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Computed theoretical power for N=100 and N=200 scenarios

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Corentin Choisy
2024-02-19 18:35:26 +01:00
parent ac9189d26a
commit 238852b08b
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Modules/ado/plus/m/metafunnel.ado Normal file
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*! Version 1.0.2, JACS, 18 August 2003
program define metafunnel
version 8.1
* Graphs funnel plot, with standard error on the vertical axis
if ("`*'" == "") {
di "Syntax is:"
di in wh "metafunnel " in gr "{ theta { se | var } | " _c
di in gr "exp(theta) | ll ul [cl] } [" _c
di in wh "if " in gr "exp] [" in wh "in " in gr "range]"
di in gr " [ " in wh ", by(" in gr "by_var"in wh ")" _c
di in gr " { " in wh "v" in gr "ar | " in wh "ci" in gr " } " _c
di in wh "nol" in gr "ines " in wh "forc" in gr "enull " _c
di in wh "rev" in gr "erse " in wh "ef" in gr "orm"
di in gr " graph_options ]"
exit
}
syntax varlist(numeric min=2 max=4) [if] [in], [ by(varname) ///
Var CI SUbtitle(str) NOLines FORCenull REVerse EForm ///
XTitle(string) YTitle(string) XScale(string) YScale(string) ///
MSymbol(string) * ]
tempvar touse theta setheta etheta zz
tempvar ll2 ul2 vl z mmm vvar w sw wl swl RRm orign
tempname oe
tokenize `varlist'
local theta `1'
if "`3'" == "" {
local setheta `2'
}
else {
tempvar ll ul cl
local ll `2'
local ul `3'
local cl `4'
}
* input error traps
if "`ci'" != "" & "`var'" != "" {
di _n as error "Error: options 'ci' and 'var' cannot " _c
di as error "be specified together."
exit
}
if "`ci'" == "ci" & "`ul'" != "" {
di _n as text "Note: option 'ci' specified."
}
if "`ci'" == "ci" & "`ul'" == "" {
di _n as error "Error: option 'ci' specified but varlist " _c
di as error "has only 2 variables."
exit
}
if "`ci'" != "ci" & "`var'" != "var" & "`ul'" != "" {
di _n as text "Warning: varlist has 3 variables but option " _c
di as text "'ci' not specified; 'ci' assumed."
local ci "ci"
local var ""
}
if "`var'" == "var" & "`ul'" != "" {
di _n as error "Error: option 'var' specified but varlist " _c
di as error "has more than 2 variables."
exit
}
if "`var'" == "var" & "`ul'" == "" {
di _n as text "Note: option 'var' specified."
}
if "`var'" != "var" & "`ul'" == "" {
di _n as text "Note: default data input format (theta, " _c
di as text "se_theta) assumed."
}
* Select data to analyze
mark `touse' `if' `in'
if "`ul'" == "" {
markout `touse' `theta' `setheta'
}
else {
markout `touse' `theta' `ll' `ul'
}
preserve
quietly keep if `touse'
quietly count
if r(N)==0 {
di as error "No observations with nonmissing values of `by'"
exit 999
}
* initial calculations...
if "`var'" == "var" {
qui replace `setheta' = sqrt(`setheta')
}
if "`ci'" == "ci" {
di _n as text "Warning: ci option assumes that ratio measures are being used"
capture confirm variable `cl'
if _rc~=0 {
qui gen `zz' = invnorm(.975)
}
else {
qui replace `cl' = `cl' * 100 if `cl' < 1
qui gen `zz' = -1 * invnorm((1- `cl' / 100) / 2 )
qui replace `zz' = invnorm(.025) if `zz'==.
