Outcome 50-100%","Outcome Worse"),
values=c("Outcome Free"="black",
"Outcome 0-50%"="black",
"Outcome 50-100%"="black",
"Outcome Worse"="black"))
outcome_bar_graph <- outcome_bar_graph + scale_fill_manual(name="",
breaks=c("Outcome Free","Outcome 0-50%","Outcome 50-100%","Outcome Worse"),
values=c("green","yellow","white","red"))
outcome_bar_graph <- outcome_bar_graph + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,size=4))
outcome_bar_graph <- outcome_bar_graph + labs(title=paste(gsub(" ","",paste(t,"'s")),"Outcome Response"),
x="Time on Therapy",
y="% of Time Period on Therapy")
outcome_bar_graph <- outcome_bar_graph + theme(axis.title.y=element_text(angle=90,size=6))
return(outcome_bar_graph)
}
## Create and save FILA_SEIZURE_BAR_GRAPH.jpeg
s.bar_graph <- data.frame(PERIOD=character(),PERCENT=integer(),SECTION=character(),stringsAsFactors=FALSE)
s.bar_graph[1:((dim(seizure_bar_table)[1])*4),c("PERIOD")] <- rep(as.character(seizure_bar_table$START_DATE[1:length(seizure_bar_table$START_DATE)]),each=4)
s.bar_graph[,c("PERIOD")] <- paste(as.character(seizure_bar_table$START_DATE[ceiling(as.numeric(rownames(s.bar_graph))/4)]),"-",as.character(seizure_bar_table$END_DATE[ceiling(as.numeric(rownames(s.bar_graph))/4)]))
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==1,c("PERCENT")] <- seizure_bar_table$SEIZURE_FREE
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==1,c("SECTION")] <- "Seizure Free"
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==2,c("PERCENT")] <- seizure_bar_table$SEIZURE_0_TO_50
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==2,c("SECTION")] <- "Seizures 0-50%"
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==3,c("PERCENT")] <- seizure_bar_table$SEIZURE_50_TO_100
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==3,c("SECTION")] <- "Seizures 50-100%"
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==0,c("PERCENT")] <- seizure_bar_table$SEIZURE_GREATER_THAN_100
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==0,c("SECTION")] <- "Seizures Worse"
seizure_bar_graph <- s.graph(s.bar_graph,name,FALSE)
## Create and save FILA_MED_BAR_GRAPH.jpeg
m.bar_graph <- data.frame(PERIOD=character(),PERCENT=integer(),SECTION=character(),stringsAsFactors=FALSE)
m.bar_graph[1:((dim(seizure_bar_table)[1])*4),c("PERIOD")] <- rep(as.character(seizure_bar_table$START_DATE[1:length(seizure_bar_table$START_DATE)]),each=4)
m.bar_graph[,c("PERIOD")] <- paste(as.character(seizure_bar_table$START_DATE[ceiling(as.numeric(rownames(m.bar_graph))/4)]),"-",as.character(seizure_bar_table$END_DATE[ceiling(as.numeric(rownames(m.bar_graph))/4)]))
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==1,c("PERCENT")] <- med_bar_table$MED_FREE
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==1,c("SECTION")] <- "Med Free"
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==2,c("PERCENT")] <- med_bar_table$MED_0_TO_50
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==2,c("SECTION")] <- "Meds 0-50%"
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==3,c("PERCENT")] <- med_bar_table$MED_50_TO_100
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==3,c("SECTION")] <- "Meds 50-100%"
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==0,c("PERCENT")] <- med_bar_table$MED_GREATER_THAN_100
