cd "D:\Office work\Dr. Fahmida chowdhury\2020\Vitamin D Manuscript"
use "Vitamin-D main phase_10-12-.2019.dta",clear 
**use "C:\Users\fahmida_chow\Dropbox\Vitamin_D\Vitamin D\Vitamin D data\Do file\Vitamin-D main phase_10-12-.2019.dta",clear 
***Table 1***
*Relapse_3m_cough_cold Relapse_3m_pneumonia Relapse_3_m_severe_Pneumonia 


tabstat age_pt,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest  age_pt,by(allocation_group)
gen age_cat12=(age_pt>12)
median age_pt,by(allocation_group)
tab sex_pt allocation_group,col chi

gen underweight=(Z_WA<-3)
replace underweight=. if Z_WA==.
tab underweight allocation_group,col chi

gen wasting=(Z_WL<-3)
replace wasting=. if Z_WL==.
tab wasting allocation_group,col chi


tab pedal_edema allocation_group,col chi
recode breast_feeding (9=.)
tab breast_feeding allocation_group,col chi


recode exclusive_breast_feeding (9=.)
tab exclusive_breast_feeding allocation_group,col chi

tabstat mother_age,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest  mother_age,by(allocation_group)
median mother_age,by(allocation_group)

recode education_mother (3/5=3)
tab education_mother allocation_group,col chi nolab


tab family_TB allocation_group,col chi 
tab family_respiratory allocation_group,col chi 

recode past_pneumonia (2/4=1) (1=0)
lab drop past_pneumonia
lab define pneum_past 1"pneumonia" 0"No pneumonia"
lab values  past_pneumonia pneum_past
tab past_pneumonia allocation_group,col chi 

tab cook_bed allocation_group,col chi 

gen outdoor_daily_ct=(outdoor_daily>.5)
replace outdoor_daily_ct=. if outdoor_daily==.
tab outdoor_daily_ct allocation_group,col chi

recode percentage_body (.=0)
tab percentage_body allocation_group,col chi


tab underweight allocation_group,col chi

lab drop smoking_history
recode smoking_history (2/5=1) (1=0)
lab define smoking_past 1"Smoking" 0"No Smoking"
lab values  smoking_history smoking_past
tab smoking_history allocation_group,col chi 
 

recode  room_household (2/4=2)
lab define room_household 1"Single" 2"More"
lab values  room_household room_household

tab room_household allocation_group,col chi 

recode monthly_income(9999=.)
ttest  monthly_income,by(allocation_group)


***Table 2***
egen duration_ill=rowmax(dia_duration cough_duration running_nose_duration fever_duration vomiting_duration poor_intake_duration lethargy_duration convulsion_duration)
tabstat duration_ill,stat(N mean sd median iqr p25 p75) by(allocation_group) 
median duration_ill,by(allocation_group)

ttest   admission_height,by(allocation_group)
ttest   admission_weight,by(allocation_group)
ttest   Radial_Pulse,by(allocation_group)
ttest   temp,by(allocation_group)
ttest   Res_rate,by(allocation_group)
ttest   spo2,by(allocation_group)
tab hypoxaemia allocation_group,col chi

recode vit_d3_admission (99=.)
ttest   vit_d3_admission,by(allocation_group)

*tabstat vit_d3_admission,stat(N mean sd median iqr p25 p75) by(allocation_group) 
*median vit_d3_admission,by(allocation_group)

ttest   ca_admission,by(allocation_group)

tabstat CRP,stat(N mean sd median iqr p25 p75) by(allocation_group) 
median CRP,by(allocation_group)
tab fever_admission allocation_group,col chi
tab LCWI allocation_group,col chi
tab crackles allocation_group,col chi

tab rhonchi   allocation_group,col chi
tab grunting   allocation_group,col chi
tab vomiting_admission   allocation_group,col chi
tab lethargy_admission   allocation_group,col chi

recode dehydration (9=.)
tab dehydration   allocation_group,col chi

tabstat vit_d3_discharge,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   vit_d3_discharge,by(allocation_group)

