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219 lines
6.5 KiB
Plaintext
219 lines
6.5 KiB
Plaintext
7 months ago
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*! baplot.ado version 1.21 written by PTS (p.seed@umds.ac.uk) (STB-55: sbe33)
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*! Produces Bland-Altman plots for two variables
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*! See Bland & Altman Lancet Feb 8 1986, pp 307-310
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*!
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*! syntax: baplot var1 var2 if in, symbol(symbol) format(%6.3f) avlab("Average") difflab("Difference") yline(str) textsize(#) other graph options
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* Now allows choice of symbol, and extra ylines Feb 8 1996
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* larger plotting symbols for overlapping points
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* Silly comparisons taken out
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cap prog drop baplot
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prog define baplot
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version 6.0
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* set trace off
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syntax varlist(min=2 max=2 numeric) [if] [in], /*
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*/ [Symbol(string) format(string) avlab(string) difflab(string) /*
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*/ novars noGRaph ci zero mean yline(string) diag saving(string) /*
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*/ text(real 100) ratio(real 1) *]"
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parse "`varlist'", parse(" ")
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local m1 "`1'"
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local m2 "`2'"
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if "`symbol'" == "" { local symbol "o" }
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if "`format'" == "" {local format "%6.3f" }
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if "`saving'" ~= "" { local saving "saving(`saving')"}
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if "`ci'" ~= "" {local mean = "mean" }
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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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tempvar av diff
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if "`avlab'" == "" { local avlab "Average"}
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if lower("`avlab'") == "nolab" { local avlab " "}
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if "`difflab'" == "" { local difflab "Difference" }
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if lower("`difflab'") == "nolab" { local difflab " "}
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qui gen `av' = (`m1' + `m2')/2
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qui gen `diff' = `m1' - `m2'
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label var `av' "`avlab'"
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label var `diff' "`difflab'"
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qui summ `diff' if `touse'
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local xbar = _result(3)
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local sd = _result(4)^.5
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local n = _result(2)
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local se = `sd'/`n'^.5
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local t = invt(_result(2)-1, .95)
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local lrr = `xbar' - 2*`sd'
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local urr = `xbar' + 2*`sd'
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local min = _result(5)
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local max = _result(6)
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local lcb = `xbar' - `t'*`se'
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local ucb = `xbar' + `t'*`se'
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summ `av', meanonly
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local xmin = _result(5)
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local xmax = _result(6)
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local yline "`lrr', `urr'"
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if "`ci'" ~= "" {
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local yline "`yline', `lcb', `ucb'"
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}
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if "`mean'" ~= "" | "`zero'" == "" {local yline "`yline', `xbar'"}
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if "`zero'" ~= "" {local yline "`yline', 0"}
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qui corr `av' `diff'
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local r = _result(4)
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local n = _result(1)
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local sig = tprob(`n'-2, `r'*((`n'-2)/(1-`r'^2))^.5)
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#delim ;
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di in gr _n "Bland-Altman comparison of `m1' and `m2'";
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di in gr "Limits of agreement (Reference Range for difference): " in ye `format' `lrr'
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in gr " to " in ye `format' `urr' ;
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di in gr "Mean difference: " in ye `format' `xbar'
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in gr " (CI " in ye `format' `lcb'
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in gr " to " in ye `format' `ucb'
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in gr ") ";
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di in gr "Range : " in ye `format' `xmin'
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in gr " to " in ye `format' `xmax';
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di in gr "Pitman's Test of difference in variance: r = " in ye `format' `r'
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in gr ", n = " in ye `n'
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in gr ", p =" in ye `format' `sig' ;
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#delim cr
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if "`vars'" ~= "" {
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qui corr `m1' `m2', cov
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local tau = _result(4)
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qui summ `m1'
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local err1 = _result(4) - `tau'
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qui summ `m2'
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local err2 = _result(4) - `tau'
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di in gr "Estimated variance of true measure: " in ye `format' `tau'
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di in gr "Estimated error variance (`1'): " in ye `format' `err1'
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di in gr "Estimated error variance (`2'): " in ye `format' `err2'
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di in gr "Very low or negative error variances may indiate that modelling assumptions are violated."
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}
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global S_1 `xbar'
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global S_2 `lrr'
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global S_3 `urr'
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if "`graph'" == "" & "`diag'" == "" {
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sort `diff' `av'
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tempvar f n
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qui by `diff' `av': gen `f' = _N if `diff' ~= . & `av' ~= .
