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301 lines
8.0 KiB
Plaintext
301 lines
8.0 KiB
Plaintext
9 months ago
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*! bamat Version 1.2.2 written 11 June 1997 by P T Seed (STB-55: sbe33)
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*!
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*! A matrix of Bland-Altman plots for a series of variables
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*! bamat varlist, graph_options
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* Amended 7 August 1998 to allow for saving graphs
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*
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* Amended 3 May 2000 by arr@stata to suppress intermediary graphs and
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* display only the final matrix of Bland-Altman plots
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prog define bamat
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version 5.0
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local varlist "req ex min(3)"
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local if "opt"
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local in "opt"
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local options "noTABle TItle(string) saving(string) data nograph markout FORmat(string) XLAbel(string) YLAbel(string) text(str) *"
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parse "`*'"
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if index("`options'","xlab") ~= 0 | index("`options'","ylab") ~= 0 {
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di in red "xlabel and ylabel without values not permitted"
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exit 198
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}
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parse "`varlist'", parse(" ")
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if "`table'" == "notable" & "`graph'" == "nograph" & "`data'" == "" {
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di in red "Either table data or graph options must be chosen"
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exit 194 }
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preserve
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tempvar touse
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mark `touse' `if'
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if "`markout'" ~= "" {markout `touse' `varlist'}
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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 "`table'" ~= "notable" {
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_table `varlist' if `touse', format(`format') `data'
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}
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if "`graph'" ~= "nograph" |"`data'" ~= "" {
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_limits `varlist' if `touse'
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if "`xlabel'" == "" | "`xlabel'" == "xlabel" {
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_mynnum xlabel $xmin $xmax
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local xlabel "xlabel($xlabel)"
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}
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else {local xlabel "xlabel(`xlabel')" }
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if "`ylabel'" == "" {
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_mynnum ylabel $ymin $ymax
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local ylabel "ylabel($ylabel)"
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}
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else {local ylabel "ylabel(`ylabel')" }
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#delim ;
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di _n in gr "Range of x values is " in ye %6.0g $xmin in gr " to " in ye %6.0g $xmax
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in gr ", range of y values is " in ye %6.0g $ymin in gr " to " in ye %6.0g $ymax;
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#delim cr
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if "`title'" == "" {_graph `varlist' if `touse', `graph' `saving' `xlabel' `ylabel' `data' `options' }
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else {_graph `varlist' if `touse', title("`title'") `graph' `saving' `xlabel' `ylabel' `data' `options' }
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}
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end bamat
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prog define _table
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local varlist "req ex"
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local if "opt"
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local options "data format(str)"
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parse "`*'"
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tempvar touse
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mark `touse' `if'
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di in gr _new "Reference ranges for differences between two methods""
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#delimit;
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di in gr _new(2) "Method 1" _col(10) "Method 2" _col(20) "Mean"
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_col(30) "[95% Reference Range]"
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_col(54) "Minimum" _col(64) "Maximum" ;
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#delimit cr
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di in gr _dup(70) "-"
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tempvar av diff
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qui gen `av' = .
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qui gen `diff' = .
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local nvar : word count `varlist'
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local i = 2
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while `i' <= `nvar' {
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local j = 1
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while `j' < `i' {
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* di "i = |`i'|, j = |`j'|"
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qui replace `diff' = ``i'' - ``j'' `if'
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label var `diff' " "
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qui replace `av' = (``i'' + ``j'')/2 `if'
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label var `av' " "
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qui summ `diff' `if'
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local mean = _result(3)
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local lrr = `mean' - 2*_result(4)^.5
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local urr = `mean' + 2*_result(4)^.5
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local min = _result(5)
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local max = _result(6)
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di in gr "``i''" _col(10) "``j''" _col(20) in ye `format' `mean' /*
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*/ _col(30) `format' `lrr' _col(40) `format' `urr' _col(52) `format' `min' _col(62) `format' `max'
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local j = `j' +1
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}
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local i = `i' + 1
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}
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di in gr _dup(70) "-"
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end _table
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prog define _data
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local av `1'
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local diff `2'
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local m1 `3'
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local m2 `4'
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di _n in gr _dup(40) "-"
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di in gr "Data for graph comparing `m1' and `m2'"
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di in gr "Difference" _col(20) "Average"
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di in gr _dup(40) "-"
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local k = 1
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while `k' <= _N {
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if `av'[`k'] ~= . & `diff'[`k'] ~= . { di `diff'[`k'] _col(20) `av'[`k'] }
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local k = `k' + 1
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}
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di in gr _dup(40) "-" _n
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end _data
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prog define _graph
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local varlist "req ex"
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local if "req"
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local options "title(str) saving(str) xlabel(str) ylabel(str) nograph data *"
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parse "`*'",
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if "`saving'" ~= "" { local saving "saving(`saving')" }
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local nvar : word count `varlist'
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tempvar diff av
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qui gen `diff' = .