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==0,c("SECTION")] <- "Meds Worse"
med_bar_graph <- m.graph(m.bar_graph,name,FALSE)
## Create and save FILA_OUTCOME_BAR_GRAPH.jpeg
o.bar_graph <- data.frame(PERIOD=character(),PERCENT=integer(),SECTION=character(),stringsAsFactors=FALSE)
o.bar_graph[1:((dim(seizure_bar_table)[1])*4),c("PERIOD")] <- rep(as.character(seizure_bar_table$START_DATE[1:length(seizure_bar_table$START_DATE)]),each=4)
o.bar_graph[,c("PERIOD")] <- paste(as.character(seizure_bar_table$START_DATE[ceiling(as.numeric(rownames(o.bar_graph))/4)]),"-",as.character(seizure_bar_table$END_DATE[ceiling(as.numeric(rownames(o.bar_graph))/4)]))
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==1,c("PERCENT")] <- outcome_bar_table$OUTCOME_FREE
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==1,c("SECTION")] <- "Outcome Free"
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==2,c("PERCENT")] <- outcome_bar_table$OUTCOME_0_TO_50
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==2,c("SECTION")] <- "Outcome 0-50%"
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==3,c("PERCENT")] <- outcome_bar_table$OUTCOME_50_TO_100
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==3,c("SECTION")] <- "Outcome 50-100%"
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==0,c("PERCENT")] <- outcome_bar_table$OUTCOME_GREATER_THAN_100
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==0,c("SECTION")] <- "Outcome Worse"
outcome_bar_graph <- o.graph(o.bar_graph,name,FALSE)
print("Type 'yes' if you wish to save all graphs in the same folder as this patient's OUTCOME_DATA_CLINICAL file. Type 'no' if you would like for it to be in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to save this patient's graphs in")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
file <- gsub(" ","",paste(patient,"_SEIZURE_BAR_GRAPH.jpeg"))
ggsave(seizure_bar_graph,filename=file,width=6,height=4)
print("Seizure bar graph created and saved")
file <- gsub(" ","",paste(patient,"_MED_BAR_GRAPH.jpeg"))
ggsave(med_bar_graph,filename=file,width=6,height=4)
print("Med bar graph created and saved")
file <- gsub(" ","",paste(patient,"_OUTCOME_BAR_GRAPH.jpeg"))
ggsave(outcome_bar_graph,filename=file,width=6,height=4)
print("Outcome bar graph created and saved")
print("Type 'yes' if you wish to save this patient's MED_SEIZURE_OUTCOME_BAR_TABLE file in the same folder as this patient's OUTCOME_DATA_CLINICAL file. Type 'no' if you would like for it to be in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to save this patient's MED_SEIZURE_OUTCOME_BAR_TABLE file in")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
## Create and save FILA_MED_SEIZURE_OUTCOME_BAR_TABLE.xlsx
print(paste("Saving med/seizure/outcome bar table as",gsub(" ","",paste(patient,"_MED_SEIZURE_OUTCOME_BAR_TABLE.xlsx")),"in directory",getwd()))
bar_table <- cbind.data.frame(seizure_bar_table,med_bar_table,outcome_bar_table)
xlsx <- "MED_SEIZURE_OUTCOME_BAR_TABLE.xlsx"
xlsx <- gsub(" ","",paste(patient,"_",xlsx))
xlsx::write.xlsx2(bar_table,file=xlsx,showNA=FALSE,row.names=FALSE)
}
jonathanelee1993/clinicalresponsepackage documentation built on May 19, 2019, 7:28 p.m.