recode ca_discharge (99=.)
tabstat ca_discharge,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   ca_discharge,by(allocation_group)

tabstat phosphorus,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   phosphorus,by(allocation_group)

tabstat al_phosphatase,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   al_phosphatase,by(allocation_group)

tabstat PTH_admission,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   PTH_admission,by(allocation_group)

tabstat PTH_discharge,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   PTH_discharge,by(allocation_group)

tabstat vitamin_D_diet,stat(N mean sd median iqr p25 p75) by(allocation_group) 
ttest   vitamin_D_diet,by(allocation_group)

tab final_outcome,gen(final_outcome_)

tab final_outcome_1 allocation_group,col chi   
tab final_outcome_2 allocation_group,col chi   
tab final_outcome_3 allocation_group,col chi
tab final_outcome_4 allocation_group,col chi
tab final_outcome_5 allocation_group,col chi

tab  allocation_group


*tab Followup_outcome allocation_group, col chi nolab
tab Followup_outcome allocation_group if Followup_outcome<9, col chi

/***Table 3***
tab CXR_admission allocation_group,col chi
tab CXR_discharge allocation_group,col chi*/

***Table 3***

recode normalization_rr (.=0)

tabstat normalization_rr,stat(N mean sd median iqr p25 p75) by(allocation_group) 

*keep if underweight==1
stset  normalization_rr 
stcox allocation_group underweight allocation_group##underweight
stcox age_cat12  
stcox  allocation_group 

sts graph,by(allocation_group)
stset,clear

tabstat resolution_LCWI,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_LCWI
stcox allocation_group underweight allocation_group##underweight

stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_hypoxaemia,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_hypoxaemia
stcox age_cat12  
stcox allocation_group underweight allocation_group##underweight

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_pneumonia,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_pneumonia
stcox age_cat12  
stcox  allocation_group 
sts graph,by(allocation_group)
stcox allocation_group underweight allocation_group##underweight

stset,clear

tabstat duration_hospital,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  duration_hospital
stcox age_cat12  
stcox allocation_group underweight allocation_group##underweight

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

*total Relapse_3m_cough_cold Relapse_3_m_severe_Pneumonia Relapse_3m_pneumonia ,over(  allocation_group)
*total Relapse_cough_cold Relapse_pneumonia Relapse_severe_pneumonia ,over(  allocation_group)

*poisson Relapse_3m_pneumonia  allocation_group, irr
*poisson Relapse_3_m_severe_Pneumonia  allocation_group, irr
*poisson Relapse_3m_cough_cold  allocation_group, irr



****D3 vit admin***
gen vitd3_admin=(vit_d3_admission<50)

logistic vitd3_admin i.education_mother
gen mother_age_group=mother_age<18
logistic vitd3_admin i.mother_age_group

****Table 3: under 50 deficient vit d3 ***

gen vitd3_admin=(vit_d3_admission<50)
tab vitd3_admin allocation_group,col chi
keep if vitd3_admin==1
recode normalization_rr (.=0)

tabstat normalization_rr,stat(N mean sd median iqr p25 p75) by(allocation_group) 

stset  normalization_rr
stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_LCWI,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_LCWI
stcox age_cat12  
stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_hypoxaemia,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_hypoxaemia
stcox age_cat12  
stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_pneumonia,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_pneumonia
stcox age_cat12  
stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat duration_hospital,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  duration_hospital
stcox age_cat12  
stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear



****Table 3: above 50 sufficient vit d3 ***

gen vitd3_admin=(vit_d3_admission<50)
keep if vitd3_admin==0
recode normalization_rr (.=0)

tabstat normalization_rr,stat(N mean sd median iqr p25 p75) by(allocation_group) 

stset  normalization_rr
stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_LCWI,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_LCWI
stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat resolution_hypoxaemia,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_hypoxaemia
stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear


tabstat resolution_pneumonia,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  resolution_pneumonia
stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

tabstat duration_hospital,stat(N mean sd median iqr p25 p75) by(allocation_group) 
stset  duration_hospital
stcox age_cat12  