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qui gen `av' = .
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label var `diff' " "
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label var `av' " "
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local gonoff : set graphics
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set graphics off
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local i = 1
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while `i' <= `nvar' {
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local j = 1
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while `j' <= `nvar' {
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qui replace `diff' = ``i'' - ``j'' `if'
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qui replace `av' = (``i'' + ``j'')/2 `if'
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tempfile g`i'`j'
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local graph2 "`graph2' `i'`j'"
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local graphs "`graphs' `g`i'`j''"
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if `i' == `j' & "`graph'" == "" { _namegr ``i'', saving(`g`i'`j'', replace) }
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* set trace on
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else if `i' ~= `j'{
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qui summ `diff'
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local mean = _result(3)
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local lrr = _result(3) - 2*_result(4)^.5
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local urr = _result(3) + 2*_result(4)^.5
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if "`graph'" == "" {
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sort `diff' `av'
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* set trace off
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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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qui graph `diff' `av' `if' & `n' == 1 [fw=`f'], xlabel(`xlabel') /*
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*/ylabel(`ylabel') `options' saving(`g`i'`j'', replace) yline(`lrr', `mean', `urr')
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}
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if "`data'" ~= "" { _data `av' `diff' ``i'' ``j''}
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}
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local j = `j' + 1
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}
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local i = `i' + 1
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}
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set graphics `gonoff'
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if "`graph'" == "" { graph using `graphs', title("`title'") `saving' }
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end _graph
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prog define _namegr
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local varlist "req ex"
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local options "saving(string)"
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parse "`*'"
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local f1 = 3000
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local f2 = 1400
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parse "`varlist'", parse (" ")
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local lab1 : var label `1'
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if "`lab1'" == "" { local lab1 "`1'" }
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qui gph open, saving(`saving')
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qui gph font `f1' `f2'
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qui gph text 11188 16000 0 0 `lab1'
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qui gph close
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end _namegr
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prog define _limits
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local varlist "req ex"
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local if "opt"
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parse "`*'"
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tempvar av diff
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qui gen `diff' = `2' - `1'
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qui gen `av' = (`2' + `1')/2
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qui summ `av' `if'
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global xmin = _result(5)
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global xmax = _result(6)
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qui summ `diff' `if'
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global ymin = _result(5)
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global ymax = _result(6)
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local nvar : word count `varlist'
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local i = 3
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while `i' <= `nvar' {
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local j = 1
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while `j' < `i' {
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qui replace `diff' = ``i'' - ``j'' `if'
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qui replace `av' = (``i'' + ``j'')/2 `if'
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qui summ `av' `if'
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if _result(5) < $xmin { global xmin = _result(5) }
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if _result(6) > $xmax { global xmax = _result(6) }
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qui summ `diff' `if'
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if _result(5) < $ymin { global ymin = _result(5) }
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if _result(6) > $ymax { global ymax = _result(6) }
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local j = `j' + 1
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}
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local i = `i' + 1
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}
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if $ymax + $ymin > 0 { global ymin = -$ymax }
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else { global ymax = -$ymin }
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end _limits
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prog define _mynnum
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*! _mynnum Version 1.00 20/3/1997 PTS
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*! a version of nicenum to handle numbers less than 1
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*! usage: _mynnum global_macro minimum maximum mumber_of_ticks
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version 5.0
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local macro "`1'"
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if `2' ~= `3' {
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if `2' < `3' {
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local min `2'
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local max `3'
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}
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else {
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local min `3'
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local max `2'
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}
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}
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else {
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di in red "Numbers do not differ"
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exit 198
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}
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local nticks `4'
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if "`nticks'" == "" { local nticks = 5 }
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else { cap confirm integer `nticks'
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assert `nticks' > 2
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if _rc ~= 0 {
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di in red "Number of ticks requested must be at least 2"
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exit 198
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}
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}
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local gap = 10^(int(log10(`max' - `min'))-1)
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local nt = int((`max' - `min' )/`gap') + 1
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while `nt' < `nticks' {
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local gap = `gap'/10
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local nt = int((`max' - `min' )/`gap') + 1
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}
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if `nt' > `nticks' - 1 {
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local gap = `gap' * 2
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local nt = int((`max' - `min' )/`gap') + 1
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}
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if `nt' > `nticks' - 1 {
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local gap = `gap' * 2.5
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}
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if `nt' > `nticks' - 1 {
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local gap = `gap' * 2
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}
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local tick = `gap'*int(`min'/`gap')
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while `tick' > `min' { local tick = `tick' - `gap' }
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global `macro' "`tick'"
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while `tick' < `max' {
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local tick = `tick' + `gap'
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global `macro' "$`macro', `tick'"
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}
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end _mynnum
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