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#' Calculate outcome
#'
#' This function allow you to calculate a patient's outcome (i.e. it creates the OUTCOME_DATA_CLINICAL
#' file and the MED_SEIZURE_OUTCOME_BAR_TABLE files, as well as creates bar graphs for seizure score,
#' med score, and outcome for each period of 30 days)
#' @keywords outcome
#' @export
#' @import ggplot2
#' @import openxlsx
#' @examples
#' calculate_outcome()
calculate_outcome <- function() {
print("Input the identifier that signify the patient we are doing calculations for")
print("Example: FILA")
patient <- readline(prompt="Enter here: ")
# Directory for the clinic visit source file: G:\MySQL Database\Demographics
print("Input the directory that you wish to draw the CLINIC_VISIT_SOURCE file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
cvs <- "CLINIC_VISIT_SOURCE.xlsx"
cvs <- read.xlsx(cvs,sheet=1,detectDates=TRUE)
print("Type 'yes' if the DEMOGRAPHICS_SOURCE file can be found in the same folder as the CLINIC_VISIT_SOURCE table. Type 'no' if it is in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to draw the DEMOGRAPHICS_SOURCE file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
demo <- "DEMOGRAPHICS_SOURCE.xlsx"
demo <- read.xlsx(demo,sheet=1,detectDates=TRUE)
print("Type 'yes' if this patient's SEIZURE_DATA_CLINICAL file can be found in the same folder as the DEMOGRAPHICS_SOURCE table. Type 'no' if it is in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to draw this patient's SEIZURE_DATA_CLINICAL file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
s.clinical <- "SEIZURE_DATA_CLINICAL.xlsx"
s.clinical <- gsub(" ","",paste(patient,"_",s.clinical))
s.clinical <- read.xlsx(s.clinical,sheet=1,detectDates=TRUE)
print("Type 'yes' if this patient's MED_DATA_CLINICAL file can be found in the same folder as this patient's SEIZURE_DATA_CLINICAL table. Type 'no' if it is in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to draw this patient's MED_DATA_CLINICAL file from")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
m.clinical <- "MED_DATA_CLINICAL.xlsx"
m.clinical <- gsub(" ","",paste(patient,"_",m.clinical))
m.clinical <- read.xlsx(m.clinical,sheet=1,detectDates=TRUE)
mrnumber <- unique(s.clinical$MRNUMBER)
name <- unique(demo[demo$MRNUMBER==mrnumber,colnames(demo)=="FIRST"])
cvs <- cvs[!is.na(cvs$MRNUMBER),]
cvs <- unique(cvs[cvs$MRNUMBER==mrnumber,colnames(cvs)=="MRNUMBER" | colnames(cvs)=="DATE"])
cvs$DATE <- as.Date(cvs$DATE)
## Create and save FILA_OUTCOME_DATA_CLINICAL.xlsx
outcome <- data.frame(MRNUMBER=integer(),DATE=as.Date(as.character()),DAY_TYPE=integer(),OUTCOME_DAY=integer(),OUTCOME_30_DAYS=integer())
outcome[1:dim(s.clinical)[1],] <- c(s.clinical[,colnames(s.clinical)=="MRNUMBER" | colnames(s.clinical)=="DATE" | colnames(s.clinical)=="DAY_TYPE"],NA,NA)
outcome[,4] <- (s.clinical$SEIZURE_RESPONSE_DAY+m.clinical$MED_RESPONSE_DAY)/2
outcome[,5] <- (s.clinical$SEIZURE_RESPONSE_30_DAYS+m.clinical$MED_RESPONSE_30_DAYS)/2
print("Type 'yes' if you wish to save the OUTCOME_DATA_CLINICAL file in the same folder as this patient's MED_DATA_CLINICAL table. Type 'no' if you would like for it to be in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to save this patient's OUTCOME_DATA_CLINICAL file in")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
