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512 lines
13 KiB
Plaintext
512 lines
13 KiB
Plaintext
9 months ago
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// program runs old graph command in tandem
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// should be able to use other Stata 10 graph options in `options' once removed
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// allow labelling of data points? Can extra plots be added?
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*! version 1.22 Sep2003
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*! version 2.01 Jul2008
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*Can add lines corresponding to RR, OR and RD measures. Allows the analyst to see the
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*line fitted to the points (p1,p0)
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*Also has logit option added
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*2008 update by Ross Harris
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program define labbe
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version 8
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syntax varlist(min=4 max=4) [if] [in] /*
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*/ [, RR(string) RRN(string) RD(string) OR(string) NULL PERCent noWT XLOg YLOg /*
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*/ SAving(string) YLAbel(string) XLAbel(string) YSCale(string) XSCale(string) LOGIT NOLEGend /*
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*/ id(varname) CLOCKvar(varname) gap(real 1) textsize(real 1) symbol(string) wgt(varname) * ]
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local lines = 0
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local cmd_legend = ""
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preserve
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if "`if'`in'"!="" {
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qui keep `if' `in'
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}
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parse "`varlist'", parse(" ")
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tempvar r1 r2 N /* id yrange xrange hsqrwt */
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if ~( `1'>=0 & `2'>=0 & `3'>=0 & `4'>=0 ) {
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di in re "Negative cell counts encountered"
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exit 198
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}
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qui gen `r1'=`1'/(`1'+`2')
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qui gen `r2'=`3'/(`3'+`4')
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cap assert ((`r1'>=0 & `r1'<=1) | `r1'==.) & ((`r2'>=0 & `r2'<=1 ) | `r2'==. )
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if _rc!=0 {
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di in re "Data incorrectly specified"
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exit 198
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}
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qui gen `N' =`1'+`2'+`3'+`4'
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if "`wt'"=="" {
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if "`wgt'" != ""{
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local weight "[weight=`wgt']"
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}
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else{
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local weight "[weight=`N']"
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}
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}
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*display logit scale if needed
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if "`logit'"!="" {
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cap {
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assert (`r1'>0) & (`r2'>0)
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assert (`r1'<1) & (`r2'<1)
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}
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if _rc!=0 {
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di in re "Non-finite values encountered"
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exit
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}
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qui replace `r1'=log(`r1'/(1-`r1'))
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qui replace `r2'=log(`r2'/(1-`r2'))
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local subtitl ", logit scale"
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}
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label var `r1' "Event rate group 1`subtitl'"
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label var `r2' "Event rate group 2`subtitl'"
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if strpos("`options'","xtitle(") == 0 & strpos("`options'","ytitle(") == 0{
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local ytitle "Event rate group 1`subtitl'"
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local xtitle "Event rate group 2`subtitl'"
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}
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if "`percent'"!="" {
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if "`logit'"!="" {
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di in re "percent option not valid with logit"
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exit
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}
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qui replace `r1'=100*`r1'
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qui replace `r2'=100*`r2'
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local scale=100
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}
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else {
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local scale=1
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}
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if ("`xlog'`ylog'"!="") {
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if ("`logit'"!="") {
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di in re "Cannot use logit and xlog or ylog"
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exit
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}
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if "`rr'`or'`rd'`rrn'"!="" {
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di in re "Cannot use rr(), or(), rd() or rrn() with xlog or ylog"
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exit
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}
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}
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if "`xlabel'`ylabel'`yscale'`xscale'"=="" {
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local zero=0
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if "`percent'"!="" {
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if "`xlog'`ylog'"!="" {
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local zero=1
