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917 lines
24 KiB
Plaintext
917 lines
24 KiB
Plaintext
7 months ago
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*! v2.6.1 Roger Harbord 4 Nov 2008
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program define metareg, eclass byable(recall)
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version 7
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if replay() {
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if "`e(cmd)'" !="metareg" {
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error 301 /* last estimates not found */
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}
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if _by() {
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error 190 /* request may not be combined with by */
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}
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Display `0'
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exit
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}
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syntax varlist(min=1 numeric) [if] [in] , [ /*
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*/ wsse(varname numeric) /*
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*/ EForm /*
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*/ NOCONStant /*
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*/ MM /*
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*/ REML /*
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*/ EB /*
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*/ Knapphartung /*
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*/ z /* standard normal w/o K-H modification to variance
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*/ Level(passthru) /*
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*/ PERMute(string) /*
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*/ Graph /* produce a bubble plot
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*/ RAndomsize /* marker size according to random-effects weights
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*/ TAU2test /* tests for tau2=0 residual het test
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*/ LOg /* maximize_option
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*/ TOLerance(real 1e-6) /* maximize_option also used by eb method
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*/ ITERate(integer 100) /* maximize_option - default 16000 is too large!
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*/ wsvar(varname numeric)/* undoc'd, for compat with v1 ( wsvar = wsse^2 )
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*/ bsest(string) /* undoc'd, for compat with v1
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*/ tdist /* undoc'd, use t-distib w/o K-H variance mod'n
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*/ ORIGinal /* undoc'd, use version 1 (metareg_orig)
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*/ LRtau2 /* undoc'd, for compat with v.2.2 on SSC
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*/ NOITer /* passed through to metareg_orig
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*/ NOTAUComp /* no comparison of tau2 with constant-only model;
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for use by permute() option
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*/ * /* other `options', parsed by -mlopts-
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*/ ]
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marksample touse
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tokenize `varlist'
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local y `1' /* study estimate */
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qui count if `touse'
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local nobs = r(N)
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if r(N) == 0 {
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error 2000 /* no observations */
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}
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if r(N) <= `: word count `*'' {
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error 2001 /* insufficient observations */
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}
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macro shift 1
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_rmcoll `*' if `touse', `noconstant'
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local xvars `r(varlist)'
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mlopts mlopts, `options' iterate(`iterate') /* Parse maximize_options */
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if "`wsse'"=="" & "`wsvar'"=="" {
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di as error "wsse() option required"
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exit 100
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}
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if "`wsse'"!="" & "`wsvar'"!="" {
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di as error "options wsse() and wsvar() cannot both be specified"
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exit 198
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}
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if "`wsse'"!="" {
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capture assert `wsse' > 0 if `touse'
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if _rc {
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di as error "zero or negative wsse() not allowed"
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exit 499
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}
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tempvar wsvar
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qui gen `wsvar' = `wsse'^2 if `touse'
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}
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if "`wsvar'"!="" {
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capture assert `wsvar' > 0 if `touse'
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if _rc {
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di as error "zero or negative wsvar() not allowed"
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exit 499
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}
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}
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if "`noconstant'"!="" {
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/* local nvar : word count `varlist' */
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if `: word count `varlist'' == 1 {
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di as error "independent variables required with " /*
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*/ "noconstant option"
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exit 102
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}
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}
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local wc : word count "`mm' `reml' `eb'"
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if `wc' > 1 {
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di as error "Only one of options mm, reml and eb can be specified"
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exit 198
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}
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local wc : word count "`mm' `reml' `eb' `bsest'"
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if `wc' > 1 {
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di as error "Option bsest() cannot be used with options mm, reml or eb"
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exit 198
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}
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if "`bsest'"!="reml" & "`bsest'"!="ml" & "`bsest'"!="eb" /*
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*/ & "`bsest'"!="mm" & "`bsest'"!="" {
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di as error "Between study variance estimation method invalid:"
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di as error "should be either reml, ml, eb or mm"
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exit 198
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}
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if "`bsest'" == "" {
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if "`mm'" != "" | "`permute'" != "" { /* MM is default with permute */
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local bsest "mm"
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}
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else if "`eb'" != "" {
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local bsest "eb"
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}
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else { /* REML is default otherwise */
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local bsest "reml"
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}
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}
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if "`bsest'" =="ml" {
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di as text /*
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*/ "Option bsest(ml) not supported by version 2 of metareg."