stcox  allocation_group 
sts graph,by(allocation_group)
stset,clear

**** deficient vit d3 category ***
*on admission
recode allocation_group (1=0)(2=1)
lab define group_st 1"B" 0"A"
lab values  allocation_group group_st

gen vitd3_deficiency_adm=(vit_d3_admission>=50)
lab define vitd3_deficiency_adm 1"Sufficient" 0"Insufficient"
lab values vitd3_deficiency_adm vitd3_deficiency_adm
tab vitd3_deficiency_adm allocation_group,col chi


replace vitd3_deficiency=2 if (vit_d3_admission>= 37.6 & vit_d3_admission<50)
replace vitd3_deficiency=3 if (vit_d3_admission> 12.5  &vit_d3_admission<37.6)
replace vitd3_deficiency=4 if (vit_d3_admission<=12.5  &vit_d3_admission!=.)

lab define vit_deficient 1"Sufficient" 2"Insufficient" 3"Deficient" 4"Severely deficient" 
lab values vitd3_deficiency vit_deficient

tab vitd3_deficiency allocation_group,col chi

*at discharge
gen vitd3_deficiency=(vit_d3_discharge>=50)
lab define vit_deficient 1"Sufficient" 0"Insufficient"
lab values vitd3_deficiency vit_deficient
tab vitd3_deficiency allocation_group,col chi

replace vitd3_deficiency=2 if (vit_d3_discharge>= 37.6 & vit_d3_discharge<50)
replace vitd3_deficiency=3 if (vit_d3_discharge> 12.5  &vit_d3_discharge<37.6)
replace vitd3_deficiency=4 if (vit_d3_discharge<=12.5  &vit_d3_discharge!=.)

lab define vit_deficient 1"Sufficient" 2"Insufficient" 3"Deficient" 4"Severely deficient" 
lab values vitd3_deficiency vit_deficient

tab vitd3_deficiency allocation_group,col chi

*Table 4:

ren Relapse_pneumonia Relapse_6m_pneumonia
ren Relapse_severe_pneumonia Relapse_6_m_severe_Pneumonia
ren Relapse_cough_cold Relapse_6m_cough_cold

gen Relapse_6m_pneumonia_cat=0 if (Relapse_6m_pneumonia==0)
replace Relapse_6m_pneumonia_cat=1 if Relapse_6m_pneumonia==1
replace Relapse_6m_pneumonia_cat=2 if Relapse_6m_pneumonia>1
replace Relapse_6m_pneumonia_cat=. if Relapse_6m_pneumonia==.
tab Relapse_6m_pneumonia_cat allocation_group,col chi


poisson allocation_group i.Relapse_6m_pneumonia_cat ,irr

gen Relapse_6_m_severe_Pneumonia_cat=0 if(Relapse_6_m_severe_Pneumonia==0)
replace Relapse_6_m_severe_Pneumonia_cat=1 if Relapse_6_m_severe_Pneumonia==1
replace Relapse_6_m_severe_Pneumonia_cat=2 if Relapse_6_m_severe_Pneumonia>1
replace Relapse_6_m_severe_Pneumonia_cat=. if Relapse_6_m_severe_Pneumonia==.
tab Relapse_6_m_severe_Pneumonia_cat allocation_group,col
poisson allocation_group i.Relapse_6_m_severe_Pneumonia_cat,irr 

gen Relapse_6m_cough_cold_cat=0 if(Relapse_6m_cough_cold==0)
replace Relapse_6m_cough_cold_cat=1 if Relapse_6m_cough_cold==1
replace Relapse_6m_cough_cold_cat=2 if Relapse_6m_cough_cold>1
replace Relapse_6m_cough_cold_cat=. if Relapse_6m_cough_cold==.
tab Relapse_6m_cough_cold_cat allocation_group,col chi
poisson allocation_group i.Relapse_6m_cough_cold_cat ,irr
 

***Forest plot****

metan hr hr_l hr_u,label(namevar=Outcomes) by(group) effect(HR) nooverall lcols(Outcomes) null(1) xlabel(.5, 1, 1.5, 2, 2.5, 3, 3.5) force