print(paste("Saving data clinical outcome table as",gsub(" ","",paste(patient,"_OUTCOME_DATA_CLINICAL.xlsx")),"in directory",getwd()))
xlsx <- "OUTCOME_DATA_CLINICAL.xlsx"
xlsx <- gsub(" ","",paste(patient,"_",xlsx))
xlsx::write.xlsx2(outcome,file=xlsx,showNA=FALSE,row.names=FALSE)
bar_table_dates <- cvs$DATE[which(cvs$DATE %in% outcome$DATE)]
mrn <- cvs$MRNUMBER[1:length(bar_table_dates)]
bar_table_dates <- cbind.data.frame(mrn,bar_table_dates)
seizure_bar_table <- data.frame(MRNUMBER=integer(),START_DATE=as.Date(as.character()),END_DATE=as.Date(as.character()),SEIZURE_FREE=integer(),SEIZURE_0_TO_50=integer(),SEIZURE_50_TO_100=integer(),SEIZURE_GREATER_THAN_100=integer())
seizure_bar_table[1:dim(bar_table_dates)[1],] <- NA
seizure_bar_table$MRNUMBER <- mrn
seizure_bar_table$START_DATE <- bar_table_dates$bar_table_dates
seizure_bar_table$END_DATE[1:dim(seizure_bar_table)[1]-1] <- bar_table_dates$bar_table_dates[2:dim(seizure_bar_table)[1]]-1
seizure_bar_table$END_DATE[dim(seizure_bar_table)[1]] <- max(outcome$DATE)
med_bar_table <- data.frame(MED_FREE=integer(),MED_0_TO_50=integer(),MED_50_TO_100=integer(),MED_GREATER_THAN_100=integer())
med_bar_table[1:dim(bar_table_dates)[1],] <- NA
outcome_bar_table <- data.frame(OUTCOME_FREE=integer(),OUTCOME_0_TO_50=integer(),OUTCOME_50_TO_100=integer(),OUTCOME_GREATER_THAN_100=integer())
outcome_bar_table[1:dim(bar_table_dates)[1],] <- NA
dates <- data.frame(TABLEDATES=as.Date(as.character()))
dates[1:(length(seizure_bar_table$START_DATE)+1),] <- NA
dates[1:length(seizure_bar_table$START_DATE),] <- seizure_bar_table$START_DATE
dates[dim(dates)[1],] <- seizure_bar_table$END_DATE[length(seizure_bar_table$END_DATE)]+1
for (j in 2:length(dates$TABLEDATES)) {
## Create table of values used to create FILA_SEIZURE_BAR_GRAPH.jpeg
s.totalnumdays <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j],])
s.totalfreedays <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY==0,])/s.totalnumdays
s.total0to50days <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY>0 & s.clinical$SEIZURE_RESPONSE_DAY<=50,])/s.totalnumdays
s.total50to100days <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY>50 & s.clinical$SEIZURE_RESPONSE_DAY<=100,])/s.totalnumdays
s.totalgreater100days <- nrow(s.clinical[s.clinical$DATE>=dates$TABLEDATES[j-1] & s.clinical$DATE<dates$TABLEDATES[j] & s.clinical$SEIZURE_RESPONSE_DAY>100,])/s.totalnumdays
seizure_bar_table$SEIZURE_FREE[j-1] <- round(s.totalfreedays*100,2)
seizure_bar_table$SEIZURE_0_TO_50[j-1] <- round(s.total0to50days*100,2)
seizure_bar_table$SEIZURE_50_TO_100[j-1] <- round(s.total50to100days*100,2)
seizure_bar_table$SEIZURE_GREATER_THAN_100[j-1] <- round(s.totalgreater100days*100,2)
## Create table of values used to create FILA_MED_BAR_GRAPH.jpeg
m.totalnumdays <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j],])
m.totalfreedays <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY==0,])/m.totalnumdays
m.total0to50days <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY>0 & m.clinical$MED_RESPONSE_DAY<=50,])/m.totalnumdays
m.total50to100days <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY>50 & m.clinical$MED_RESPONSE_DAY<=100,])/m.totalnumdays
m.totalgreater100days <- nrow(m.clinical[m.clinical$DATE>=dates$TABLEDATES[j-1] & m.clinical$DATE<dates$TABLEDATES[j] & m.clinical$MED_RESPONSE_DAY>100,])/m.totalnumdays
med_bar_table$MED_FREE[j-1] <- round(m.totalfreedays*100,2)