}
qui gen `setheta' = ( ln(`ul') - ln(`ll')) / 2 / `zz'
qui replace `theta' = ln(`theta')
}
* Graph options
if "`xtitle'" == "" {
local xti : variable label `theta'
if "`xti'" == "" {
local xti "`theta'"
}
}
else if "`xtitle'" ~= "" {
local xti "`xtitle'"
}
if "`ytitle'" == "" {
local yti : variable label `setheta'
if "`yti'" == "" {
local yti "s.e. of `theta'"
}
}
else if "`ytitle'" ~= "" {
local yti "`ytitle'"
}
capture assert "`ysca'"==""
if _rc~=0 {
display as error "ysca option not permitted"
exit 999
}
if "`yscale'"~="" {
local chkrev=index("`yscale'","rev")
display "chkrev: `chkrev'"
if `chkrev'~=0 & "`reverse'"=="" {
local ysca "`yscale'"
}
if `chkrev'==0 & "`reverse'"=="" {
local ysca "`yscale' reverse"
}
if `chkrev'~=0 & "`reverse'"~="" {
display "Parsing yscale: ,`yscale' "
tokenize `yscale'
while "`1'"~="" {
if index("`1'","rev")==0 {
local ysca "`ysca' `1'"
}
mac shift
}
}
if `chkrev'==0 & "`reverse'"~="" {
local ysca "`yscale'"
}
}
if "`yscale'"=="" {
if "`reverse'"=="" {
local ysca "reverse"
}
if "`reverse'"~="" {
local ysca "noreverse"
}
}
if "`subtitle'" == "" {
local subtitle = "Funnel plot with pseudo 95% confidence limits"
}
else if "`subtitle'" == "." { /* "." means blank it out */
local subtitle "" ""
}
local subtitle "subtitle(`subtitle')"
if "`msymbol'"=="" {
local symopt "O T S D + X Oh Th Sh Dh o t s d x oh th sh dh p"
}
if "`msymbol'"~="" {
local symopt "`msymbol'"
}
local msymbol "msymbol(`symopt')"
qui {
gen `orign'=_n
gen `vvar' = `setheta'^2
gen `w' = 1/`vvar'
egen `sw' = sum(`w') if `touse'
gen `wl' = `w' * `theta'
egen `swl' = sum(`wl') if `touse'
sort `orign'
gen `RRm' = `swl' / `sw'
local rxl=`RRm'[1]
scalar `oe' = `RRm'
egen `mmm' = min(`RRm')
replace `RRm' = `mmm' if `setheta' == 0
if "`forcenull'"~="" {
local rxl=0
}
sort `orign'
local obs1=_N+1
local obs2=_N+2
local obs3=_N+3
local obs4=_N+4
local obs5=_N+5
local obs6=_N+6
set obs `obs6'
replace `orign'=_n
replace `theta'=`rxl' in `obs1'
replace `theta'=`rxl' in `obs3'
gen `ll2' = 0 in `obs1'
gen `ul2' = 0 in `obs3'
sort `orign'
qui summ `setheta'
local maxse=r(max)
replace `theta' = `rxl'-(1.96*`maxse') in `obs2'
replace `theta' = `rxl'+(1.96*`maxse') in `obs4'
replace `ll2' = `maxse' in `obs2'
replace `ul2' = `maxse' in `obs4'
gen `vl' = 0 in `obs5'
replace `vl' = `maxse' in `obs6'
replace `theta' = `rxl' in `obs5'
replace `theta' = `rxl' in `obs6'
label var `ll2' "Lower CI"
label var `ul2' "Lower CI"
label var `vl' "Pooled"
if "`forcenull'"~="" {
label var `vl' "No effect"
}
}
* list `setheta' `ll2' `ul2' `vl' `theta' `orign'
* display "RRm: `rxl'"
local funopt "yscale(`ysca') `subtitle' ytitle("`yti'") xtitle("`xti'")"
if "`by'"=="" {
local yvar "`setheta'"
local legopt "legend(off)"
}
if "`by'"~="" {
qui levels `by', local(bylev)
local lev: word count `bylev'
if `lev'>20 {
di as text "Note: distinct group markers available for only 19 groups"
}
sort `orign'
qui drop if `by'==.&_n<`obs1'
qui count if `by'~=.
if r(N)==0 {
di as error "No observations with nonmissing values of `by'"
exit 999
}
forvalues b=1/`lev' {
local bylab ""
local bygroup: word `b' of `bylev'
tempname bg`b'
qui gen `bg`b''=`setheta' if `by'==`bygroup'
local bylab: label (`by') `b'
if "`bylab"=="" {
label variable `bg`b'' "`by'=`b'"
}
if "`bylab"~="" {
label variable `bg`b'' "`bylab'"
}
}
local yvar "`bg1'-`bg`lev''"
} /* end by processing */
if "`nolines'"=="nolines"&"`eform'"=="" {
* display "clause 1"
twoway (scatter `yvar' `theta', `legopt' `msymbol') ///
if `touse', `funopt' `options'
}
if "`nolines'"==""&"`eform'"=="" {
* display "clause 2"
twoway (scatter `yvar' `theta', `legopt' `msymbol') ///
(line `ll2' `ul2' `vl' `theta', msymbol(none none none) ///
clcolor(black black black) clpat(dash dash solid) ///
clwidth(medium medium medium)) ///
if `touse', `funopt' `options'
}
if "`eform'"~="" {
gen `etheta'=exp(`theta')
if "`xtitle'"=="" {
local xti : variable label `theta'
if "`xti'" == "" {
local xti "exp(`theta'), log scale"
}
else if "`xti'" ~= "" {
local xti "exp(`xti'), log scale"
}
}
capture assert "`xsca'"==""
if _rc~=0 {
display as error "xsca option not permitted"
exit 999
}
if "`xscale'"~="" {
local chklog=index("`xscale'","log")
if `chklog'==0 {
local xsca "`xscale' log"
}
else if `chklog'~=0 {
local xsca "`xscale'"
}
}
else if "`xscale'"=="" {
local xsca "log"
}
if "`nolines'"=="nolines" {
* display "clause 3"
twoway (scatter `yvar' `etheta', `legopt' `msymbol') ///
if `touse', `funopt' xscale(`xsca') `options'
}
if "`nolines'"=="" {
* display "clause 4"
local rxl=exp(`rxl')
twoway (scatter `yvar' `etheta', `legopt' `msymbol') ///
(line `ll2' `ul2' `vl' `etheta', msymbol(none none none) ///
clcolor(black black black) clpat(dash dash solid) ///
clwidth(medium medium medium)) ///
if `touse', `funopt' xscale(`xsca') `options'
}
}
end