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}
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local ylabel "ylabel(`zero',25,50,75,100)"
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local xlabel "xlabel(`zero',25,50,75,100)"
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}
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if "`percent'"=="" & "`logit'"=="" {
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if "`xlog'`ylog'"!="" {
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local zero=0.01
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}
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local ylabel "ylabel(`zero',0.25,0.5,0.75,1)"
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local xlabel "xlabel(`zero',0.25,0.5,0.75,1)"
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}
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if "`percent'"=="" & "`logit'"!="" {
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*make own labels if on logit scale
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qui sum `r1'
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local r1min=r(min)
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local r1max=r(max)
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qui sum `r2'
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local r2min=r(min)
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local r2max=r(max)
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local lo=min(`r1min',`r2min')
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local hi=max(`r1max',`r2max')
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local ylabel "ylabel(`lo',`hi')"
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local xlabel "xlabel(`lo',`hi')"
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}
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}
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else {
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if "`ylabel'"!="" {
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local ylabel "ylabel(`ylabel')"
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}
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if "`xlabel'"!="" {
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local xlabel "xlabel(`xlabel')"
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}
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if "`yscale'"!="" {
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local yscale "yscale(range(`yscale'))"
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}
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if "`xscale'"!="" {
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local xscale "xscale(range(`xscale'))"
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}
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}
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if "`saving'"!="" {
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local saving "saving(`saving')"
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}
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*graph `r1' `r2' `weight' , `options' `xlog' `ylog' `xlabel' `ylabel' `xscale' `yscale'
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*gph open, `saving'
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*graph
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local ay=r(ay)
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local by=r(by)
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local ax=r(ax)
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local bx=r(bx)
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local ymax=r(ymax)
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local ymin=r(ymin)
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local xmax=r(xmax)
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local xmin=r(xmin)
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local Grmax=min(`ymax', `xmax')
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local Grmin=max(`ymin', `xmin')
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local xvals = subinstr("`xlabel'","xlabel(","",.)
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local yvals = subinstr("`ylabel'","ylabel(","",.)
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local xvals = subinstr("`xvals'",")","",.)
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local yvals = subinstr("`yvals'",")","",.)
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local xvals2 = subinstr("`xscale'","xscale(range(","",.)
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local yvals2 = subinstr("`yscale'","yscale(range(","",.)
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local xvals2 = subinstr("`xvals2'","))","",.)
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local yvals2 = subinstr("`yvals2'","))","",.)
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// need to find graph widths etc. manually
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qui summ `r1'
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local ymin = r(min)
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local ymax = r(max)
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if "`yvals'" != ""{
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local ymin = min(`ymin',`yvals')
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local ymax = max(`ymax',`yvals')
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}
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if "`yvals2'" != ""{
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local ymin = min(`ymin',`yvals2')
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local ymax = max(`ymax',`yvals2')
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}
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qui summ `r2'
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local xmin = r(min)
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local xmax = r(max)
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if "`xvals'" != ""{
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local xmin = min(`xmin',`xvals')
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local xmax = max(`xmax',`xvals')
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}
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if "`xvals2'" != ""{
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local xmin = min(`xmin',`xvals2')
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local xmax = max(`xmax',`xvals2')
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}
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local aspect = (`ymax'-`ymin')/(`xmax'-`xmin')
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*trap errors :RR, OR,RRN need to be positive; RD in range -1 to 1
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local flag= 0
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*gph font 300 200
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if "`xlog'"!="" {
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local xlog "log"
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}
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if "`ylog'"!="" {