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qui by `diff' `av': gen `n' = _n if `diff' ~= . & `av' ~= .
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graph `diff' `av' if `touse' & `n' == 1 [fw=`f'], symbol(`symbol') `xlabel' `ylabel' yline(`yline') `saving' `options'
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}
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else if "`diag'" ~= "" {
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local nobs = _N + 1
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qui set obs `nobs'
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qui replace `m2' = 0 if `m2' == .
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* loa
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tempvar lb ub
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qui gen `ub' = `m2' + `xbar' + 2*`sd'
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qui replace `ub' = . if `ub' < 0
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summ `ub', mean
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qui replace `ub' = . if `ub' > _result(5) & `ub' < _result(6)
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qui gen `lb' = `m2' + `xbar' - 2*`sd'
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summ `lb', mean
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if _result(5) < 0 {
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qui replace `lb' = . if `lb' < 0
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local nobs = _N + 1
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qui set obs `nobs'
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qui replace `lb' = 0 if _n == _N
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qui replace `m2' = 2*`sd' - `xbar' if _n == _N
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}
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summ `lb', mean
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qui replace `lb' = . if `lb' > _result(5) & `lb' < _result(6)
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* ci
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if "`ci'" ~= "" {
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tempvar lci uci
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qui gen `lci' = `m2' + `xbar' - invt(`n'-1,0.95)*`sd'/`n'^.5
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qui gen `uci' = `m2' + `xbar' + invt(`n'-1,0.95)*`sd'/`n'^.5
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summ `lci', mean
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if _result(5) < 0 {
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qui replace `lci' = . if `lci' < 0
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local nobs = _N + 1
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qui set obs `nobs'
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qui replace `lci' = 0 if _n == _N
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qui replace `m2' = invt(`n'-1,0.95)*`sd'/`n'^.5 - `xbar' if _n == _N
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}
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summ `uci', mean
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if _result(5) < 0 {
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qui replace `uci' = . if `uci' < 0
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local nobs = _N + 1
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qui set obs `nobs'
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qui replace `uci' = 0 if _n == _N
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qui replace `m2' = - invt(`n'-1,0.95)*`sd'/`n'^.5 - `xbar' if _n == _N
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}
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summ `lci', mean
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qui replace `lci' = . if `lci' > _result(5) & `lci' < _result(6)
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summ `uci', mean
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qui replace `uci' = . if `uci' > _result(5) & `lci' < _result(6)
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}
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summ `m2' if `m2' ~= ., mean
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tempvar diag
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* zero
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if "`zero'" ~= "" | "`mean'" == "" {
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qui gen `diag' = `m2' if `m2' == _result(5) | `m2' == _result(6)
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}
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* mean
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else {
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qui gen `diag' = `m2' + `xbar' if `m2' == _result(5) | `m2' == _result(6)
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summ `diag', mean
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if _result(5) < 0 {
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qui replace `diag' = . if `diag' < 0
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local nobs = _N + 1
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qui set obs `nobs'
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qui replace `diag' = 0 if _n == _N
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qui replace `m2' = - `xbar' if _n == _N
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}
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}
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sort `m1' `m2'
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tempvar f n
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qui by `m1' `m2': gen `f' = _N
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qui by `m1' `m2': gen `n' = _n
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if ("`xlabel'" == "" | "`ylabel'" == "") & index("`options'","xlab") == 0 & index("`options'","ylab") == 0 {
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nicenum labels = 0 `m1' `m2'
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local xlabel xlab($labels)
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local ylabel ylab($labels)
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}
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local r_tx = int(923 * `text'/100)
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local c_tx = int(444 * `text'/100)
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local c_min = int(16000 - (23063*`ratio'/2))
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local c_max = int(16000 + (23063*`ratio'/2))
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di "bbox(0,`c_min',23063,`c_max',`r_tx',`c_tx',0) "
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gph open, `saving'
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graph `m1' `diag' `ub' `lb' `lci' `uci' `m2' if `n' == 1 [fw=`f'], /*
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*/ `xlabel' `ylabel' s(oiiiii) c(.lllll) sort /*
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*/ bbox(0,`c_min',23063,`c_max',`r_tx',`c_tx',0) `options'
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gph close
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}
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end
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exit
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