stata_code.do

set trace off
set more off
clear all

global dir_main "C:\Projects\Occasional\20190802Adalberto"
global dir_figs  "${dir_main}\_figs"
global dir_dict  "${dir_main}\_dict"
global dir_dta "${dir_main}\_data"

global dir_DATA "C:\data"
global dir_SHAPE "${dir_DATA}\_shape"
global dir_UNcode "${dir_DATA}\UNcode"
global dir_UNDPpop "${dir_DATA}\UNDPpop"
global dir_CI5plus "${dir_DATA}\CI5plus"
global dir_CI5XI "${dir_DATA}\CI5XI"
global dir_GLOBO2018 "${dir_DATA}\Globocan2018"
global dir_GHE "${dir_DATA}\GHE_mortality"
global dir_WHO_mortality  "${dir_DATA}\WHO_mortality"

global dir_inkbash  "C:\Projects\inkbash"
global dir_fix_label  "${dir_inkbash}\fix_label"

global dir_maps_data "C:\Projects\Standard_maps\_data"


*begin trend panel


	use  "${dir_dta}\nordpred_testis_output_recent.dta", clear

	replace py = 0 if age == 18
	replace cases = 0 if age == 18
	replace cases = 0 if cases < 0


	CSU_ASR age cases py,var_age_gr(country*)  by( country* base    year gof np  ) standardE("st_err")  var_ASR("asr") 

	merge m:1 country_code  using   "${dir_dta}\pop_estimate.dta"
	drop _m



	sort  country_code  year 
	format temp_ratio %4.1f

	CSU_country_info country_code
	drop continent* country_iso3

	sort  area_label country_code  year 
	egen dummy_country = group(country_code)

	tempfile temp_graph
	save `temp_graph' ,replace

	use `temp_graph' ,clear
	keep country* area* 
	duplicates drop 
	gsort area* country_label 
	bys area_code :gen order = _n
	gen str_order = string(order,"%02.0f") 
	drop order 
	tempfile temp_order
	save `temp_order' ,replace

	use `temp_graph' ,clear
	merge m:1 area* country* using `temp_order'
	drop _m 
	sort country* year 
	save `temp_graph' ,replace

	sum asr
	tab year

	forvalues i =1/ 26 {

		use `temp_graph' ,clear
		
		keep if dummy_country == `i'
		
		
		drop if year < 1975
		sum year
		local min_y = r(min)
		if mod( `min_y', 10) == 0 {
			local min2_y = `min_y'
		}
		else {
			local min2_y = `min_y'+5
		}
		
		local title_graph = country_label
		
		if national == 0 {
			local title_graph = "`title_graph'*"
			local subtitle_graph = "*: based on regional registries" 
		}
		else {
			local subtitle_graph = "" 
		}

		
		
		
		 # delimit ;
		twoway 
			
			(connected asr year if  base<=2 , lcolor( "25 113 159") lwidth(medthick) msymbol(none)  mlabcolor(black))
			(connected asr year if  base>=2 , lcolor( "25 113 159") lwidth(medthick) lpattern(dash) msymbol(none)  mlabcolor(black)) // 

			
				, 
				
				title( `title_graph', color(black))
				//caption( `subtitle_graph', size(2))
				ytitle( "Age standardized incidence rate per 100,000",size(small)) 
				yscale(  log range(0.9 17) titlegap(5)) // titlegap(1)
				ylabel( 1 1.2 1.5 2 2.5 3 4 5 6 7 8 9 10 12 13 15 17    , labels labsize(small) angle(horizontal) format(%3s) grid glwidth(vthin) glcolor(gs13)) 
				ymtick(0.9 (0.1) 2.5 2.5 (0.5) 5 5 (1) 17   , nolabels grid glwidth(vthin) glcolor(gs13)) 
				xtitle( "Year" ,size(small) ) 
				xscale( titlegap(3))
				xlabel( 1980 (10) 2030, labsize(small) valuelabel grid glwidth(vthin) glcolor(gs13) )  // labgap(1)
				xmtick( 1980 (5) 2035 , nolabels grid glwidth(vthin) glcolor(gs13)) 
				xline( 1980 ,   lwidth(vthin) lcolor(gs13)) 
				legend(off)
				name(graph`i', replace)
				graphregion(style(none) istyle(none))
				plotregion(style(none) istyle(none))
				ysize(10) xsize(7)  

			;
			
