CDCCR: What the package does (short line)

#'Turn list of co/chronic mobidity and mental health into "ture" and "false"
#'
#' @param x the levels for patients in the original data frame to be turned into "ture" and "false"
#' @param possible numbers of possible levels for co/chronic mobidity and mental health
#' @return vectors of "ture" and "false" according to the levels of co/chronic mobidity and mental health
extractmorbidity=function(x,possible) #possible=#of possible values for 16 or 23 values for chronic / co-mobidity
{
  if(x[1]==999||is.na(x[1]))
  {
    return(rep(F,possible))
  }else{
    has=rep(F,possible)
    for(i in x){
      has[i]=T
    }
    return(has)
  }
}

hasrepeat=function(x,possible)
{
  tab=table(x)
  m=max(tab)
  w=names(which.max(tab))
  ifelse(m>1,w,NA)
}

#x=c(2,3,2,3,4)
#table(x)
#tab=table(t(data2[2,14:23]))
#tab["23"]

#'built a function that will count numbers of 23(mental health in comorbidity) in one patient
count23=function(x)
{
  tab=table(t(x))
  ans=ifelse(is.na(tab["23"]),0,tab["23"])
}


#'built a function that count the total numbers of actual mental health issue for each patient 
countmh=function(x)
{
  return(sum(table(t(x))))
}



#made fuction that label the specific values of each co-mobidity
extractco=function(x)
{
  thenames=c("Other","Eat","Hypert","Cardio","Kidney","Retino","Wounds","Neuro","Liver",
             "Vascular","Obesity","Cancer","Lipidd",
             "Thyroid","Dementia","Pulmon","sleep",
             "HIV","Pancreas","Celiac","Genetic","Deafblind","Mental") 
  M=extractmorbidity(x,23)
  names(M)=thenames
  return(M)
  
}


#made functionthat label the specific values for each chronic-morbidity
extractchronic=function(x)
{
  thenames=c("COther","CNeuro","CRetino","CBlind","CCardio","CWounds",
             "Amput","Skin","Lipo","Hypo",
             "Diabetic","Foot","Stiff","Hear","Frac","Nephro")
  M=extractmorbidity(x,16)
  names(M)=thenames
  return(M)
}

extractMH=function(x)
{
  thenames=c("depress","OCD","schizophrenia","alcoholism","bipolar","anxiety","develop","delusional",
             "psychosis","mood","drug","adjustment","alzheimers","cognitive","personality","klinfelter",
             "PTSD","agaraphobia","binge","panic","cope","socialanx","manic","hoarding","eating","maladaptive",
             "imsomnia","clusterc","schizo","ADD","generalizeanx","addiction")
  M=extractmorbidity(x,32)
  names(M)=thenames
  return(M)
}









# read data in from csv
# 
# a paragraph with more details about function
# 
# @param file.name name of imported file
#
# @return dataframe containing all variables as appropriatly dates, factor and logicals
# @export 
# @import dplyr
# @import lubridate
library(dplyr)
Readdata=function(file.name)
  {
  data=read.csv("../inst/extdata/finaldata.csv",header=T)
  #refer the column names by numbers
  
  #take the rows that are not NA for location and gender
  #cut = converted the numbers into factors --> converted the numbers to factors of the following variables
  #library(dplyr)
  data %>%
    dplyr::slice(1:622) ->data2
  
  
  locationf=cut(data2[,2],breaks=c(0,1.2,3),labels=c("HALTON","MISSISSAUGA"))
  
  
  genderf=cut(data2[,4],breaks=c(0,1.5,3),labels=c("M","F"))
  
  agef=cut(data2[,3],breaks=c(15,35,55,75,95))
  
  repeatreferral=cut(data2[,7],breaks=c(-1,0.5,2),labels=c("No","Yes"))
  
  
  referralfrom=cut(data2[,8],breaks=c(-1,1.5,2.5,3.5,4.5,6),labels=c("primary","self","specialist","hospital","DEC"))
  
  
  socialissue=cut(data2[,9],breaks=c(0,1.5,2.5,3.5,4.5,5.5,6.5,7.5,8.5,9.5,11,1000),
                  labels=c("social","community","income","elderly","smoke","drugs","housing","mobility","language","education","none"))
#consider changing the short names to the actual names  
  
  profcareplan=cut(data2[,64],breaks=c(-1,0.5,2,1000),labels=c("No","Yes","N/A"))
  
  
  SelfMGoals=cut(data2[,65],breaks=c(-1,0.5,2,1000),labels=c("No","Yes","N/A"))
  
