//FPM
  	//Load the data from step 03
	import delimited "pseudo_dataset.csv", clear 


	sum  dep_1_time death_time
	tab1 dep_1_status death_status

	
	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4	
	//Define the transition matrix
	mat tmat= (.,1\.,.)
	//Msset the data
	msset, transmatrix(tmat)  id(id)  times(dep_1_time ) states(dep_1_status ) 
	gen _newt=_stop-_start 

	//Place basic variables first
	order id  _from _to _start _stop _status 	
	//save "${N}/01_MSM_FPM_pseudodata.dta", replace
	export delimited using "01_MSM_FPM_pseudodata.csv", replace	


		
	//CR
  	//Load the data from step 03
	import delimited "pseudo_dataset.csv", clear 

	sum dep_1_status dep_1_time
	sum death_status death_time
	
   	msset, id(id)  times(dep_1_time death_time) states(dep_1_status death_status) 
	//Define Transition matrix
   	 mat tmat1 =  r(transmatrix)  
	mat li tmat1
	gen _newt=_stop-_start 
	
	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4

	//Place basic variables first
	order id  _from _to _start _stop _status 	
	//save "${N}/02_MSM_CR_pseudodata.dta", replace
	export delimited using "02_MSM_CR_pseudodata.csv", replace	

	
		
	//MSMsimple
  	//Load the data from step 03
	//use "${N}/pseudo_dataset.dta", clear
	import delimited "pseudo_dataset.csv", clear 

	sum dep_1_status dep_1_time
	sum death_status death_time
	
	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4
	
	mat tmat= (.,1,2\.,.,3\.,.,.)
	msset, transmatrix(tmat)  id(id) times(dep_1_time death_time) states(dep_1_status death_status) 
	gen _newt=_stop-_start 

	//Place basic variables first
	order id  _from _to _start _stop _status 	
	//save "${N}/03_MSM_MSMsimple_pseudodata.dta", replace
	export delimited using "03_MSM_MSMsimple_pseudodata.csv", replace

	/**********************************************************************************/
/*******************MSM 4 state unidirectional structure make*****************************/
/**********************************************************************************/

	//Load the data from step 08a
	//use "${N}/pseudo_dataset.dta", clear
	import delimited "pseudo_dataset.csv", clear

	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4

	//MSM PD structure
	

		mat tmat4= (.,1,.,2\.,.,3,4\.,.,.,5\.,.,.,.)
		
	
	
		preserve
		keep dep_1_time pd_1_time death_time
		order dep_1_time pd_1_time death_time
		local x 
		foreach var of varlist _all {
			local x `x' `var'
		}
		restore
		
		preserve
		keep dep_1_status pd_1_status death_status
		order dep_1_status pd_1_status death_status
		local y 
		foreach var of varlist _all {
			local y `y' `var'
		}
		restore
	
		msset, transmatrix(tmat4)  id(id) times("`x'") states("`y'") 
	
		//msset, transmatrix(tmat4)  id(lpnr) times(dep_1th_time postdep_1_time_pd death_time) states(dep_1th_status postdep_1_status_pd death_status) 

		//Place basic variables first
		order id  _trans _from _to _start _stop _status 	

		gen _newt=_stop-_start 

		//save "${N}/04_MSM_MSMpd_pseudodata.dta", replace
		export delimited using "04_MSM_MSMpd_pseudodata.csv", replace	
	
		
	
	/**********************************************************************************/
/*******************MSM bidirectional structure make*****************************/
/**********************************************************************************/

	//Load the data from step 08a
	//use "${N}/pseudo_dataset.dta", clear
	import delimited "pseudo_dataset.csv", clear

	global nstates=13
	
	
	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4

	//stset with death as the failure variable and eofdate the time variable 
	//with startdate as the left truncation variable
	//We will thus create the variables _t, _t0 that will used to create variables _start _stop

