#!/usr/bin/Rscript   
getwd()
setwd('~/git/mosaic_2020/')
getwd()
########################################################################
# TASK: Run regression analysis
# clinical params and npa meds
########################################################################

#====================
# Input: source data
#====================
source("data_extraction_formatting_clinical.R")

# quick sanity checks
table(clinical_df_ics$ia_exac_copd==1 & clinical_df_ics$asthma == 1)
table(fp_adults$ia_exac_copd==1 & fp_adults$asthma == 1)
table(fp_adults_na$ia_exac_copd==1 & fp_adults_na$asthma == 1)

table(clinical_df_ics$asthma)

if ( length(cols_to_extract) == length(clinical_cols) + length(sig_npa_cols) ){
  cat("PASS: extracting clinical and sign npa cols")
} else{
  cat("FAIL: could not find cols to extract")
  quit()
}

fp_adults_reg = fp_adults[, cols_to_extract]
fp_adults_reg_na = fp_adults_na[, cols_to_extract]

#--------------------
# Data reassignment
#--------------------
my_data = fp_adults_reg
my_data_na = fp_adults_reg_na

table(my_data$ia_exac_copd==1 & my_data$asthma == 1)
table(my_data_na$ia_exac_copd==1 & my_data_na$asthma == 1)

# clear variables
rm(fp_adults, fp_adults_na, clinical_df_ics, clinical_df_ics_na)

#########################################################################
#============================
# Identifying column types: Reg data
#===========================
cols_to_omit = c("mosaic", "flustat", "onset_2_initial", "ia_exac_copd")

my_reg_data  = my_data[!colnames(my_data)%in%cols_to_omit]

my_vars = colnames(my_reg_data)
my_vars

lapply(my_reg_data, class)

check_int_vars = my_vars[lapply(my_reg_data, class)%in%c("integer")]
check_num_vars = my_vars[lapply(my_reg_data, class)%in%c("numeric")]
check_charac_vars =  my_vars[lapply(my_reg_data, class)%in%c("character")]
check_factor_vars =  my_vars[lapply(my_reg_data, class)%in%c("factor")]

cat("\nNo. of int cols:", length(check_int_vars)
    , "\nNo. of num cols:", length(check_num_vars)
    , "\nNo. of char cols:", length(check_charac_vars)
    , "\nNo. of factor cols:", length(check_factor_vars)
    )

# convert char vals to int as these should be int
my_reg_data[,check_charac_vars] =  lapply(my_reg_data[,check_charac_vars], as.integer)
str(my_reg_data$sfluv)


numerical_vars = c("age"
                   , "vl_pfu_ul_npa1"
                   , "los"
                   , "onset2final"
                   , "onsfindeath"
                   , "o2_sat_admis")






my_reg_data[numerical_vars] <- lapply(my_reg_data[numerical_vars], as.numeric)

my_reg_params = my_vars

na_count = sapply(my_reg_data, function(x) sum(is.na(x)));na_count 
names(na_count)[na_count>0]

vars_to_factor = my_vars[!my_vars%in%numerical_vars]

# convert to factor
lapply(my_reg_data, class)
my_reg_data[vars_to_factor] <- lapply(my_reg_data[vars_to_factor], as.factor)
factor_vars <- colnames(my_reg_data)[lapply(my_reg_data, class) == "factor"]
table(factor_vars)

# check again
lapply(my_reg_data, class)


# all parasm for reg
my_reg_params = c("age"
                   , "vl_pfu_ul_npa1"
                   , "los"
                   , "onset2final"
                   #, "onsfindeath"
                   #, "o2_sat_admis"
                   , "death" 
                   , "obesity"
                   , "sfluv"
                   , "h1n1v"
                   , "gender"
                   , "asthma"
                   , "ethnicity"
                   , "smoking"
                   , "ia_cxr"
                   , "max_resp_score"
                   , "T1_resp_score"
                   , "com_noasthma"
                   , "T2_resp_score"
                   , "inresp_sev"
                   , "steroid"
                   , "age_bins"
                   , "o2_sat_bin"
                   , "onset_initial_bin"
                   , "steroid_ics"
                   , "t1_resp_recoded")

#=================
# reg data prepare
#=================
pv1 = "death"
pv2 = "t1_resp_recoded"

#reg_params1 =  factor_vars[!factor_vars%in%pv1]
#reg_params_mixed =  my_vars[!my_vars%in%pv1]

########################################################################
#=================
# outcome2
#=================
#-----------------------------
# outcome: death + obesity
# data: fp adults
#-----------------------------
my_reg_params1 = my_reg_params[!my_reg_params%in%c("death", "obesity")]

for(i in my_reg_params1) { 
  #print (i)
  p_form = as.formula(paste("death ~ obesity + ", i ,sep = ""))
  print(p_form)
  model_reg = glm(p_form , family = binomial, data = my_reg_data)
  print(summary(model_reg))
  print(exp(cbind(OR = coef(model_reg), confint(model_reg))))
  #print (PseudoR2(model_reg))
  print(nobs(model_reg))
  cat("=================================================================================\n")
}