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local ylog "log"
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}
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if "`null'"!="" {
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*Draw null line
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if `ymin' < `xmin'{
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local Axco0 = `xmin'
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local Ayco0 = `xmin'
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}
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else{
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local Axco0 = `ymin'
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local Ayco0 = `ymin'
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}
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if `ymax' > `xmax'{
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local Axco1 = `xmax'
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local Ayco1 = `xmax'
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}
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else{
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local Axco1 = `ymax'
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local Ayco1 = `ymax'
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}
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local cmd_null = "(scatteri `Ayco0' `Axco0' `Ayco1' `Axco1', recast(line) lpattern(dash) lcolor(gs6))"
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local lines = `lines'+1
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local q = char(34)
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local cmd_legend = "`cmd_legend' `lines' "+ `"`q'"' + "Null" + `"`q'"'
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}
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if "`or'"!="" & "`logit'"=="" {
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*gph pen 5
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parse "`or'", parse(",")
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while "`1'"!="" {
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local or_gph=`1'
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if (`or_gph'<=0 ) {
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local flag=10
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}
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else {
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if `ymin' > `scale'*(`or_gph'*`xmin'/(`scale'*1-`xmin'+(`or_gph'*`xmin'))) {
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local yco0=`ymin'
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local xco0=`ymin'/(`scale'*`or_gph'+`ymin'-`ymin'*`or_gph')
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}
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else {
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local yco0=`scale'*`or_gph'*`xmin'/(`scale'*1-`xmin'+(`or_gph'*`xmin'))
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local xco0=`xmin'
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}
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local Ayco0=`ay'*`yco0' + `by'
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local Axco0=`ax'*`xco0' + `bx'
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if `xmax' < (`scale'*`ymax'/(`scale'*`or_gph'+`ymax'-(`or_gph'*`ymax'))) {
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local cgermax = `xmax'
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}
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else {
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local cgermax = (`scale'*`ymax'/(`scale'*`or_gph'+`ymax'-(`or_gph'*`ymax')))
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}
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local cger=`xco0'
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while `cger'<=`cgermax' {
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local cger = `cger'+`scale'*0.005
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local tger = `scale'*`or_gph'*`cger'/(`scale'*1-`cger'+(`or_gph'*`cger'))
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local Ayco1= `ay'*`tger'+`by'
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local Axco1= `ax'*`cger'+`bx'
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local sub_cmds "`sub_cmds' `tger' `cger'"
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local Ayco0=`Ayco1'
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local Axco0=`Axco1'
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}
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local cmd_or "(scatteri `sub_cmds', recast(line) lcolor(maroon))"
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local lines = `lines'+1
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local q = char(34)
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local cmd_legend = `"`cmd_legend'"' + " `lines' " + `"`q'"' + "Odds ratio" + `"`q'"'
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}
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mac shift 2
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}
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}
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if "`or'"!="" & "`logit'"!="" {
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*gph pen 9
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parse "`or'", parse(",")
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while "`1'"!="" {
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if (`1'<=0 ) {
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local flag=10
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}
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else {
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local or_lgph=log(`1')
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if `ymin' > `xmin'+`or_lgph' {
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local yco0=`ymin'
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local xco0=`ymin'-`or_lgph'
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}
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else {
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local yco0=`xmin'+`or_lgph'
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local xco0=`xmin'
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}
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if `ymax' >`xmax'+`or_lgph' {
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local yco1=`xmax'+`or_lgph'
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local xco1=`xmax'
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}
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else {
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local yco1=`ymax'
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local xco1=`ymax'-`or_lgph'
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}
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local Ayco0=`ay'*`yco0' + `by'
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local Axco0=`ax'*`xco0' + `bx'
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local Ayco1=`ay'*`yco1' + `by'
