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270 lines
8.0 KiB
Plaintext
270 lines
8.0 KiB
Plaintext
*! Date : 19 May 2009
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*! Version : 1.12
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*! Authors : Adrian Mander
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*! Email : adrian.mander@mrc-bsu.cam.ac.uk
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*! Description : Bland-Altman plots with trend adjustment
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/*
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17/5/06 v1.3 add-in the middle line
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6/10/06 v1.4 Handle multiple data points at the same point by using frequency option
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Also add Scatter option just to add options to the scatter part of the plot
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2/9/07 v1.5 Changed version from 8 to 9.2
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11/12/07 v1.6 Extended the shaded area
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14/12/07 v1.7 Add limits of agreement into the info option
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11/2/08 v1.8 BUGs fixed and extended the shading to the xlimits
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17/4/08 v1.9 BUG fix.. the info limits were the wrong way round!
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9/5/08 v1.10 Allowing shading to extend beyond data to any limit you like
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11/5/08 v1.11 Added the range to be displayed for the averages
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19/5/2009 v1.12 Changed email address
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11/6/12 v1.13 Added extra option for titles and number of decimal places in display
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*/
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prog def batplot, rclass
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version 9.2
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syntax varlist (min=2 max=2) [if] [in] [,NOtrend INFO VALabel(varname) MOPTIONS(string asis) XLABel(numlist) SHADING(numlist min=2 max=2) SCatter(string asis) NOGraph DP(int 2) *]
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local gopt "`options'"
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if "`moptions'"~="" local mopt `"moptions(`moptions')"'
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preserve
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tempvar touse
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mark `touse' `if' `in'
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markout `touse' `m1' `m2'
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qui keep if `touse'
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if "`xlabel'"~="" {
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local glab `"xlabel(`xlabel')"'
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local i 0
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foreach xv of local xlabel {
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if `i++'==0 local sxmin "`xv'"
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local sxmax "`xv'"
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}
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local shade "shade(`sxmin' `sxmax')"
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}
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/* To stop the shading going the whole length of the x-axis */
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if "`shading'"~="" {
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local i 0
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foreach s of local shading {
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if `i++'==0 local smin "`s'"
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else local smax "`s'"
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}
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if `smin'<`smax' local shade "shade(`smin' `smax')"
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else local shade "shade(`smax' `smin')"
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}
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/* NOW do the trend version */
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if "`valabel'"~="" local add "val(`valabel')"
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_calctrend `varlist', `gopt' `notrend' `info' `add' `mopt' sc(`scatter') `glab' `shade' `nograph' dp(`dp')
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return local mean = "`r(mean)'"
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return local b0 = "`r(b0)'"
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return local b1 = "`r(b1)'"
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return local c0 = "`r(c0)'"
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return local c1 = "`r(c1)'"
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return local eqn = "`r(eqn)'"
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return local upper = "`r(upper)'"
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return local lower = "`r(lower)'"
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restore
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end
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/* calculate trend and do a BA plot with trend */
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prog def _calctrend,rclass
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syntax [varlist] [,NOTREND INFO VALabel(varname) MOPTIONS(string asis) SCatter(string asis) shade(numlist) NOGraph DP(int 2) *]
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local xopt "`options'"
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if "`shade'"~="" {
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local i 0
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foreach s of local shade {
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if `i++'==0 local a "`s'"
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local b "`s'"
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}
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local sxmin = `a'
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local sxmax = `b'
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}
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local i 1
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foreach var of varlist `varlist' {
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local v`i++' "`var'"
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}
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tempvar av diff
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qui gen `av' = (`v1' + `v2')/2
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qui gen `diff' = `v1' - `v2'
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local ytit "Difference (`v1'-`v2')"
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local xtit "Average of `v1' and `v2'"
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lab var `diff' "Diff"
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lab var `av' "Mean"
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if "`notrend'"~="" {
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qui summ `diff'
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local xbar = `r(mean)'
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local sd = `r(Var)'^.5
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local n = `r(N)'
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local se = `sd'/`n'^.5
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local t = invttail(`n'-1, .95)
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local lrr = `xbar' - invnorm(0.975)*`sd' /* 95% lower limit of agreement */
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local urr = `xbar' + invnorm(0.975)*`sd' /* 95% upper limit of agreement */
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local mrr = `xbar' /* 95% mean agreement */
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di "{text}Mean difference = {res}`mrr'"
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di "{text}Limits of agreement = ({res}`lrr'{text},{res}`urr'{text})"
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local min = `r(min)'
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local max = `r(max)'
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local lcb = `xbar' - `t'*`se'
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local ucb = `xbar' + `t'*`se'
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qui summ `av'
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local xmin = `r(min)'
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local xmax = `r(max)'
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local a : di %5.3f `xmin'
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local b : di %5.3f `xmax'
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local range = "Averages lie between `a' and `b'"
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di "{text}Averages lie between {res} `a' {text}and {res}`b'"
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qui corr `av' `diff'
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local r = `r(rho)'
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local n = `r(N)'
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local sig = ttail(`n'-2, `r'*((`n'-2)/(1-`r'^2))^.5)
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tempvar uy ly my
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/* The bit to extend the shade */
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local obs =`c(N)'+2
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qui set obs `obs'
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if "`sxmin'"~="" qui replace `av'=`sxmin' in `obs--'
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if "`sxmax'"~="" qui replace `av'=`sxmax' in `obs'
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qui gen `uy' = `urr'
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qui gen `ly' = `lrr'
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qui gen `my' = `mrr'
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sort `av'
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if "`info'"~="" {
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local te1:di %6.3f `mrr'
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local te2:di %6.3f `lrr'
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local te3:di %6.3f `urr'
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qui count if (`diff'>`urr' | `diff'<`lrr' ) & `diff'~=.