#-----------------------------
# outcome: death
# data: fp adults
#-----------------------------
my_reg_params1v2 = my_reg_params[!my_reg_params%in%c("death")]

for(i in my_reg_params1v2) { 
  #print (i)
  p_form = as.formula(paste("death ~ ", i ,sep = ""))
  print(p_form)
  model_reg = glm(p_form , family = binomial, data = my_reg_data)
  print(summary(model_reg))
  print(exp(cbind(OR = coef(model_reg), confint(model_reg))))
  #print (PseudoR2(model_reg))
  print(nobs(model_reg))
  cat("=================================================================================\n")
}
########################################################################
#=================
# outcome2
#=================
#-----------------------------
# outcome: t1_resp_recoded + obesity
# data: fp adults
#-----------------------------
my_reg_params2 = my_reg_params[!my_reg_params%in%c("death"
                                                   , "obesity"
                                                   , "t1_resp_recoded"
                                                   , "T1_resp_score")]

for(i in my_reg_params2) { 
  #print (i)
  p_form = as.formula(paste("t1_resp_recoded ~ obesity + ", i ,sep = ""))
  print(p_form)
  model_reg = glm(p_form , family = binomial, data = my_reg_data)
  print(summary(model_reg))
  print(exp(cbind(OR = coef(model_reg), confint(model_reg))))
  #print (PseudoR2(model_reg))
  print(nobs(model_reg))
  cat("=================================================================================\n")
}


#-----------------------------
# outcome: t1_resp_recoded
# data: fp adults
#-----------------------------
my_reg_params2v2 = my_reg_params[!my_reg_params%in%c("death"
                                                   #, "obesity"
                                                   , "t1_resp_recoded"
                                                   , "T1_resp_score")]

for(i in my_reg_params2v2) { 
  #print (i)
  p_form = as.formula(paste("t1_resp_recoded ~ ", i ,sep = ""))
  print(p_form)
  model_reg = glm(p_form , family = binomial, data = my_reg_data)
  print(summary(model_reg))
  print(exp(cbind(OR = coef(model_reg), confint(model_reg))))
  #print (PseudoR2(model_reg))
  print(nobs(model_reg))
  cat("=================================================================================\n")
}

########################################################################
# Full model
########################################################################

full_mod = glm(death ~ obesity +
                 age + 
                 #age_bins + 
                 obesity +
                 asthma + 
                 t1_resp_recoded + 
                 #ia_cxr
                , family = "binomial", data = my_reg_data)

summary(full_mod)



########################################################################
# mediators
########################################################################
sig_npa_cols = c("mosaic", sig_npa_cols)

my_med_sig = fp_adults[, sig_npa_cols]

my_reg_data_med = merge(clinical_df_ics, my_med_sig
                        , by = intersect(names(clinical_df_ics), names(my_med_sig))
)

#-----------------------------
# outcome: death + obesity
# data: fp adults
#-----------------------------
#my_reg_params_meds =  c(my_reg_params, sig_npa_cols)
my_reg_params_meds =  colnames(my_reg_data_med)
my_reg_params_meds1 = my_reg_params_meds[!my_reg_params_meds%in%c("mosaic", "flustat"
                                                                  , "onset_2_initial"
                                                                  , "onsfindeath"
                                                                  , "ia_exac_copd"
                                                                  , "death"
                                                                  , "obesity")]



for(i in my_reg_params_meds1) { 
  #print (i)
  p_form = as.formula(paste("death ~ obesity + ", i ,sep = ""))
  print(p_form)
  model_reg = glm(p_form , family = binomial, data = my_reg_data_med)
  print(summary(model_reg))
  print(exp(cbind(OR = coef(model_reg), confint(model_reg))))
  #print (PseudoR2(model_reg))
  print(nobs(model_reg))
  cat("=================================================================================\n")
}

#-----------------------------
# outcome: t1_resp_recoded ~ obesity + asthma
# data: fp adults
#-----------------------------
my_reg_params_meds2v2 = my_reg_params_meds[!my_reg_params_meds%in%c("mosaic"
                                                                    , "flustat"
                                                                    , "onset_2_initial"
                                                                    , "onsfindeath"
                                                                    , "ia_exac_copd"
                                                                    , "death"
                                                                    , "t1_resp_recoded"
                                                                    , "T1_resp_score"
                                                                    , "asthma")]



for(i in my_reg_params_meds2v2) { 
  #print (i)
  p_form = as.formula(paste("t1_resp_recoded ~ obesity + asthma + ", i ,sep = ""))
  print(p_form)
  model_reg = glm(p_form , family = binomial, data = my_reg_data_med)
  print(summary(model_reg))
  print(exp(cbind(OR = coef(model_reg), confint(model_reg))))
  #print (PseudoR2(model_reg))
  print(nobs(model_reg))
  cat("=================================================================================\n")
}