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di as text "Calling version 1.06 (sbe23):" _n(1)
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metareg_orig `0'
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exit
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}
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if "`knapphartung'" !="" & "`z'" != "" {
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di as error "Options knapphartung and z cannot both be specified"
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exit 198
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}
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if "`tdist'" != "" & ( "`z'" != "" | "`knapphartung'" !="" ) {
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di as error "Option t cannot be specified with options knapphartung or z"
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exit 198
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}
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if "`original'" =="original" {
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di as text "Calling metareg version 1.06 (sbe23):" _n(1)
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metareg_orig `0'
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exit
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}
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if "`log'"=="" {
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local log "nolog"
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}
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if "`lrtau2'" != "" {
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local tau2test tau2test
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}
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if "`permute'" != "" {
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if "`xvars'" == "" {
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di as error "Option permute() requires at least one covariate"
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exit 198
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}
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Permute, y(`y') xvars(`xvars') wsvar(`wsvar') permute(`permute') ///
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nobs(`nobs') `noconstant' ///
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bsest(`bsest') `knapphartung' `z' ///
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level(`level') touse(`touse')
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exit
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}
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/*** begin main code ***/
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tempvar w hat v resid
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tempname remll_c remll sumw tau2 tau2mm b V Q df_Q tau2_0
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quietly {
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/** (get starting values using) method-of-moments **/
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gen `w'=1/`wsvar' if `touse'
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summ `w' if `touse', meanonly
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scalar `sumw'=r(sum)
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/* use regress not vwls so can predict hat */
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regress `y' `xvars' [iw=`w'] if `touse', `noconstant'
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predict `hat' if `touse', hat
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/* H_ii where H = X(X'WX)^{-1}X', W=diag(w) */
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replace `hat'=`hat'*`w'^2 if `touse' /* Tr( WX(X'WX)^{-1}X'W ) */
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/* iweights mess up residual df so compute it : */
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scalar `df_Q' = `nobs' - e(df_m) - ("`noconstant'" == "")
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scalar `Q' = e(rss)
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summ `hat' if `touse', meanonly
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scalar `tau2' = (`Q' - `df_Q') / ( `sumw' - r(sum))
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/* truncate at zero */
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scalar `tau2' = max(`tau2', 0)
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/* Fit constant-only model to compare tau2
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NB can't compare different fixed-effect models using REML log-L */
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if "`noconstant'" == "" & "`notaucomp'"=="" & "`xvars'" != "" {
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metareg `y' if `touse', wsvar(`wsvar') bsest(`bsest') notaucomp
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scalar `tau2_0' = e(tau2)
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}
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} /* end quietly */
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if "`bsest'" == "reml" { /* *** REML start *** */
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global REML_x `xvars' /* betas not estimated by ml so pass X as global*/
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global REML_nocons `noconstant' /* have to pass as global too */
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/* fit comparison fixed-effect (tau2=0) model*/
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ml model d0 metareg_ll (`y' `wsvar' = ) /*
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*/ if `touse', maximize init(_cons=0) /*
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*/ search(off) iterate(0) nowarning nolog
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scalar `remll_c' = e(ll) /* log-L, comparison model */
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/* estimate tau2 using ml */
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local tau2mm = max(`tau2', 1e-4) /* init doesn't work with scalar */
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ml model d0 metareg_ll (`y' `wsvar' = ) if `touse',/*
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*/ maximize init(_cons=`tau2mm') search(off) nopreserve noscvars /*
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*/ `log' tolerance(`tolerance') `mlopts'
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if "`e(converged)'" != "1" {
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di as error "WARNING: REML estimation of tau2 failed to converge."
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di as error "Estimates may be wrong."
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di as error "Try adding mm option to use method-of-moments".