  
  ExtentSelfM=cut(data2[,66],breaks=c(-1,0.5,1.5,2.5,3.5,1000),labels=c("None","Some","Most","All","N/A"))
  
  
  Pdischwithtrans=cut(data2[,67],breaks=c(-1,0.5,2,1000),labels=c("No","Yes","N/A"))
  
  
  DischSt=cut(data2[,69],breaks=c(0,1.5,2.5,3.5),labels=c("withdrawal","discharged","death"))
  
  
  Endorefer=cut(data2[,87],breaks=c(-1,0.5,2),labels=c("no","yes"))
  
  
  #extract the dates and truned them into Rdate
  #obtain different duration between admit date and discharge date
  
  #library(lubridate)
  referdate=lubridate::dmy(data2[,6])
  
  
  admitdate=lubridate::dmy(data2[,34])
  
  
  dischargedate=lubridate::dmy(data2[,68])
  
  
  
  #dis - data2[,73] #column 73 is numbers of weeeks between admitdate and discharge date as calculated in spreadsheet
  #summary(as.numeric(dis) - data2[,73])  #checking if the calculation is consisting
  #column Bu- Time in CCDC doesn't appear in the final spread sheet
  
  #co-mo is from column 14-23
  #chronic comlication is from column 24-33
  
  #made the function for "T=pts has both morbidity and F=pts doesn't have morbidity"
  
  
  
  
  
  como=t(apply(data2[,14:23],1,extractco))
  comorep=apply(data2[,14:23],1,hasrepeat)
  comorep
  comomhrep=apply(data2[,14:23],1,count23)
  comomhrep #'counted numbers of "23" for each patient among the comorbidity columns 
  actualmhrep=apply(data2[,74:78],1,countmh)
  actualmhrep #'counted numbers of actual mental health issue for each patient among the mental health sections
  difference=actualmhrep-comomhrep
  which(difference!=0)
  #'#'there are a lot of difference= 96 patients have different value 
  #'this show which patients have different total numbers of actual mental health issues than the mental health issue from comorbidity section
  which(comomhrep>1)
  table(comomhrep)
  table(comorep)
  which(!is.na(comorep))
  #only co-morbidity has a lot of repeats 
  
  chronic=t(apply(data2[,24:33],1,extractchronic))
  chronicrep=apply(data2[,24:33],1,hasrepeat)
  chronicrep
  table(chronicrep)
  
  MH=t(apply(data2[,74:78],1,extractMH))
  head(MH)
  MHrep=apply(data2[,74:78],1,hasrepeat)
  MHrep
  table(MHrep)
  
  como=as.data.frame(como)
  chronic=as.data.frame(chronic)
  MH=as.data.frame(MH)
  
  
  
  #make a new dataframe (note that chronic and como factors are displaced one after the other, and chronics factors start from "Cother")
  dataframe=data.frame(locationf,age=data2[,3],genderf,distance=data2[,5],referdate,repeatreferral,referralfrom,socialissue,
                       data2[,10:13],como,chronic,admitdate,data2[,35:49],DCweight=as.numeric(data2[,50]),data2[,51:63],profcareplan,
                       SelfMGoals,ExtentSelfM,Pdischwithtrans,dischargedate,DischSt,data2[,70:73],MH,data2[,79:86],Endorefer)
  
  
  #column 59-60: treat 999 N/A 
  return(dataframe)
}











dataframe=Readdata()
head(dataframe)
#'1a.Numbers of male and female patients from each site:
outofregions <- table(dataframe$locationf,dataframe$genderf)
outofregions
prop.table(outofregions,margin=1)
#'no effect of genders - same percentage of males and females from both regions 

boxplot(dataframe$age~dataframe$locationf)
#'outlier on Missussauga site
#'no great difference in midean and spread for both sites

boxplot(dataframe$distance~dataframe$locationf)
#'one outlier on the Halton site (mistake: still need to get permission from PI to change 750 to 7.5)

#'1b.numbers of patients with each social issue:
socialissues <- table(dataframe$socialissue)
socialissues
plot(dataframe$socialissue,las=2)
#'compare to the impactful issues you mentioned, the following social issues appears to be more frequent: low income, social support, smoking, elderly 

#'1c.numbers of patients with each co-morbidity 
a=subset(dataframe, select=c("Other","Eat","Hypert","Cardio","Kidney","Retino","Wounds",
                             "Neuro","Liver","Vascular","Obesity","Cancer","Lipidd","Thyroid","Dementia",
                             "Pulmon","sleep","HIV","Pancreas","Celiac","Celiac","Deafblind","Mental"))
a

library(tidyr)
library(dplyr)
a %>% gather(col,v,Other:Mental) %>% table()
#'1c.the co-morbidities with the highest frequency:Lipidd