		# delimit cr
		
		
		local area_code = area_code
		local str_order = str_order
		local title_graph = country_label 		
		
		graph export "${dir_inkbash}\trend_panel\temp\graph_`area_code'_`str_order'.eps", as(eps) replace

	}
	 

*end 

*begin pie


		local sex 0
	local x 6
	local top = `x' - 1

	insheet using "${dir_GHE}\GHE_mortality_2016.csv", clear


	keep if country_code == 76 // 170 

	keep if sex == `sex' 
	keep if inrange(age,0,6)
	keep if inlist(ghe_level,0,2)

	collapse (sum) cases, by(ghe*)

	gsort -cases
	gen rk_cases =_n
	keep if rk_cases <= `x'
	list

	tempfile temp_tot
	save `temp_tot', replace

	use `temp_tot', replace
	gen percent = cases/cases[1]*100 


	forvalue i = 1(1)`top' {
		replace percent = percent[_n] - percent[_n+`i'] if rk == 1
	}

	list ghe_cause percent
		
	use `temp_tot', replace
	replace rk_cases = rk_cases -1

	forvalue i = 1(1)`top' {
		replace cases = cases[_n] - cases[_n+`i'] if rk == 0
	}

	replace rk = `x' if rk == 0 

	csv_merge  ghe_code using "${dir_DATA}\_dict\cancer_color_2018.csv", master_key(10) using_key(10)
	keep if _m == 3
	drop _m 
	sort  rk 


	forvalue i = 0(1)`x' {
		local color`i' = color[`i']
	}

	replace ghe_cause = "Other causes" if ghe_code == 0

	#delimit ;
	 
	graph pie cases , 	
			over(rk) 
			angle(90) 
			
			pie(1, color (`color1'))               
			pie(2, color (`color2'))            				
			pie(3, color (`color3'))                         
			pie(4, color (`color4'))  
			pie(5, color (`color5'))     				
			pie(6, color (`color6')) 
			pie(7, color (`color7'))
			pie(8, color (`color8'))
			pie(9, color (`color9'))
			pie(10, color (`color10'))
			pie(11, color (`color11'))			

			plabel(1 percent, size(medium) color (black) gap(10))
			plabel(2 percent, size(medium) color (black) gap(10))
			plabel(3 percent, size(medium) color (black) gap(10))
			plabel(4 percent, size(medium) color (black) gap(10))
			plabel(5 percent, size(medium) color (black) gap(10))
			plabel(6 percent, size(medium) color (black) gap(10))	
			plabel(6 percent, size(medium) color (black) gap(10))	
			plabel(7 percent, size(medium) color (black) gap(10))	
			plabel(8 percent, size(medium) color (black) gap(10))	
			plabel(9 percent, size(medium) color (black) gap(10))	
			plabel(10 percent, size(medium) color (black) gap(10))	
			plabel(11 percent, size(medium) color (black) gap(10))	
			
			legend(off) 
			graphregion(style(none) istyle(none))
			plotregion(style(none) istyle(none))
	;
	#delimit cr

	graph export "${dir_inkbash}\pie\temp\temp.eps", as(eps) replace

	keep rk ghe_cause cases
	outsheet using  "${dir_inkbash}\pie\temp\cancer_info.csv", comma replace

*end 



*begin top5 pie bar auto



local sex 0
local country 900

		
	
	use "${dir_GLOBO2018}\Globocan_asr_cases_cumrisk_CRC.dta", clear
	drop asr cumrisk 
	keep if sex == `sex'

	drop if inlist(cancer_code,17,37,38,40) // drop skin, other cancer and unspecified cancer 
	
	//regroup for cancer_tabacco related 
	replace cancer_code =15 if inlist(cancer_code ,1,2,3,4,5,6,7,8,9,11,13,14,15,23,29,30 )
	replace cancer_label = "Smoking related cancer" if cancer_code ==15 
	
	collapse (sum) cases (mean) py, by (type sex cancer* country*)
	
	keep if country_code == `country'
	tab country_label

	collapse (sum) cases py, by(type sex cancer*) 

	gsort +type sex -cases
	bys type sex  : gen rk_cases =_n
	keep if rk_cases <= 6

	
	
	tempfile temp_tot
	save `temp_tot', replace
	
	gen percent = 0 
	forvalues i = 0(1)5 {
		replace percent = (cases/(cases[_n-`i']))*100 if rk == `i' +1
	}
	