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}
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macro drop REML_x
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macro drop REML_nocons
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scalar `tau2' = max( _b[_cons], 0)
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if `tau2' > 0 {
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scalar `remll' = e(ll)
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}
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else {
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scalar `remll' = `remll_c'
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}
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} /* REML end */
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if "`bsest'" == "eb" { /* *** EB start *** */
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local oldtau2=-1
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local j=0
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while abs((`tau2'-`oldtau2')/(`oldtau2'+1e-8)) >= `tolerance' {
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local j = `j'+1
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tempvar wt ypred wtsq numi
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local oldtau2=`tau2'
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qui {
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gen `wt'=(`wsvar'+`tau2')^-1 if `touse'
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regress `y' `xvars' [aw=`wt'] if `touse'
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predict `ypred' if `touse'
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gen `wtsq'=`wt'^2 if `touse'
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gen `numi'=(`wt')*(((e(N)/e(df_r))*((`y'-`ypred')^2))-`wsvar') if `touse'
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summ `numi' if `touse', meanonly
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local num=r(sum)
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summ `wt', meanonly
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local tau2=`num'/r(sum)
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}
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if "`log'" == "log" {
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di as txt "Iteration " `j' ": tau^2 = " as res `tau2'
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}
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}
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local tau2 = max(`tau2',0)
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} /* EB end*/
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/** estimate final model by weighted LS **/
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quietly {
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gen `v' = `wsvar' + `tau2'
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regress `y' `xvars' [iw=1/`v'] if `touse', mse1 `noconstant'
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matrix `b' = e(b)
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matrix `V' = e(V)
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local df_m = e(df_m)
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/** knapp and hartung variance adjustment **/
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if "`z'" == "" & "`tdist'" == "" {
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tempname vkh
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predict `resid' if `touse', resid
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replace `resid' = `resid'*`resid' / `v' if `touse'
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summarize `resid' if `touse', meanonly
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local qkh = r(sum) / `df_Q'
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matrix `V' = `V' * max(1, `qkh')
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}
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} /* end quietly */
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estimates post `b' `V', depname(`y') obs(`nobs') esample(`touse')
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estimates scalar tau2 = `tau2'
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estimates scalar df_m = `df_m'
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estimates scalar Q = `Q'
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estimates scalar df_Q = `df_Q'
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estimates scalar I2 = max( ( `Q' - `df_Q' ) / `Q', 0 )
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if "`z'" == "" { /* post df_r so get t & F tests not z and chi2 */
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estimates scalar df_r = `df_Q'
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}
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if "`tdist'" =="" & "`z'" == "" {
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estimates scalar q_KH = `qkh'
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}
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if "`wsse'" == "" {
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estimates local wsvar "`wsvar'"
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}
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else {
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estimates local wsse "`wsse'"
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}
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if "`bsest'" == "mm" {
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estimates local method "Method of moments"
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}
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if "`bsest'" == "eb" {
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estimates local method "Empirical Bayes"
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}
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if "`bsest'" == "reml" {
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estimates local method "REML"
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/* return reml log-l in e(remll) NOT e(ll)
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to ensure can't do inappropriate lrtest of fixed effects */
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estimates scalar remll = `remll'
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if "`remll_c'" != "" {
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estimates scalar remll_c = `remll_c'
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if (e(remll) < e(remll_c)) | (`tau2' <= 0) {
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estimates scalar chi2_c = 0
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}
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else {
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estimates scalar chi2_c = 2*(e(remll)-e(remll_c))
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}
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}
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}