#' 1c.average # of co-morbidities
sumofcomofoeachpt=apply(a,1,sum) #'how many como each pt has
summary(sumofcomofoeachpt) #each pt have avg 3 como

#'1c.numbers of patients with each chronic-morbidity 
b=subset(dataframe, select=c("COther","CNeuro","CRetino","CBlind","CCardio","CWounds","Amput","Skin","Lipo","Hypo",
                             "Diabetic","Foot","Stiff","Hear","Frac","Nephro"))
b
b %>% gather(col,v,COther:Nephro) %>% table()

#' 1c.average # of chronic-morbidities
sumofchronicfoeachpt=apply(b,1,sum) #'how many chronicmo each pt has
summary(sumofchronicfoeachpt) #each pt have avg 1 chronic


#'1c.numbers of patients with mental health as co-morbidity:
comomental <- table(dataframe$Mental)
comomental
which(dataframe$Mental)
#'it appears that 189 patients have mental health issue as comorbidity, but there are lots of repeats (refers to line 184-185)
#'need to verify with PI 

#'numbers of patients with "other" as co-morbidity
conmoother <- table(dataframe$Other)
conmoother
which(dataframe$Other)
#335 vs. 230 --> very big difference 

#'numbers of patients with "eat" as co-morbidity
comoeat <- table(dataframe$Eat)
comoeat
#this is the same total numbers as per excel calculated

chronicother <- table(dataframe$COther)
chronicother

chronicamputation <- table(dataframe$Amput)
chronicamputation
#chronic numebrs are correct, no repeats 

#' 1c.the range of co-morbidities/complication?? --> ask her



#' 1d. How many has mental health as one of the co-morbidities(protions of F and M have metal health issue as co-morbidity) 
comomental <- table(dataframe$Mental,dataframe$genderf)
comomental
prop.table(comomental,margin=2)
#'among Male, only 25% have mental health issues, but higher proportion of female than male have mental health issue 

#' #7.logistic data-mental vs. admit A1C
logisticmentaladmitedA1C=glm(Mental~admit.A1C,data=dataframe,family="binomial")
summary(logisticmentaladmitedA1C)
#'not significant (re-do this one with final data)

#' #8.logistic data-mental vs. discharged A1C
logisticmentaldischargedA1C=glm(Mental~D.C.A1C,data=dataframe,family="binomial")
summary(logisticmentaldischargedA1C)
#'almost significant
#'slope is positive = meaning as discharged A1C level increase, the patients are more likely to have mental health issue as one of co-morbidity
#this regression model "true" (2nd one after "false")




#' 2a.comparing admit and discharged clinical metrics 
aggregate(cbind(admit.A1C,D.C.A1C)~genderf+agef,data=dataframe,mean)
#'average Dischaged A1C level is lower for both male and female! --> good/strong evidence + the effect is also consistant (As the change is about the same for both gender) 
#'(however, the target is 6-7, both male and female patients are above target)

library(dplyr)
library(tidyr)
library(ggplot2)

dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=A1C))+geom_boxplot()+facet_grid(admitdischarge~agef)
#'older pts have lower discharged A1C value + consistant difference between two genders 
#'+ A1C values goes down as age increase 
dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n(),ybar=mean(A1C))
#' resonably large frequency for each age group
#'ask for her age group! 
dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  filter(is.na(A1C)) %>% select(c(admitdischarge,A1C)) 
#'found 116 NA(missing values) for A1C in total (more for discharged A1C)

#'2a.Lipids level(HDL cholesterol):
aggregate(cbind(admit.HDL.Cholesterol, D.C.HDL.Cholesterol)~genderf+agef,data=dataframe,mean)
#lower discharged HDL cholesterol level in male, but same for female 

dataframe %>% gather(admitdischarge,LipidHDL,c(admit.HDL.Cholesterol, D.C.HDL.Cholesterol)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=LipidHDL))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,LipidHDL,c(admit.HDL.Cholesterol, D.C.HDL.Cholesterol)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2a.Lipids level(LDL cholesterol):
aggregate(cbind(admit.LDL.Cholesterol, D.C.LDL.Cholesterol)~genderf+agef,data=dataframe,mean)
#both male and female have lower discharged LDL cholesterol levle = good thing! 