	list


		*begin pie
		

		use `temp_tot', replace

		gen prop5 = 0 if rk == 1
		replace prop5 = 1 if rk > 1

		collapse (sum) cases, by(type prop5)
		gen percent = (cases - cases[_n+1])*100 / cases if prop5 == 0
		replace percent = cases *100 / cases[_n-1] if prop5 == 1 
		
		forvalue i = 0(1)2 {
		
		#delimit ;
			 
			graph pie percent if type == `i', 	
					over(prop5) 
					angle(90) 
					
					pie(2,  color (26 98 162))
					pie(1,  color ( 220 220 220))

					plabel(2 percent, size(medium) color (black) gap(5))
					plabel(1 percent, size(medium) color (black) gap(5))
					
					legend(off) 
					name(pie_`i', replace)
				graphregion(style(none) istyle(none))
				plotregion(style(none) istyle(none))
			;
			#delimit cr
			
			graph export "${dir_inkbash}\pie_bar\temp\pie`i'.eps", as(eps) replace

			
		}

			


		

		*end

		*begin bar
		

		
		forvalue i = 0(1)2 {
		
			use `temp_tot', replace
			replace rk_cases = rk_cases -1
			drop if rk_cases == 0

			merge m:1 cancer_code using "${dir_DATA}\_dict\cancer_color_2018.dta"
			keep if _m == 3
			drop _m
			sort type rk 
			
			keep if type == `i'

			local color1= color[1]
			local color2= color[2]
			local color3= color[3]
			local color4= color[4]
			local color5= color[5]


			drop cancer* sex color
			reshape wide cases, i(type) j(rk)

			local total = cases1 + cases2 + cases3 + cases4 + cases5
			gen bar1 = cases1 / `total'  
			gen bar2 = cases2 / `total'  
			gen bar3 = cases3 / `total'  
			gen bar4 = cases4 / `total'  
			gen bar5 = cases5 / `total'  

			# delimit;
				graph bar (asis) bar5 bar4 bar3 bar2 bar1  , 
					stack
					yscale(off)
					bar(1, color ( `color5')) 
					bar(2, color ( `color4')) 
					bar(3, color ( `color3')) 
					bar(4, color ( `color2')) 
					bar(5, color ( `color1')) 
					ylabel(,nolabels noticks nogrid)
					legend(off)
					xsize(4)
					ysize(10)
					name(bar_`i', replace)
					graphregion(style(none) istyle(none))
					plotregion(style(none) istyle(none))
					;
					
			# delimit cr
			
			graph export "${dir_inkbash}\pie_bar\temp\bar`i'.eps", as(eps) replace

			
			
			}

		use `temp_tot', replace
		replace rk_cases = rk_cases -1
		drop if rk_cases == 0
		merge m:1 cancer_code using "${dir_DATA}\_dict\cancer_color_2018.dta"
		keep if _m == 3
		drop _m 

		gsort type -rk 
		by type : egen tot=total(cases)
		by type  : gen pos = sum(cases)
		replace pos = pos - (cases/2) 
		replace pos = ((pos/tot)*312.001) + 98.582 - 7.2755
		replace pos = ((pos - 59.833)/1.33333)*(-1) 
		drop py color 
		gsort type rk
		keep cancer_label pos
		list
		outsheet using "${dir_inkbash}\pie_bar\temp\cancer_label.csv", comma replace

		
		use `temp_tot', replace

		quietly gen prop5 = 0 if rk == 1
		quietly replace prop5 = 1 if rk > 1
		gsort type +prop
		quietly collapse (sum) cases, by(type prop5)
		keep cases 
		outsheet using "${dir_inkbash}\pie_bar\temp\cancer_number.csv", comma replace
		

		
		*end
		
	

*end 



*begin top5 pie bar auto



forvalue a = 0(1)2 {
	forvalue b = 981(1)984 {
	
		if `a' == 0 {
			local sex_lab "both" 
		}
		else if `a' == 1{
			local sex_lab "male"
		
		}
		else if `a' == 2{
			local sex_lab "female"
		}
		
		if `b' == 981 {
			local country_lab "very" 
		}
		else if `b' == 982{
			local country_lab "high"
		
		}
		else if `b' == 983{
			local country_lab "medium"
		
		}
		else if `b' == 984{
			local country_lab "low"
		