med_bar_table$MED_0_TO_50[j-1] <- round(m.total0to50days*100,2)
med_bar_table$MED_50_TO_100[j-1] <- round(m.total50to100days*100,2)
med_bar_table$MED_GREATER_THAN_100[j-1] <- round(m.totalgreater100days*100,2)
## Create table of values used to create FILA_OUTCOME_BAR_GRAPH.jpeg
o.totalnumdays <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j],])
o.totalfreedays <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY==0,])/o.totalnumdays
o.total0to50days <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY>0 & outcome$OUTCOME_DAY<=50,])/o.totalnumdays
o.total50to100days <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY>50 & outcome$OUTCOME_DAY<=100,])/o.totalnumdays
o.totalgreater100days <- nrow(outcome[outcome$DATE>=dates$TABLEDATES[j-1] & outcome$DATE<dates$TABLEDATES[j] & outcome$OUTCOME_DAY>100,])/o.totalnumdays
outcome_bar_table$OUTCOME_FREE[j-1] <- round(o.totalfreedays*100,2)
outcome_bar_table$OUTCOME_0_TO_50[j-1] <- round(o.total0to50days*100,2)
outcome_bar_table$OUTCOME_50_TO_100[j-1] <- round(o.total50to100days*100,2)
outcome_bar_table$OUTCOME_GREATER_THAN_100[j-1] <- round(o.totalgreater100days*100,2)
}
s.graph <- function(s.bar_graph,t,di) {
if (di==TRUE) {
s.bar_graph$PERIOD <- seq(1:(length(s.bar_graph$PERIOD)))
s.bar_graph$PERIOD <- paste("Month",s.bar_graph$PERIOD)
}
seizure_bar_graph <- ggplot(data=s.bar_graph,aes(x=PERIOD,y=PERCENT,fill=SECTION,colour=SECTION))
seizure_bar_graph <- seizure_bar_graph + geom_bar(stat="identity")
seizure_bar_graph <- seizure_bar_graph + scale_colour_manual(name="",
breaks=c("Seizure Free","Seizures 0-50%","Seizures 50-100%","Seizures Worse"),
values=c("Seizure Free"="black",
"Seizures 0-50%"="black",
"Seizures 50-100%"="black",
"Seizures Worse"="black"))
seizure_bar_graph <- seizure_bar_graph + scale_fill_manual(name="",
breaks=c("Seizure Free","Seizures 0-50%","Seizures 50-100%","Seizures Worse"),
values=c("white","green","yellow","red"))
seizure_bar_graph <- seizure_bar_graph + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,siz=3))
seizure_bar_graph <- seizure_bar_graph + labs(title=paste(gsub(" ","",paste(t,"'s")),"Seizure Response"),
x="Time on Therapy",
y="% of Time Period on Therapy")
seizure_bar_graph <- seizure_bar_graph + theme(axis.title.y=element_text(angle=90,size=6))
return(seizure_bar_graph)
}
m.graph <- function(m.bar_graph,t,di) {
med_bar_graph <- ggplot(data=m.bar_graph,aes(x=PERIOD,y=PERCENT,fill=SECTION,colour=SECTION))
med_bar_graph <- med_bar_graph + geom_bar(stat="identity")
med_bar_graph <- med_bar_graph + scale_colour_manual(name="",
breaks=c("Med Free","Meds 0-50%","Meds 50-100%","Meds Worse"),
values=c("Med Free"="black",
"Meds 0-50%"="black",
"Meds 50-100%"="black",
"Meds Worse"="black"))
med_bar_graph <- med_bar_graph + scale_fill_manual(name="",
breaks=c("Med Free","Meds 0-50%","Meds 50-100%","Meds Worse"),
values=c("white","green","yellow","red"))
med_bar_graph <- med_bar_graph + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,size=4))
med_bar_graph <- med_bar_graph + labs(title=paste(gsub(" ","",paste(t,"'s")),"Med Response"),
x="Time on Therapy",
y="% of Time Period on Therapy")
med_bar_graph <- med_bar_graph + theme(axis.title.y=element_text(angle=90,size=6))
return(med_bar_graph)
}
o.graph <- function(o.bar_graph,t,di) {
outcome_bar_graph <- ggplot(data=o.bar_graph,aes(x=PERIOD,y=PERCENT,fill=SECTION,colour=SECTION))