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local Axco1=`ax'*`xco1' + `bx'
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if ( (`ymax'>`yco0') & (`xmax'>`xco0') & (`ymin'<`yco1') & (`xmin'<`xco1') ) {
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*gph line `Ayco0' `Axco0' `Ayco1' `Axco1'
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local cmd_or2 = "(scatteri `yco0' `xco0' `yco1' `xco1', recast(line) lcolor(maroon))"
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local lines = `lines'+1
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local q = char(34)
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local cmd_legend = `"`cmd_legend'"' + " `lines' " + `"`q'"' + "Odds ratio" + `"`q'"'
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}
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}
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mac shift 2
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}
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}
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if "`rr'"!="" {
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if "`logit'"!="" {
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di in re "rr option not valid with logit"
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exit
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}
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*gph pen 6
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parse "`rr'", parse(",")
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while "`1'"!="" {
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local rr_gph=`1'
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if (`rr_gph'<=0 ) {
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local flag=10
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}
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else {
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if `ymin' > `rr_gph'*`xmin' {
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local yco0=`ymin'
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local xco0=`ymin'/`rr_gph'
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}
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else {
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local yco0=`rr_gph'*`xmin'
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local xco0=`xmin'
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}
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if `ymax' > `rr_gph'*`xmax' {
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local yco1=`rr_gph'*`xmax'
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local xco1=`xmax'
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}
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else {
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local yco1=`ymax'
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local xco1=`ymax'/`rr_gph'
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}
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local Ayco0=`ay'*`yco0' + `by'
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local Axco0=`ax'*`xco0' + `bx'
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local Ayco1=`ay'*`yco1' + `by'
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local Axco1=`ax'*`xco1' + `bx'
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if ( (`ymax'>`yco0') & (`xmax'>`xco0') & (`ymin'<`yco1') & (`xmin'<`xco1') ) {
|
||
|
|
*gph line `Ayco0' `Axco0' `Ayco1' `Axco1'
|
||
|
|
local cmd_rr = "(scatteri `yco0' `xco0' `yco1' `xco1', recast(line) lcolor(dkgreen))"
|
||
|
|
local lines = `lines'+1
|
||
|
|
local q = char(34)
|
||
|
|
local cmd_legend = `"`cmd_legend'"' + " `lines' " + `"`q'"' + "Risk ratio" + `"`q'"'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
mac shift 2
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`rrn'"!="" {
|
||
|
|
if "`logit'"!="" {
|
||
|
|
di in re "rrn option not valid with logit"
|
||
|
|
exit
|
||
|
|
}
|
||
|
|
*gph pen 7
|
||
|
|
parse "`rrn'", parse(",")
|
||
|
|
while "`1'"!="" {
|
||
|
|
local rrn_gph=`1'
|
||
|
|
if (`rrn_gph'<=0 ) {
|
||
|
|
local flag=10
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
if `ymin' > (`scale'*(1 -`rrn_gph') + `rrn_gph'*`xmin') {
|
||
|
|
local yco0=`ymin'
|
||
|
|
local xco0=(`ymin'+`scale'*(`rrn_gph'-1))/`rrn_gph'
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
local yco0=`scale'*(1-`rrn_gph') + `rrn_gph'*`xmin'
|
||
|
|
local xco0=`xmin'
|
||
|
|
}
|
||
|
|
if `ymax' >(`scale'*(1-`rrn_gph') + `rrn_gph'*`xmax' ) {
|
||
|
|
local yco1=`scale'*(1-`rrn_gph') + `rrn_gph'*`xmax'
|
||
|
|
local xco1=`xmax'
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
local yco1=`ymax'
|
||
|
|
local xco1=(`ymax'+`scale'*(`rrn_gph'-1))/`rrn_gph'
|
||
|
|
}
|
||
|
|
local Ayco0=`ay'*`yco0' + `by'
|
||
|
|
local Axco0=`ax'*`xco0' + `bx'
|
||
|
|
local Ayco1=`ay'*`yco1' + `by'
|
||
|
|
local Axco1=`ax'*`xco1' + `bx'
|
||
|
|
if ( (`ymax'>`yco0') & (`xmax'>`xco0') & (`ymin'<`yco1') & (`xmin'<`xco1') ) {
|
||
|
|
*gph line `Ayco0' `Axco0' `Ayco1' `Axco1'
|
||
|
|
local cmd_rrn = "(scatteri `yco0' `xco0' `yco1' `xco1', recast(line) lcolor(ltgreen))"
|
||
|
|
local lines = `lines'+1
|
||
|
|
local q = char(34)
|
||
|
|
local cmd_legend = `"`cmd_legend'"' + " `lines' " + `"`q'"' + "Risk ratio (non-event)" + `"`q'"'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
mac shift 2
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`rd'"!="" {
|
||
|
|
if "`logit'"!="" {
|
||
|
|
di in re "rd option not valid with logit"
|
||
|
|
exit
|
||
|
|
}
|
||
|
|
*gph pen 8
|
||
|
|
parse "`rd'", parse(",")
|
||
|
|
while "`1'"!="" {
|
||
|
|
local rd_gph=`1'
|
||
|
|
if (`rd_gph'<=-1 | `rd_gph'>=1 ) {
|
||
|
|
local flag=10
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
if `ymin' > `xmin'+`scale'*`rd_gph' {
|
||
|
|
local yco0=`ymin'
|
||
|
|
local xco0=`ymin'-`scale'*`rd_gph'
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
local yco0=`xmin'+`scale'*`rd_gph'
|
||
|
|
local xco0=`xmin'
|
||
|
|
}
|
||
|
|
if `ymax' >`xmax'+`rd_gph' {
|
||
|
|
local yco1=`xmax'+`scale'*`rd_gph'
|
||
|
|
local xco1=`xmax'
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
local yco1=`ymax'
|
||
|
|
local xco1=`ymax'-`scale'*`rd_gph'
|
||
|
|
}
|
||
|
|
local Ayco0=`ay'*`yco0' + `by'
|
||
|
|
local Axco0=`ax'*`xco0' + `bx'
|
||
|
|
local Ayco1=`ay'*`yco1' + `by'
|
||
|
|
local Axco1=`ax'*`xco1' + `bx'
|
||
|
|
if ( (`ymax'>`yco0') & (`xmax'>`xco0') & (`ymin'<`yco1') & (`xmin'<`xco1') ) {
|
||
|
|
*gph line `Ayco0' `Axco0' `Ayco1' `Axco1'
|
||
|
|
local cmd_rd = "(scatteri `yco0' `xco0' `yco1' `xco1', recast(line) lcolor(olive))"
|
||
|
|
local lines = `lines'+1
|
||
|
|
local q = char(34)
|
||
|
|
local cmd_legend = `"`cmd_legend'"' + " `lines' " + `"`q'"' + "Risk difference" + `"`q'"'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
mac shift 2
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
*gph close
|
||
|
|
if `flag'>1 {
|
||
|
|
display _n "Note: some effect sizes are outside valid ranges"
|
||
|
|
}
|
||
|
|
|
||
|
|
// RJH EDIT
|
||
|
|
// sort out xlabel etc. later
|
||
|
|
|
||
|
|
local xlabel = subinstr("`xlabel'", "," ," " ,.)
