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350 lines
8.9 KiB
Plaintext
350 lines
8.9 KiB
Plaintext
7 months ago
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*! Version 1.0.2, JACS, 18 August 2003
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program define metafunnel
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version 8.1
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* Graphs funnel plot, with standard error on the vertical axis
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if ("`*'" == "") {
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di "Syntax is:"
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di in wh "metafunnel " in gr "{ theta { se | var } | " _c
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di in gr "exp(theta) | ll ul [cl] } [" _c
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di in wh "if " in gr "exp] [" in wh "in " in gr "range]"
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di in gr " [ " in wh ", by(" in gr "by_var"in wh ")" _c
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di in gr " { " in wh "v" in gr "ar | " in wh "ci" in gr " } " _c
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di in wh "nol" in gr "ines " in wh "forc" in gr "enull " _c
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di in wh "rev" in gr "erse " in wh "ef" in gr "orm"
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di in gr " graph_options ]"
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exit
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}
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syntax varlist(numeric min=2 max=4) [if] [in], [ by(varname) ///
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Var CI SUbtitle(str) NOLines FORCenull REVerse EForm ///
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XTitle(string) YTitle(string) XScale(string) YScale(string) ///
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MSymbol(string) * ]
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tempvar touse theta setheta etheta zz
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tempvar ll2 ul2 vl z mmm vvar w sw wl swl RRm orign
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tempname oe
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tokenize `varlist'
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local theta `1'
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if "`3'" == "" {
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local setheta `2'
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}
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else {
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tempvar ll ul cl
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local ll `2'
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local ul `3'
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local cl `4'
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}
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* input error traps
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if "`ci'" != "" & "`var'" != "" {
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di _n as error "Error: options 'ci' and 'var' cannot " _c
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di as error "be specified together."
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exit
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}
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if "`ci'" == "ci" & "`ul'" != "" {
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di _n as text "Note: option 'ci' specified."
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}
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if "`ci'" == "ci" & "`ul'" == "" {
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di _n as error "Error: option 'ci' specified but varlist " _c
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di as error "has only 2 variables."
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exit
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}
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if "`ci'" != "ci" & "`var'" != "var" & "`ul'" != "" {
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di _n as text "Warning: varlist has 3 variables but option " _c
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di as text "'ci' not specified; 'ci' assumed."
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local ci "ci"
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local var ""
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}
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if "`var'" == "var" & "`ul'" != "" {
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di _n as error "Error: option 'var' specified but varlist " _c
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di as error "has more than 2 variables."
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exit
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}
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if "`var'" == "var" & "`ul'" == "" {
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di _n as text "Note: option 'var' specified."
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}
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if "`var'" != "var" & "`ul'" == "" {
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di _n as text "Note: default data input format (theta, " _c
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di as text "se_theta) assumed."
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}
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* Select data to analyze
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mark `touse' `if' `in'
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if "`ul'" == "" {
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markout `touse' `theta' `setheta'
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}
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else {
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markout `touse' `theta' `ll' `ul'
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}
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preserve
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quietly keep if `touse'
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quietly count
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if r(N)==0 {
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di as error "No observations with nonmissing values of `by'"
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exit 999
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}
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* initial calculations...
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if "`var'" == "var" {
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qui replace `setheta' = sqrt(`setheta')
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}
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if "`ci'" == "ci" {
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di _n as text "Warning: ci option assumes that ratio measures are being used"
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capture confirm variable `cl'
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if _rc~=0 {
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qui gen `zz' = invnorm(.975)
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}
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else {
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qui replace `cl' = `cl' * 100 if `cl' < 1
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qui gen `zz' = -1 * invnorm((1- `cl' / 100) / 2 )
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qui replace `zz' = invnorm(.025) if `zz'==.
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}
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qui gen `setheta' = ( ln(`ul') - ln(`ll')) / 2 / `zz'
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qui replace `theta' = ln(`theta')
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}
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* Graph options
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if "`xtitle'" == "" {
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local xti : variable label `theta'
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if "`xti'" == "" {
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local xti "`theta'"
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}
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}
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else if "`xtitle'" ~= "" {
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local xti "`xtitle'"
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}
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if "`ytitle'" == "" {
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local yti : variable label `setheta'
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if "`yti'" == "" {
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local yti "s.e. of `theta'"
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}
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}
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else if "`ytitle'" ~= "" {
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local yti "`ytitle'"
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}
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capture assert "`ysca'"==""
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if _rc~=0 {
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display as error "ysca option not permitted"
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exit 999
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}
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if "`yscale'"~="" {
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local chkrev=index("`yscale'","rev")
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display "chkrev: `chkrev'"
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if `chkrev'~=0 & "`reverse'"=="" {
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local ysca "`yscale'"
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}
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if `chkrev'==0 & "`reverse'"=="" {
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local ysca "`yscale' reverse"
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}
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if `chkrev'~=0 & "`reverse'"~="" {
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display "Parsing yscale: ,`yscale' "
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tokenize `yscale'
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while "`1'"~="" {
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if index("`1'","rev")==0 {
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local ysca "`ysca' `1'"
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}
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mac shift
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}
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}
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if `chkrev'==0 & "`reverse'"~="" {
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local ysca "`yscale'"
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}
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}
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if "`yscale'"=="" {
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if "`reverse'"=="" {
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local ysca "reverse"
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}
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if "`reverse'"~="" {
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local ysca "noreverse"
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}
