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*! bamat Version 1.2.2 written 11 June 1997 by P T Seed (STB-55: sbe33)
*!
*! A matrix of Bland-Altman plots for a series of variables
*! bamat varlist, graph_options
* Amended 7 August 1998 to allow for saving graphs
*
* Amended 3 May 2000 by arr@stata to suppress intermediary graphs and
* display only the final matrix of Bland-Altman plots
prog define bamat
version 5.0
local varlist "req ex min(3)"
local if "opt"
local in "opt"
local options "noTABle TItle(string) saving(string) data nograph markout FORmat(string) XLAbel(string) YLAbel(string) text(str) *"
parse "`*'"
if index("`options'","xlab") ~= 0 | index("`options'","ylab") ~= 0 {
di in red "xlabel and ylabel without values not permitted"
exit 198
}
parse "`varlist'", parse(" ")
if "`table'" == "notable" & "`graph'" == "nograph" & "`data'" == "" {
di in red "Either table data or graph options must be chosen"
exit 194 }
preserve
tempvar touse
mark `touse' `if'
if "`markout'" ~= "" {markout `touse' `varlist'}
if "`format'" == "" { local format "%6.3f" }
if "`saving'" ~= "" { local saving "saving(`saving')" }
if "`table'" ~= "notable" {
_table `varlist' if `touse', format(`format') `data'
}
if "`graph'" ~= "nograph" |"`data'" ~= "" {
_limits `varlist' if `touse'
if "`xlabel'" == "" | "`xlabel'" == "xlabel" {
_mynnum xlabel $xmin $xmax
local xlabel "xlabel($xlabel)"
}
else {local xlabel "xlabel(`xlabel')" }
if "`ylabel'" == "" {
_mynnum ylabel $ymin $ymax
local ylabel "ylabel($ylabel)"
}
else {local ylabel "ylabel(`ylabel')" }
#delim ;
di _n in gr "Range of x values is " in ye %6.0g $xmin in gr " to " in ye %6.0g $xmax
in gr ", range of y values is " in ye %6.0g $ymin in gr " to " in ye %6.0g $ymax;
#delim cr
if "`title'" == "" {_graph `varlist' if `touse', `graph' `saving' `xlabel' `ylabel' `data' `options' }
else {_graph `varlist' if `touse', title("`title'") `graph' `saving' `xlabel' `ylabel' `data' `options' }
}
end bamat
prog define _table
local varlist "req ex"
local if "opt"
local options "data format(str)"
parse "`*'"
tempvar touse
mark `touse' `if'
di in gr _new "Reference ranges for differences between two methods""
#delimit;
di in gr _new(2) "Method 1" _col(10) "Method 2" _col(20) "Mean"
_col(30) "[95% Reference Range]"
_col(54) "Minimum" _col(64) "Maximum" ;
#delimit cr
di in gr _dup(70) "-"
tempvar av diff
qui gen `av' = .
qui gen `diff' = .
local nvar : word count `varlist'
local i = 2
while `i' <= `nvar' {
local j = 1
while `j' < `i' {
* di "i = |`i'|, j = |`j'|"
qui replace `diff' = ``i'' - ``j'' `if'
label var `diff' " "
qui replace `av' = (``i'' + ``j'')/2 `if'
label var `av' " "
qui summ `diff' `if'
local mean = _result(3)
local lrr = `mean' - 2*_result(4)^.5
local urr = `mean' + 2*_result(4)^.5
local min = _result(5)
local max = _result(6)
di in gr "``i''" _col(10) "``j''" _col(20) in ye `format' `mean' /*
*/ _col(30) `format' `lrr' _col(40) `format' `urr' _col(52) `format' `min' _col(62) `format' `max'
local j = `j' +1
}
local i = `i' + 1
}
di in gr _dup(70) "-"
end _table
prog define _data
local av `1'
local diff `2'
local m1 `3'
local m2 `4'
di _n in gr _dup(40) "-"
di in gr "Data for graph comparing `m1' and `m2'"
di in gr "Difference" _col(20) "Average"
di in gr _dup(40) "-"
local k = 1
while `k' <= _N {
if `av'[`k'] ~= . & `diff'[`k'] ~= . { di `diff'[`k'] _col(20) `av'[`k'] }
local k = `k' + 1
}
di in gr _dup(40) "-" _n
end _data
prog define _graph
local varlist "req ex"
local if "req"
local options "title(str) saving(str) xlabel(str) ylabel(str) nograph data *"
parse "`*'",
if "`saving'" ~= "" { local saving "saving(`saving')" }
local nvar : word count `varlist'
tempvar diff av
qui gen `diff' = .