		}


		
		
		use "${dir_GLOBO2018}\Globocan_asr_cases_cumrisk_CRC.dta", clear
		drop asr cumrisk 
		keep if sex == `a'

		drop if inlist(cancer_code,17,37,38,40) // drop skin, other cancer and unspecified cancer 
		keep if country_code == `b'
		tab country_label

		collapse (sum) cases py, by(type sex cancer*) 

		gsort +type sex -cases
		bys type sex  : gen rk_cases =_n
		keep if rk_cases <= 6
		list


		tempfile temp_tot
		save `temp_tot', replace

			*begin pie
			

			use `temp_tot', replace

			gen prop5 = 0 if rk == 1
			replace prop5 = 1 if rk > 1

			collapse (sum) cases, by(type prop5)
			gen percent = (cases - cases[_n+1])*100 / cases if prop5 == 0
			replace percent = cases *100 / cases[_n-1] if prop5 == 1 
			
			forvalue i = 0(1)2 {
			
			#delimit ;
				 
				graph pie percent if type == `i', 	
						over(prop5) 
						angle(90) 
						
						pie(2,  color (26 98 162))
						pie(1,  color ( 220 220 220))

						plabel(2 percent, size(medium) color (black) gap(5))
						plabel(1 percent, size(medium) color (black) gap(5))
						
						legend(off) 
						name(pie_`i', replace)
					graphregion(style(none) istyle(none))
					plotregion(style(none) istyle(none))
				;
				#delimit cr
				
				graph export "${inkbash}\pie_bar\temp\pie_`country_lab'_`sex_lab'_`i'.eps", as(eps) replace

				
			}

				


			

			*end

			*begin bar
			

			
			forvalue i = 0(1)2 {
			
				use `temp_tot', replace
				replace rk_cases = rk_cases -1
				drop if rk_cases == 0

				merge m:1 cancer_code using "${dir_DATA}\_dict\cancer_color_2018.dta"
				keep if _m == 3
				drop _m
				sort type rk 
				
				keep if type == `i'

				local color1= color[1]
				local color2= color[2]
				local color3= color[3]
				local color4= color[4]
				local color5= color[5]


				drop cancer* sex color
				reshape wide cases, i(type) j(rk)

				local total = cases1 + cases2 + cases3 + cases4 + cases5
				gen bar1 = cases1 / `total'  
				gen bar2 = cases2 / `total'  
				gen bar3 = cases3 / `total'  
				gen bar4 = cases4 / `total'  
				gen bar5 = cases5 / `total'  

				# delimit;
					graph bar (asis) bar5 bar4 bar3 bar2 bar1  , 
						stack
						yscale(off)
						bar(1, color ( `color5')) 
						bar(2, color ( `color4')) 
						bar(3, color ( `color3')) 
						bar(4, color ( `color2')) 
						bar(5, color ( `color1')) 
						ylabel(,nolabels noticks nogrid)
						legend(off)
						xsize(4)
						ysize(10)
						name(bar_`i', replace)
						graphregion(style(none) istyle(none))
						plotregion(style(none) istyle(none))
						;
						
				# delimit cr
				
				graph export "${inkbash}\pie_bar\temp\bar_`country_lab'_`sex_lab'_`i'.eps", as(eps) replace

				
				
				}

			use `temp_tot', replace
			replace rk_cases = rk_cases -1
			drop if rk_cases == 0
			merge m:1 cancer_code using "${dir_DATA}\_dict\cancer_color_2018.dta"
			keep if _m == 3
			drop _m 

			gsort type -rk 
			by type : egen tot=total(cases)
			by type  : gen pos = sum(cases)
			replace pos = pos - (cases/2) 
			replace pos = ((pos/tot)*312.001) + 98.582 - 7.2755
			replace pos = ((pos - 59.833)/1.33333)*(-1) 
			drop py color 
			gsort type rk
			keep cancer_label pos
			list
			outsheet using "${inkbash}\pie_bar\temp\cancer_label_`country_lab'_`sex_lab'.csv", comma replace

			
			use `temp_tot', replace

			quietly gen prop5 = 0 if rk == 1
			quietly replace prop5 = 1 if rk > 1
			gsort type +prop
			quietly collapse (sum) cases, by(type prop5)
			keep cases 
			outsheet using "${inkbash}\pie_bar\temp\cancer_number_`country_lab'_`sex_lab'.csv", comma replace
			

			
			*end
		}
	}

*end