outcome_bar_graph <- outcome_bar_graph + geom_bar(stat="identity")
outcome_bar_graph <- outcome_bar_graph + scale_colour_manual(name="",
breaks=c("Outcome Free","Outcome 0-50%","Outcome 50-100%","Outcome Worse"),
values=c("Outcome Free"="black",
"Outcome 0-50%"="black",
"Outcome 50-100%"="black",
"Outcome Worse"="black"))
outcome_bar_graph <- outcome_bar_graph + scale_fill_manual(name="",
breaks=c("Outcome Free","Outcome 0-50%","Outcome 50-100%","Outcome Worse"),
values=c("green","yellow","white","red"))
outcome_bar_graph <- outcome_bar_graph + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,size=4))
outcome_bar_graph <- outcome_bar_graph + labs(title=paste(gsub(" ","",paste(t,"'s")),"Outcome Response"),
x="Time on Therapy",
y="% of Time Period on Therapy")
outcome_bar_graph <- outcome_bar_graph + theme(axis.title.y=element_text(angle=90,size=6))
return(outcome_bar_graph)
}
## Create and save FILA_SEIZURE_BAR_GRAPH.jpeg
s.bar_graph <- data.frame(PERIOD=character(),PERCENT=integer(),SECTION=character(),stringsAsFactors=FALSE)
s.bar_graph[1:((dim(seizure_bar_table)[1])*4),c("PERIOD")] <- rep(as.character(seizure_bar_table$START_DATE[1:length(seizure_bar_table$START_DATE)]),each=4)
s.bar_graph[,c("PERIOD")] <- paste(as.character(seizure_bar_table$START_DATE[ceiling(as.numeric(rownames(s.bar_graph))/4)]),"-",as.character(seizure_bar_table$END_DATE[ceiling(as.numeric(rownames(s.bar_graph))/4)]))
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==1,c("PERCENT")] <- seizure_bar_table$SEIZURE_FREE
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==1,c("SECTION")] <- "Seizure Free"
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==2,c("PERCENT")] <- seizure_bar_table$SEIZURE_0_TO_50
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==2,c("SECTION")] <- "Seizures 0-50%"
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==3,c("PERCENT")] <- seizure_bar_table$SEIZURE_50_TO_100
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==3,c("SECTION")] <- "Seizures 50-100%"
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==0,c("PERCENT")] <- seizure_bar_table$SEIZURE_GREATER_THAN_100
s.bar_graph[as.numeric(rownames(s.bar_graph))%%4==0,c("SECTION")] <- "Seizures Worse"
seizure_bar_graph <- s.graph(s.bar_graph,name,FALSE)
## Create and save FILA_MED_BAR_GRAPH.jpeg
m.bar_graph <- data.frame(PERIOD=character(),PERCENT=integer(),SECTION=character(),stringsAsFactors=FALSE)
m.bar_graph[1:((dim(seizure_bar_table)[1])*4),c("PERIOD")] <- rep(as.character(seizure_bar_table$START_DATE[1:length(seizure_bar_table$START_DATE)]),each=4)
m.bar_graph[,c("PERIOD")] <- paste(as.character(seizure_bar_table$START_DATE[ceiling(as.numeric(rownames(m.bar_graph))/4)]),"-",as.character(seizure_bar_table$END_DATE[ceiling(as.numeric(rownames(m.bar_graph))/4)]))
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==1,c("PERCENT")] <- med_bar_table$MED_FREE
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==1,c("SECTION")] <- "Med Free"
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==2,c("PERCENT")] <- med_bar_table$MED_0_TO_50
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==2,c("SECTION")] <- "Meds 0-50%"
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==3,c("PERCENT")] <- med_bar_table$MED_50_TO_100
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==3,c("SECTION")] <- "Meds 50-100%"
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==0,c("PERCENT")] <- med_bar_table$MED_GREATER_THAN_100