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}
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if "`subtitle'" == "" {
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local subtitle = "Funnel plot with pseudo 95% confidence limits"
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}
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else if "`subtitle'" == "." { /* "." means blank it out */
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local subtitle "" ""
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}
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local subtitle "subtitle(`subtitle')"
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if "`msymbol'"=="" {
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local symopt "O T S D + X Oh Th Sh Dh o t s d x oh th sh dh p"
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}
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if "`msymbol'"~="" {
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local symopt "`msymbol'"
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}
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local msymbol "msymbol(`symopt')"
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qui {
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gen `orign'=_n
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gen `vvar' = `setheta'^2
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gen `w' = 1/`vvar'
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egen `sw' = sum(`w') if `touse'
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gen `wl' = `w' * `theta'
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egen `swl' = sum(`wl') if `touse'
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sort `orign'
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gen `RRm' = `swl' / `sw'
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local rxl=`RRm'[1]
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scalar `oe' = `RRm'
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egen `mmm' = min(`RRm')
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replace `RRm' = `mmm' if `setheta' == 0
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if "`forcenull'"~="" {
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local rxl=0
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}
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sort `orign'
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local obs1=_N+1
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local obs2=_N+2
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local obs3=_N+3
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local obs4=_N+4
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local obs5=_N+5
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local obs6=_N+6
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set obs `obs6'
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replace `orign'=_n
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replace `theta'=`rxl' in `obs1'
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replace `theta'=`rxl' in `obs3'
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gen `ll2' = 0 in `obs1'
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gen `ul2' = 0 in `obs3'
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sort `orign'
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qui summ `setheta'
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local maxse=r(max)
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replace `theta' = `rxl'-(1.96*`maxse') in `obs2'
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replace `theta' = `rxl'+(1.96*`maxse') in `obs4'
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replace `ll2' = `maxse' in `obs2'
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replace `ul2' = `maxse' in `obs4'
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gen `vl' = 0 in `obs5'
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replace `vl' = `maxse' in `obs6'
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replace `theta' = `rxl' in `obs5'
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replace `theta' = `rxl' in `obs6'
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label var `ll2' "Lower CI"
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label var `ul2' "Lower CI"
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label var `vl' "Pooled"
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if "`forcenull'"~="" {
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label var `vl' "No effect"
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}
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}
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* list `setheta' `ll2' `ul2' `vl' `theta' `orign'
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* display "RRm: `rxl'"
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local funopt "yscale(`ysca') `subtitle' ytitle("`yti'") xtitle("`xti'")"
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if "`by'"=="" {
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local yvar "`setheta'"
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local legopt "legend(off)"
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}
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if "`by'"~="" {
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qui levels `by', local(bylev)
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local lev: word count `bylev'
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if `lev'>20 {
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di as text "Note: distinct group markers available for only 19 groups"
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}
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sort `orign'
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qui drop if `by'==.&_n<`obs1'
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qui count if `by'~=.
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if r(N)==0 {
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di as error "No observations with nonmissing values of `by'"
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exit 999
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}
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forvalues b=1/`lev' {
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local bylab ""
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local bygroup: word `b' of `bylev'
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tempname bg`b'
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qui gen `bg`b''=`setheta' if `by'==`bygroup'
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local bylab: label (`by') `b'
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if "`bylab"=="" {
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label variable `bg`b'' "`by'=`b'"
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}
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if "`bylab"~="" {
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label variable `bg`b'' "`bylab'"
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}
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}
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local yvar "`bg1'-`bg`lev''"
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} /* end by processing */
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if "`nolines'"=="nolines"&"`eform'"=="" {
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* display "clause 1"
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twoway (scatter `yvar' `theta', `legopt' `msymbol') ///
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if `touse', `funopt' `options'
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}
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if "`nolines'"==""&"`eform'"=="" {
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* display "clause 2"
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twoway (scatter `yvar' `theta', `legopt' `msymbol') ///
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(line `ll2' `ul2' `vl' `theta', msymbol(none none none) ///
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clcolor(black black black) clpat(dash dash solid) ///
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clwidth(medium medium medium)) ///
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if `touse', `funopt' `options'
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}
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if "`eform'"~="" {
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gen `etheta'=exp(`theta')
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if "`xtitle'"=="" {
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local xti : variable label `theta'
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if "`xti'" == "" {
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local xti "exp(`theta'), log scale"
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}
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else if "`xti'" ~= "" {
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local xti "exp(`xti'), log scale"
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}
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}
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capture assert "`xsca'"==""
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if _rc~=0 {
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display as error "xsca option not permitted"
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exit 999
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}
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if "`xscale'"~="" {
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local chklog=index("`xscale'","log")
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if `chklog'==0 {
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local xsca "`xscale' log"
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}
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else if `chklog'~=0 {
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local xsca "`xscale'"
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}
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}
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else if "`xscale'"=="" {
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local xsca "log"
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}
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if "`nolines'"=="nolines" {
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* display "clause 3"
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twoway (scatter `yvar' `etheta', `legopt' `msymbol') ///
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if `touse', `funopt' xscale(`xsca') `options'
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}
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if "`nolines'"=="" {
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* display "clause 4"
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local rxl=exp(`rxl')
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twoway (scatter `yvar' `etheta', `legopt' `msymbol') ///
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(line `ll2' `ul2' `vl' `etheta', msymbol(none none none) ///
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clcolor(black black black) clpat(dash dash solid) ///
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clwidth(medium medium medium)) ///
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if `touse', `funopt' xscale(`xsca') `options'
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}
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}
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end
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