	// MSM bidirectional structure	
	
	//Create list of status variables for msset
	preserve
		keep dep_*_status pd_*_status death_status
		
		
		order dep_1_status pd_1_status dep_2_status pd_2_status dep_3_status pd_3_status dep_4_status pd_4_status ///
					dep_5_status pd_5_status dep_6_status , last
		
		
		order death_status, last
		local x 
		foreach var of varlist _all {
			local x `x' `var'
		}
		di "`x'"
	restore	
		
	//Create list of status variables for msset

	preserve
		
		keep dep_*_time pd_*_time death_time
		
	
		order dep_1_time pd_1_time dep_2_time pd_2_time dep_3_time pd_3_time dep_4_time pd_4_time ///
					dep_5_time pd_5_time dep_6_time , last
		
		order death_time, last
		local y 
		foreach var of varlist _all {
			local y `y' `var'
		}
		di "`y'"
	restore	
		
	global nstates: word count of `x'
	di "Number of string values: $nstates"
		
	//Automatically derive tmat
		
		matrix define tmat=J(${nstates},${nstates},.)
		mat li tmat
		
		global nstatesminus1=$nstates -1
		
		mat tmat[1,2]=1
		
		local p1=1
		local p2=2
		forval i=1(1)$nstatesminus1 {
			local iplus1=`i'+1
			mat tmat[`i',`iplus1']=`p1'
			mat tmat[`i',${nstates}]=`p2'
			local p1=`p1'+2
			local p2=`p2'+2
		}
		mat tmat[${nstatesminus1},${nstates} ]=`p1'-2
		mat li tmat
		
		msset, transmatrix(tmat)  id(id) times("`y'") states("`x'") 
	

	// Rename transitions, _from and _to variables to have the bidirectional structure
	
		bysort id (_trans): replace _trans=2 if _from==1 & _to==${nstates}

		
		local p1=4
		local p2=6
		local p3=3
		local p4=5
		forval i=1(1)$nstates {
			bysort id (_trans): replace _trans=4 if _trans==`p1' 
			bysort id (_trans): replace _trans=6 if _trans==`p2' 
			bysort id (_trans): replace _trans=3 if _trans==`p3' 
			bysort id (_trans): replace _trans=5 if _trans==`p4' 	
			local p1=`p1'+4
			local p2=`p2'+4
			local p3=`p3'+4
			local p4=`p4'+4
		}
		
		replace _from=2 if _trans==3
		replace _to  =3 if _trans==3
		
		replace _from=3 if _trans==5
		replace _to  =2 if _trans==5
		
		replace _from=2 if _trans==4
		replace _to  =4 if _trans==4
		
		replace _from=3 if _trans==6
		replace _to  =4 if _trans==6
		
		replace _to=4 if _trans==2

		
		//Place basic variables first
		order id _from _to _start _stop _status _trans	
		sort id (_start _trans)
		//replace _start=_start/365.25
		//replace _stop=_stop/365.25
		gen _newt=_stop-_start 
	
		//save "${N}/05_MSM_MSMbid_pseudodata.dta", replace
		export delimited using "05_MSM_MSMbid_pseudodata.csv", replace



	/**********************************************************************************/
/*******************MSM recurrent structure make*****************************/
/**********************************************************************************/

	//Load the data from step 08a
	//use "${N}/pseudo_dataset.dta", clear
	import delimited "pseudo_dataset.csv", clear
	
	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4

	//stset with death as the failure variable and eofdate the time variable 
	//with startdate as the left truncation variable
	//We will thus create the variables _t, _t0 that will used to create variables _start _stop
    
	global nstates=13
	
	//MSM rec structure 

	preserve
	
		mat tmat=  (.,1,.,.,.,.,.,.,.,.,.,.,2   \ ///
				.,.,3,.,.,.,.,.,.,.,.,.,4   \ ///
				.,.,.,5,.,.,.,.,.,.,.,.,6   \ ///
				.,.,.,.,7,.,.,.,.,.,.,.,8   \ ///
				.,.,.,.,.,9,.,.,.,.,.,.,10  \ ///
				.,.,.,.,.,.,11,.,.,.,.,.,12 \ ///
				.,.,.,.,.,.,.,13,.,.,.,.,14 \ ///
				.,.,.,.,.,.,.,.,15,.,.,.,16 \ ///
				.,.,.,.,.,.,.,.,.,17,.,.,18 \ ///
				.,.,.,.,.,.,.,.,.,.,19,.,20 \ ///
				.,.,.,.,.,.,.,.,.,.,.,21,22  \ ///
				.,.,.,.,.,.,.,.,.,.,.,.,23 \ /// 
				.,.,.,.,.,.,.,.,.,.,.,.,.)
						