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local nout = `r(N)'
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qui count if `diff'~=.
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local n = `r(N)'
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local pctout : di %6.2f `nout'/`n'*100
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local xopt `"`xopt' subtitle("`nout'/`n' = `pctout'% outside the limits of agreement" "Mean difference `te1'" "95% limits of agreement (`te2',`te3')" "`range'") "'
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}
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if "`valabel'"~="" {
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tempvar label
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qui gen `label' = ""
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cap confirm string variable `valabel'
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if _rc~=0 qui replace `label' = string(`valabel') if `diff'>`urr' | `diff'<`lrr'
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else qui replace `label' = `valabel' if `diff'>`urr' | `diff'<`lrr'
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local scatteropt "mlabel(`label') note(Points outside limits labelled by `valabel')"
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}
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tempvar freq
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qui bysort `diff' `av':gen `freq'=_N
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local fopt "[fw=`freq']"
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if index("`scatter'","jitter")~=0 local fopt ""
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if "`nograph'"=="" twoway (rarea `uy' `ly' `av', bc(gs13) sort) (scatter `diff' `av' `fopt', m(o) `scatteropt' `scatter' `moptions' ) (line `my' `av',lp(dash) sort ) , ////
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legend(off) ytitle(`ytit') xtitle(`xtit') xlabel(`xmin' `xmax') `xopt'
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return local lower = `lrr'
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return local upper = `urr'
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return local mean = `mrr'
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}
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else {
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qui reg `diff' `av'
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local b1 = _b[`av']
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local b0 = _b[_cons]
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local sd = `e(rmse)'
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qui predict resid , resid
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qui gen absresid = abs(resid)
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/* Analysis of the residuals */
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qui reg absresid `av'
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local c0 = _b[_cons]
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local c1=_b[`av']
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qui su `diff'
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local max = `r(max)'
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local min = `r(min)'
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qui su `av'
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local xmax = r(max)
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local xmin = r(min)
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local max: di %5.3f `xmax'
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local min: di %5.3f `xmin'
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tempvar y uy ly x
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/* The bit to extend the shade */
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local obs =`c(N)'+2
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qui set obs `obs'
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if "`sxmin'"~="" qui replace `av'=`sxmin' in `obs--'
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if "`sxmax'"~="" qui replace `av'=`sxmax' in `obs'
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sort `av'
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qui gen `y' = `b0'+`b1'*`av'
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qui gen `uy' = `b0'+`b1'*`av' + 2.46*(`c0'+`c1'*`av')
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qui gen `ly' = `b0'+`b1'*`av' - 2.46*(`c0'+`c1'*`av')
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if "`info'"~="" {
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qui count if (`diff'>`uy' | `diff'<`ly') & `diff'~=.
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local nout = `r(N)'
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qui count if `diff'~=.
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local n = `r(N)'
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local mdp = `dp'+3
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local mdp1 = `dp'+4
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local pctout : di %`mdp1'.`dp'f `nout'/`n'*100
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local te0 : di %`mdp'.`dp'f `b0'
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local te1 : di %`mdp'.`dp'f `b1'
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local te2 : di %`mdp'.`dp'f `c0'
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local te3 : di %`mdp'.`dp'f `c1'
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local xopt `"`xopt' subtitle("`nout'/`n' = `pctout'% outside the limits of agreement" "Mean Diff = `te0'+ `te1'*Average " "Limits +/- 2.46*(`te2' + `te3'*Average) ") "'
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}
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if "`valabel'"~="" {
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tempvar label
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qui gen `label' = ""
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cap confirm string variable `valabel'
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if _rc~=0 qui replace `label' = string(`valabel') if `diff'>`uy' | `diff'<`ly'
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else qui replace `label' = `valabel' if `diff'>`uy' | `diff'<`ly'
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local scatteropt "mlabel(`label') note(Points outside limits labelled by `valabel')"
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}
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tempvar freq
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qui bysort `diff' `av':gen `freq'=_N
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local fopt "[fw=`freq']"
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if index("`scatter'","jitter")~=0 local fopt ""
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if "`nograph'"=="" {
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twoway (rarea `uy' `ly' `av', bc(gs13) sort)(scatter `diff' `av' `fopt', `scatteropt' `scatter') /*
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*/(line `y' `av', lp(dash) sort) , legend(off) ytitle(`ytit') xtitle(`xtit') xlabel(`xmin' `xmax') `xopt'
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}
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return local b0 = `b0'
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return local b1 = `b1'
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return local c0 = `c0'
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return local c1 = `c1'
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return local eqn = "`b0'+`b1'*av"
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return local upper = "`b0'+`b1'*Average + 2.46*(`c0'+`c1'*Average)"
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return local lower = "`b0'+`b1'*Average - 2.46*(`c0'+`c1'*Average)"
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}
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end
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