|
||
|
|
local ylabel = subinstr("`ylabel'", "," ," " ,.)
|
||
|
|
local q = char(34)
|
||
|
|
local l2 = `lines'+1
|
||
|
|
local cmd_legend = `"`cmd_legend'"' + " `l2' " + `"`q'"' + "Studies" + `"`q'"'
|
||
|
|
if `"`cmd_legend'"' != ""{
|
||
|
|
local cmd_legend = "legend(order(" + `"`cmd_legend'"' + ") span)"
|
||
|
|
}
|
||
|
|
if "`nolegend'" != "" | (`lines' == 2 & "`null'" != "") | (`lines'<=1){
|
||
|
|
local cmd_legend = "legend(off)"
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`id'" != ""{
|
||
|
|
tempvar clockVar
|
||
|
|
local lsize = min(`textsize'*30/_N,2)
|
||
|
|
qui gen `clockVar' = `r2'<`r1'
|
||
|
|
qui replace `clockVar' = 3+`clockVar'*6
|
||
|
|
if "`clockvar'" != ""{
|
||
|
|
qui replace `clockVar' = `clockvar' if `clockvar' < . // user defined
|
||
|
|
}
|
||
|
|
tempvar r11 r22 radians
|
||
|
|
qui summ `N'
|
||
|
|
qui gen `radians' = (`clockVar'/12)*2*_pi
|
||
|
|
if `gap' == 0{
|
||
|
|
local gap = 0.0001
|
||
|
|
}
|
||
|
|
local invgap = 17/`gap' // smaller means more gap
|
||
|
|
qui gen `r11' = `r1' + `N'/r(max)*((`ymax'-`ymin')/`invgap')*cos(`radians')
|
||
|
|
qui gen `r22' = `r2' + `N'/r(max)*((`xmax'-`xmin')/`invgap')*sin(`radians')
|
||
|
|
|
||
|
|
local cmd_lab "(scatter `r11' `r22', msymbol(none) mlabel(`id') mlabvposition(`clockVar') mlabcolor(black) mlabsize(`lsize'))"
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`symbol'" == ""{
|
||
|
|
local s2 = "circle_hollow"
|
||
|
|
}
|
||
|
|
else{
|
||
|
|
local s2 = "`symbol'"
|
||
|
|
}
|
||
|
|
if "`weight'" == ""{
|
||
|
|
qui replace `r22' = `r2'
|
||
|
|
qui replace `r11' = `r1'
|
||
|
|
if "`symbol'" == ""{
|
||
|
|
local s2 = "default"
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
qui twoway `cmd_null' `cmd_or' `cmd_or2' `cmd_rr' `cmd_rrn' `cmd_rd' ///
|
||
|
|
(scatter `r1' `r2' `weight', msymbol(`s2') mcolor(navy)) `cmd_lab' ///
|
||
|
|
, `options' `xlog' `ylog' `xlabel' `ylabel' `xscale' `yscale' ///
|
||
|
|
`cmd_legend' xtitle("`xtitle'") ytitle("`ytitle'") aspect(`aspect')
|
||
|
|
|
||
|
|
restore
|
||
|
|
end
|
||
|
|
|