#for enquiries: contact harshaldeshmukh@nhs.net
#R code for FSL analysis
# calcualtes the average pre-FSL and average  post-FSL HbA1c and does a t.test, Mann-Whitney-Wilcoxon test and also does draws a boxplot of pre and post-FSL
# Calcualtes average Pre-FSL and average post-FSL gold score and and does t-test and draws box plot
# gives average of pre and post fsl hypo and hyperglycaemic-DKA related admissions and paramidic call outs

#Download and install R from here (https://www.r-project.org/)

#Save your FSL audit download in your working  folder/directory and name it file.csv.

#Save the file code FSLcode.txt the folder where you have saved your data

#Set working directory in R conosole. This is the folder where your FSL data download and Rcode file FSLcode.txt is saved. Using command below. remove the "#".

#----type>>> setwd("C:/Users/arunb/Desktop/fsldata") (--use forward slashes not backward slashes)

#Open R and Paste the command in the R console >>>> source("FSLcode_Hba1c_analysis.txt")


#reads data from the computer. 
data1<-read.csv("file.csv", header=TRUE)

#gets average of postFSL HbA1c
data1$average_preFSL<- rowMeans(data1[c('X.1.HbA1c..Xmmol.mol.', 'X2HbA1c..Xmmol.mol.','X3HbA1c..Xmmol.mol.','X4HbA1c..Xmmol.mol.','X5HbA1c..Xmmol.mol.')], na.rm=TRUE)

#gets average of postFSL HbA1c

data1$average_postFSL<- rowMeans(data1[c('follow.up...5.HbA1c.since.last.visit...OR..Xmmol.mol.', 'follow.up...4..HbA1c.since.last.visit...OR..Xmmol.mol.','follow.up...3..HbA1c.since.last.visit...OR..Xmmol.mol.','follow.up...2..HbA1c.since.last.visit.....OR..Xmmol.mol.','follow.up...1.HbA1c.since.last.visit..OR..Xmmol.mol.')], na.rm=TRUE)

#this command removes patients with no follow-up


myvars<-c("Identifier", "average_preFSL","DDSC1..Feeling.overwhelmed.by.the.demands.of.living.with.diabetes", "DDSC2..Feeling.that.I.am.often.failing.with.my.diabetes.routine", "Number.of.admissions...Hyperglycaemia.DKA", "Number.of.admissions...Hypoglycaemia", "Paramedic.call.outs...Hyperglycaemia.DKA", "Paramedic.call.outs...Hypoglycaemia", "Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.")

datapre1<-data1[myvars]

datapre1<-datapre1[complete.cases(datapre1$average_preFSL), ]


datapre1<-datapre1[!duplicated(datapre1$Identifier), ]

#####

myvars1<-c("Identifier", "average_postFSL","DDSC1..Feeling.overwhelmed.by.the.demands.of.living.with.diabetes", "DDSC2..Feeling.that.I.am.often.failing.with.my.diabetes.routine", "follow.up...Number.of.admissions...Hyperglycaemia.DKA" ,"follow.up..Number.of.admissions...Hypoglycaemia","follow.up..Paramedic.call.outs...Hyperglycaemia.DKA" , "follow.up..Paramedic.call.outs...Hypoglycaemia"  , "follow.up...Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.")


datapost1<-data1[myvars1]


datapost1<-datapost1[complete.cases(datapost1$average_postFSL), ]

datapost1<-datapost1[!duplicated(datapost1$Identifier), ]


all<-merge(datapost1,datapre1, by="Identifier", sort=TRUE, all.x=TRUE, all.y=TRUE)

all_no_dup<-all[!duplicated(all$Identifier), ]

#Does t-test and writes the output of t.test.
t.test(all_no_dup$average_postFSL,all_no_dup$average_preFSL)
capture.output(t.test(all_no_dup$average_postFSL,all_no_dup$average_preFSL),file="t.test.txt")


# Does the non-parmetric equivalent or T-test i.e. Mann-Whitney-Wilcoxon Test. prefer that you use this one 


wilcox.test(all_no_dup$average_postFSL,all_no_dup$average_preFSL)
capture.output(wilcox.test(all_no_dup$average_postFSL,all_no_dup$average_preFSL),file="wilcox.test.txt")


jpeg('HbA1c_rplot.jpg')
boxplot(all_no_dup$average_preFSL,all_no_dup$average_postFSL,
main = "Median HbA1c Pre and Post FSL",
at = c(1,2),
names = c("PreFSL", "PostFSL"),
las = 2,
col = c("black","black"),
border = "brown",
horizontal = FALSE,
notch = TRUE,
outline=FALSE)
dev.off()


t.test(all_no_dup$Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.,all_no_dup$follow.up...Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.)
capture.output(t.test(all_no_dup$Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.,all_no_dup$follow.up...Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.),file="t.test_gold_score.txt")


jpeg('Gold_score_rplot.jpg')
boxplot(all_no_dup$Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.,all_no_dup$follow.up...Assessment.of.awareness.of.hypoglycaemia..Gold.Score...Does.the.patient.know.when.hypos.are.commencing.,
main = "Median GOLD score Pre and Post FSL",
at = c(1,2),
names = c("PreFSL", "PostFSL"),
las = 2,
col = c("black","black"),
border = "brown",
horizontal = FALSE,
notch = TRUE,
outline=FALSE)
dev.off()


#Hospital admissions due to hypo
all_no_dup1<-all_no_dup[complete.cases(all_no_dup$average_postFSL), ]
sum(all_no_dup1$Number.of.admissions...Hypoglycaemia,na.rm=TRUE)
sum(all_no_dup1$follow.up..Number.of.admissions...Hypoglycaemia,na.rm=TRUE)
capture.output(sum(all_no_dup1$Number.of.admissions...Hypoglycaemia,na.rm=TRUE),file="hypo_admission_preFSL.txt")
capture.output(sum(all_no_dup1$follow.up..Number.of.admissions...Hypoglycaemia,na.rm=TRUE),file="hypo_admission_postFSL.txt")

#Hypo_para_medic_call_outs

sum(all_no_dup1$Paramedic.call.outs...Hypoglycaemia,na.rm=TRUE)
sum(all_no_dup1$follow.up..Paramedic.call.outs...Hypoglycaemia,na.rm=TRUE)
capture.output(sum(all_no_dup1$Paramedic.call.outs...Hypoglycaemia,na.rm=TRUE),file="Paramedic_hypo_calls_preFSL.txt")
capture.output(sum(all_no_dup1$follow.up..Paramedic.call.outs...Hypoglycaemia,na.rm=TRUE),file="Paramedic_hypo_calls_postFSL.txt")


# Hospital admissions due to DKA-Hyperglycaemia

all_no_dup2 <- all_no_dup1[ which(all_no_dup1$Number.of.admissions...Hyperglycaemia.DKA < 20), ]

sum(all_no_dup2$Number.of.admissions...Hyperglycaemia.DKA,na.rm=TRUE)
sum(all_no_dup2$follow.up...Number.of.admissions...Hyperglycaemia.DKA,na.rm=TRUE)
capture.output(sum(all_no_dup2$Number.of.admissions...Hyperglycaemia.DKA,na.rm=TRUE),file="DKA_admission_preFSL.txt")
capture.output(sum(all_no_dup2$follow.up...Number.of.admissions...Hyperglycaemia.DKA,na.rm=TRUE),file="DKA_admission_postFSL.txt")