		msset, transmatrix(tmat)  id(id) ///
				times(dep_1_time pd_1_time dep_2_time pd_2_time dep_3_time pd_3_time dep_4_time ///
				pd_4_time dep_5_time pd_5_time dep_6_time death_time) ///
				states(dep_1_status pd_1_status dep_2_status pd_2_status dep_3_status pd_3_status ///
				dep_4_status pd_4_status dep_5_status pd_5_status dep_6_status death_status) 
				
		//Place basic variables first
		order id _from _to _start _stop _status 	
		gen _newt=_stop-_start 
	

		forval i=1(1)23 { 	
			qui count if _trans==`i'
			di "Transition `i' is populated by `r(N)' individuals"
			qui count if _trans==`i' & _status==1
			di "In transition `i',  `r(N)' individuals experience the event"
		}
	

		//save "${N}/06_MSM_MSMrec_pseudodata.dta", replace
		export delimited using "06_MSM_MSMrec_pseudodata.csv", replace
	

	/**********************************************************************************/
/*******************MSM recurrent structure make*****************************/
/**********************************************************************************/

	//Load the data from step 08a
	//use "${N}/pseudo_dataset.dta", clear
	import delimited "pseudo_dataset.csv", clear
	
	gen casage2=case_inv*age_gr2
	gen casage3=case_inv*age_gr3
	gen casage4=case_inv*age_gr4

	//stset with death as the failure variable and eofdate the time variable 
	//with startdate as the left truncation variable
	//We will thus create the variables _t, _t0 that will used to create variables _start _stop
    
	global nstates=13
	
	//MSM rec structure 

	preserve
	
		mat tmat=  (.,1,.,.,.,.,.,.,.,.,.,.,2   \ ///
				.,.,3,.,.,.,.,.,.,.,.,.,4   \ ///
				.,.,.,5,.,.,.,.,.,.,.,.,6   \ ///
				.,.,.,.,7,.,.,.,.,.,.,.,8   \ ///
				.,.,.,.,.,9,.,.,.,.,.,.,10  \ ///
				.,.,.,.,.,.,11,.,.,.,.,.,12 \ ///
				.,.,.,.,.,.,.,13,.,.,.,.,14 \ ///
				.,.,.,.,.,.,.,.,15,.,.,.,16 \ ///
				.,.,.,.,.,.,.,.,.,17,.,.,18 \ ///
				.,.,.,.,.,.,.,.,.,.,19,.,20 \ ///
				.,.,.,.,.,.,.,.,.,.,.,21,22  \ ///
				.,.,.,.,.,.,.,.,.,.,.,.,23 \ /// 
				.,.,.,.,.,.,.,.,.,.,.,.,.)
						
		msset, transmatrix(tmat)  id(id) ///
				times(dep_1_time pd_1_time dep_2_time pd_2_time dep_3_time pd_3_time dep_4_time ///
				pd_4_time dep_5_time pd_5_time dep_6_time death_time) ///
				states(dep_1_status pd_1_status dep_2_status pd_2_status dep_3_status pd_3_status ///
				dep_4_status pd_4_status dep_5_status pd_5_status dep_6_status death_status) 
				
		//Place basic variables first
		order id _from _to _start _stop _status 	
		gen _newt=_stop-_start 
	

		forval i=1(1)23 { 	
			qui count if _trans==`i'
			di "Transition `i' is populated by `r(N)' individuals"
			qui count if _trans==`i' & _status==1
			di "In transition `i',  `r(N)' individuals experience the event"
		}
	

		//save "${N}/07_MSM_MSMbidemul_pseudodata.dta", replace
		export delimited using "07_MSM_MSMbidemul_pseudodata.csv", replace