dataframe %>% gather(admitdischarge,LipidLDL,c(admit.LDL.Cholesterol, D.C.LDL.Cholesterol)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=LipidLDL))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,LipidLDL,c(admit.LDL.Cholesterol, D.C.LDL.Cholesterol)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2a.eGFR:
aggregate(cbind(admit.eGFR, D.C.eGFR)~genderf+agef,data=dataframe,mean)
#both male and female have lower discharged eGFR levle

dataframe %>% gather(admitdischarge,eGFR,c(admit.eGFR, D.C.eGFR)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=eGFR))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,eGFR,c(admit.eGFR, D.C.eGFR)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2a.Micro Albumin
aggregate(cbind(admit.Micro.Albumin, D.C.Micro.Albumin)~genderf+agef,data=dataframe,mean)
#increase discharged microalbumin level for male, but decrease discharged microalbumin for female

dataframe %>% gather(admitdischarge,Microalbumin,c(admit.Micro.Albumin, D.C.Micro.Albumin)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=Microalbumin))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,Microalbumin,c(admit.Micro.Albumin, D.C.Micro.Albumin)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())



#'2c.Change in QoL index (emotional burden)
dataframe %>% gather(admitdischarge,emotional-burden,c(DDS.Score.Sub.scale.A_Emotional.burden..Enrollment., DDS.Score.Sub.scale.A_Emotional.Burden..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=emotional-burden))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,emotional-burden,c(DDS.Score.Sub.scale.A_Emotional.burden..Enrollment., DDS.Score.Sub.scale.A_Emotional.Burden..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2c.Change in QoL index (physician related distress)
dataframe %>% gather(admitdischarge,physician-related,c(DDS.Score.Sub.scale.B_Physician.related.distress..Enrollment., DDS.Score.Sub.scale.B_Physician.related.distress..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=physician-related))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,physician-related,c(DDS.Score.Sub.scale.B_Physician.related.distress..Enrollment., DDS.Score.Sub.scale.B_Physician.related.distress..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2c.Change in QoL index (Regimen related distress)
dataframe %>% gather(admitdischarge,Regimen-related,c(DDS.Score.Sub.scale.C_Regimen.related.distress..Enrollment., DDS.Score.Sub.scale.C_Regimen.related.distress..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=Regimen-related))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,Regimen-related,c(DDS.Score.Sub.scale.C_Regimen.related.distress..Enrollment., DDS.Score.Sub.scale.C_Regimen.related.distress..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2c.Change in QoL index (Interpersonal distress)
dataframe %>% gather(admitdischarge,interpersonal-distress,c(DDS.Score.Sub.scale.D_Interpersonal.distress..Enrollment., DDS.Score.Sub.scale.D_Interpersonal.distress..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% 
  ggplot(aes(x=genderf,y=Regimen-related))+geom_boxplot()+facet_grid(agef~admitdischarge)

dataframe %>% gather(admitdischarge,interpersonal-distress,c(DDS.Score.Sub.scale.D_Interpersonal.distress..Enrollment., DDS.Score.Sub.scale.D_Interpersonal.distress..Discharge.)) %>% 
  mutate(agef=cut(age,breaks=c(15,35,55,75,95))) %>% group_by(agef,genderf) %>% 
  summarise(n=n())

#'2d. Change in clinical metrics for subgroups: mental health patients
comomental <- table(dataframe$Mental)
comomental
aggregate(cbind(admit.HDL.Cholesterol, D.C.HDL.Cholesterol)~Mental,data=dataframe,mean)
#'patients with mental health diagnosis have almost the same HDL.cholesterol level as admission

dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  ggplot(aes(x=genderf,y=A1C))+geom_boxplot()+facet_grid(Mental~admitdischarge)
dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  group_by(Mental,genderf) %>% 
  summarise(n=n()) 

#'2d. Change in clinical metrics for subgroups: patients with wounds 
dataframe$CWounds
aggregate(cbind(admit.HDL.Cholesterol, D.C.HDL.Cholesterol)~CWounds,data=dataframe,mean)
#'patients with chronic wounds have slightly lower HDL.cholesterol level as admission

dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  ggplot(aes(x=genderf,y=A1C))+geom_boxplot()+facet_grid(CWounds~admitdischarge)
dataframe %>% gather(admitdischarge,A1C,c(admit.A1C,D.C.A1C)) %>% 
  group_by(CWounds,genderf) %>% 
  summarise(n=n()) 


#'2e.Does # social issues and co-morbidities impact health outcomes, to what extent