qui gen `av' = .
label var `diff' " "
label var `av' " "
local gonoff : set graphics
set graphics off
local i = 1
while `i' <= `nvar' {
local j = 1
while `j' <= `nvar' {
qui replace `diff' = ``i'' - ``j'' `if'
qui replace `av' = (``i'' + ``j'')/2 `if'
tempfile g`i'`j'
local graph2 "`graph2' `i'`j'"
local graphs "`graphs' `g`i'`j''"
if `i' == `j' & "`graph'" == "" { _namegr ``i'', saving(`g`i'`j'', replace) }
* set trace on
else if `i' ~= `j'{
qui summ `diff'
local mean = _result(3)
local lrr = _result(3) - 2*_result(4)^.5
local urr = _result(3) + 2*_result(4)^.5
if "`graph'" == "" {
sort `diff' `av'
* set trace off
tempvar f n
qui by `diff' `av' : gen `f' = _N if `diff' ~= . & `av' ~= .
qui by `diff' `av' : gen `n' = _n if `diff' ~= . & `av' ~= .
qui graph `diff' `av' `if' & `n' == 1 [fw=`f'], xlabel(`xlabel') /*
*/ylabel(`ylabel') `options' saving(`g`i'`j'', replace) yline(`lrr', `mean', `urr')
}
if "`data'" ~= "" { _data `av' `diff' ``i'' ``j''}
}
local j = `j' + 1
}
local i = `i' + 1
}
set graphics `gonoff'
if "`graph'" == "" { graph using `graphs', title("`title'") `saving' }
end _graph
prog define _namegr
local varlist "req ex"
local options "saving(string)"
parse "`*'"
local f1 = 3000
local f2 = 1400
parse "`varlist'", parse (" ")
local lab1 : var label `1'
if "`lab1'" == "" { local lab1 "`1'" }
qui gph open, saving(`saving')
qui gph font `f1' `f2'
qui gph text 11188 16000 0 0 `lab1'
qui gph close
end _namegr
prog define _limits
local varlist "req ex"
local if "opt"
parse "`*'"
tempvar av diff
qui gen `diff' = `2' - `1'
qui gen `av' = (`2' + `1')/2
qui summ `av' `if'
global xmin = _result(5)
global xmax = _result(6)
qui summ `diff' `if'
global ymin = _result(5)
global ymax = _result(6)
local nvar : word count `varlist'
local i = 3
while `i' <= `nvar' {
local j = 1
while `j' < `i' {
qui replace `diff' = ``i'' - ``j'' `if'
qui replace `av' = (``i'' + ``j'')/2 `if'
qui summ `av' `if'
if _result(5) < $xmin { global xmin = _result(5) }
if _result(6) > $xmax { global xmax = _result(6) }
qui summ `diff' `if'
if _result(5) < $ymin { global ymin = _result(5) }
if _result(6) > $ymax { global ymax = _result(6) }
local j = `j' + 1
}
local i = `i' + 1
}
if $ymax + $ymin > 0 { global ymin = -$ymax }
else { global ymax = -$ymin }
end _limits
prog define _mynnum
*! _mynnum Version 1.00 20/3/1997 PTS
*! a version of nicenum to handle numbers less than 1
*! usage: _mynnum global_macro minimum maximum mumber_of_ticks
version 5.0
local macro "`1'"
if `2' ~= `3' {
if `2' < `3' {
local min `2'
local max `3'
}
else {
local min `3'
local max `2'
}
}
else {
di in red "Numbers do not differ"
exit 198
}
local nticks `4'
if "`nticks'" == "" { local nticks = 5 }
else { cap confirm integer `nticks'
assert `nticks' > 2
if _rc ~= 0 {
di in red "Number of ticks requested must be at least 2"
exit 198
}
}
local gap = 10^(int(log10(`max' - `min'))-1)
local nt = int((`max' - `min' )/`gap') + 1
while `nt' < `nticks' {
local gap = `gap'/10
local nt = int((`max' - `min' )/`gap') + 1
}
if `nt' > `nticks' - 1 {
local gap = `gap' * 2
local nt = int((`max' - `min' )/`gap') + 1
}
if `nt' > `nticks' - 1 {
local gap = `gap' * 2.5
}
if `nt' > `nticks' - 1 {
local gap = `gap' * 2
}
local tick = `gap'*int(`min'/`gap')
while `tick' > `min' { local tick = `tick' - `gap' }
global `macro' "`tick'"
while `tick' < `max' {
local tick = `tick' + `gap'
global `macro' "$`macro', `tick'"
}
end _mynnum