m.bar_graph[as.numeric(rownames(m.bar_graph))%%4==0,c("SECTION")] <- "Meds Worse"
med_bar_graph <- m.graph(m.bar_graph,name,FALSE)
## Create and save FILA_OUTCOME_BAR_GRAPH.jpeg
o.bar_graph <- data.frame(PERIOD=character(),PERCENT=integer(),SECTION=character(),stringsAsFactors=FALSE)
o.bar_graph[1:((dim(seizure_bar_table)[1])*4),c("PERIOD")] <- rep(as.character(seizure_bar_table$START_DATE[1:length(seizure_bar_table$START_DATE)]),each=4)
o.bar_graph[,c("PERIOD")] <- paste(as.character(seizure_bar_table$START_DATE[ceiling(as.numeric(rownames(o.bar_graph))/4)]),"-",as.character(seizure_bar_table$END_DATE[ceiling(as.numeric(rownames(o.bar_graph))/4)]))
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==1,c("PERCENT")] <- outcome_bar_table$OUTCOME_FREE
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==1,c("SECTION")] <- "Outcome Free"
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==2,c("PERCENT")] <- outcome_bar_table$OUTCOME_0_TO_50
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==2,c("SECTION")] <- "Outcome 0-50%"
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==3,c("PERCENT")] <- outcome_bar_table$OUTCOME_50_TO_100
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==3,c("SECTION")] <- "Outcome 50-100%"
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==0,c("PERCENT")] <- outcome_bar_table$OUTCOME_GREATER_THAN_100
o.bar_graph[as.numeric(rownames(o.bar_graph))%%4==0,c("SECTION")] <- "Outcome Worse"
outcome_bar_graph <- o.graph(o.bar_graph,name,FALSE)
print("Type 'yes' if you wish to save all graphs in the same folder as this patient's OUTCOME_DATA_CLINICAL file. Type 'no' if you would like for it to be in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to save this patient's graphs in")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
file <- gsub(" ","",paste(patient,"_SEIZURE_BAR_GRAPH.jpeg"))
ggsave(seizure_bar_graph,filename=file,width=6,height=4)
print("Seizure bar graph created and saved")
file <- gsub(" ","",paste(patient,"_MED_BAR_GRAPH.jpeg"))
ggsave(med_bar_graph,filename=file,width=6,height=4)
print("Med bar graph created and saved")
file <- gsub(" ","",paste(patient,"_OUTCOME_BAR_GRAPH.jpeg"))
ggsave(outcome_bar_graph,filename=file,width=6,height=4)
print("Outcome bar graph created and saved")
print("Type 'yes' if you wish to save this patient's MED_SEIZURE_OUTCOME_BAR_TABLE file in the same folder as this patient's OUTCOME_DATA_CLINICAL file. Type 'no' if you would like for it to be in a different folder")
answer <- ""
while(tolower(answer)!="yes" & tolower(answer)!="no") {
answer <- readline(prompt="Enter here: ")
}
if (answer=="no") {
print("Input the directory that you wish to save this patient's MED_SEIZURE_OUTCOME_BAR_TABLE file in")
print("Example: C:/Folder_Name/")
directory <- readline(prompt="Enter here: ")
setwd(directory)
}
## Create and save FILA_MED_SEIZURE_OUTCOME_BAR_TABLE.xlsx
print(paste("Saving med/seizure/outcome bar table as",gsub(" ","",paste(patient,"_MED_SEIZURE_OUTCOME_BAR_TABLE.xlsx")),"in directory",getwd()))
bar_table <- cbind.data.frame(seizure_bar_table,med_bar_table,outcome_bar_table)
xlsx <- "MED_SEIZURE_OUTCOME_BAR_TABLE.xlsx"
xlsx <- gsub(" ","",paste(patient,"_",xlsx))
xlsx::write.xlsx2(bar_table,file=xlsx,showNA=FALSE,row.names=FALSE)
}
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