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if "`noconstant'" == "" & "`notaucomp'"=="" & "`xvars'" != "" {
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estimates scalar tau2_0 = `tau2_0'
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}
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/* overall F (or chi2) test */
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if "`xvars'" != "" {
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qui test `xvars'
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if "`r(chi2)'" != "" {
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estimates scalar chi2 = r(chi2)
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}
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else {
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estimates scalar F = r(F)
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}
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}
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estimates local predict "metareg_p"
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estimates local depvar "`y'"
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estimates local cmd "metareg"
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Display, `level' `eform' `tau2test'
|
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||
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if "`graph'" != "" {
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||
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if `: word count `xvars'' != 1 {
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di as error in smcl ///
|
||
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"graph option works only with a single {it:indepvar}"
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}
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else Graph `y' `xvars' `v' `w' `randomsize'
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}
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end
|
||
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|
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program define Graph
|
||
|
|
version 8.2
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||
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args y xvars v w randomsize
|
||
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||
|
|
tempvar fit
|
||
|
|
qui predict `fit'
|
||
|
|
if "`randomsize'" == "" {
|
||
|
|
local size `w'
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
local size 1/`v'
|
||
|
|
}
|
||
|
|
local yti : variable label `y'
|
||
|
|
if "`yti'" == "" {
|
||
|
|
local yti `y'
|
||
|
|
}
|
||
|
|
scatter `y' `xvars' [aw=`size'], msymbol(oh) ///
|
||
|
|
|| line `fit' `xvars', sort ///
|
||
|
|
||, legend(off) ytitle( `yti')
|
||
|
|
|
||
|
|
end
|
||
|
|
|
||
|
|
|
||
|
|
program define Display
|
||
|
|
version 7
|
||
|
|
syntax [, Level(int $S_level) EForm Tau2test q]
|
||
|
|
tempname pval i2
|
||
|
|
if "`eform'" == "eform" {
|
||
|
|
local eform eform(exp(b))
|
||
|
|
}
|
||
|
|
scalar `pval' = chi2tail(e(df_Q), e(Q))
|
||
|
|
|
||
|
|
di as txt _n "Meta-regression" /*
|
||
|
|
*/ _col(55) "Number of obs" _col(70) "= " as res %7.0f e(N)
|
||
|
|
di as res "`e(method)'" /*
|
||
|
|
*/ as txt " estimate of between-study variance" /*
|
||
|
|
*/ _col(55) "tau2" _col(70) "=" as res %8.4g e(tau2)
|
||
|
|
di as txt "% residual variation due to heterogeneity" /*
|
||
|
|
*/ _col(55) "I-squared_res" _col(70) "= " as res %6.2f 100 * e(I2) "%"
|
||
|
|
|
||
|
|
|
||
|
|
if "`e(tau2_0)'" != "" {
|
||
|
|
di as txt "Proportion of between-study variance explained" /*
|
||
|
|
*/ _col(55) "Adj R-squared " _col(70) "= " _c
|
||
|
|
di as res %6.2f 100 * ( 1 - e(tau2) / e(tau2_0) ) "%"
|
||
|
|
}
|
||
|
|
|
||
|
|
/* Overall model fit */
|
||
|
|
if e(df_m) > 1 {
|
||
|
|
di as txt "Joint test for all covariates" _c
|
||
|
|
if "`e(df_r)'" == "" {
|
||
|
|
di as txt _col(55) "Model chi2(" as res e(df_m) as txt ")" /*
|
||
|
|
*/ _col(70) "= " as res %7.2f e(chi2)
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
di as txt _col(55) "Model F(" as res e(df_m) as txt "," /*
|
||
|
|
*/ as res e(df_r) as txt ")" _col(70) "= " /*
|
||
|
|
*/ as res %7.2f e(F)
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
di as res "With" _c
|
||
|
|
if "`e(q_KH)'" == "" {
|
||
|
|
di as res "out" _c
|
||
|
|
}
|
||
|
|
di as txt " Knapp-Hartung modification" _c
|
||
|
|
|
||
|
|
if e(df_m) > 1 {
|
||
|
|
if "`e(df_r)'" == "" {
|
||
|
|
di as txt _col(55) "Prob > chi2" _col(70) "= " /*
|
||
|
|
*/ as res %7.4f chi2tail( e(df_m), e(chi2) )
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
di as txt _col(55) "Prob > F" _col(70) "= " /*
|
||
|
|
*/ as res %7.4f Ftail( e(df_m), e(df_r), e(F) )
|
||
|
|
}
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
di /* end line */
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
estimates display, level(`level') `eform'
|
||
|
|
|
||
|
|
if "`tau2test'" != "" {
|
||
|
|
di as txt "Test for residual between-study variance (of tau2=0)" /*
|
||
|
|
*/ _col(55) "Q_res (" as res %1.0f e(df_Q) as txt " df)" /*
|
||
|
|
*/ _col(70) "= " as res %7.2f e(Q)
|
||
|
|
di as txt _col(55) "Prob > Q_res" _col(70) "= " as res %7.4f `pval'
|
||
|
|
|
||
|
|
if "`e(method)'" == "REML" {
|
||
|
|
scalar `pval' = chi2tail(1, e(chi2_c))*0.5
|
||
|
|
if e(chi2_c) <=0 {
|
||
|
|
scalar `pval'= 1
|
||
|
|
}
|
||
|
|
di in smcl as txt "Likelihood-ratio test of tau2=0: " /*
|
||
|
|
*/ as txt "{help j_chibar:chibar2(01) =}" as res %6.2f e(chi2_c) /*
|
||
|
|
*/ as txt " Prob > chibar2 = " as res %7.4f `pval'
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
end
|
||
|
|
|
||
|
|
|
||
|
|
program define Permute, rclass
|
||
|
|
version 7
|
||
|
|
syntax, y(varname numeric) xvars(varlist numeric) wsvar(varname numeric) ///
|
||
|
|
permute(string) nobs(integer) [noconstant bsest(string) knapphartung z ///
|
||
|
|
level(passthru) touse(varname numeric)]
|
||
|
|
|
||
|
|
gettoken reps 0 : permute, parse(",")
|
||
|
|
confirm integer number `reps'
|
||
|
|
if `reps' < 1 {
|
||
|
|
di as err "permute() must be a positive integer"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
|
||
|
|
syntax [, Univariable Detail Verbose NOISily Joint(string) * ]
|
||
|
|
|
||
|
|
if "`verbose'" != "" { /* verbose is undoc'd synonym for detail */
|
||
|
|
local detail detail
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`xvars'" == "" {
|
||
|
|
di as error "permute() option not allowed when no covariates"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`joint'" != "" & "`univariable'" != "" {
|
||
|
|
di as error "options univariable and joint() cannot both be specified"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
|
||
|
|
if `:word count `xvars'' == 1 {
|
||
|
|
local univariable /* ensure unset if only one xvar */
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`univariable'" == "" {
|
||
|
|
di as txt _n(1) "Monte Carlo permutation test for meta-regression"
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
di as txt _n(1) in smcl /*
|
||
|
|
*/ "Monte Carlo permutation test for {it:single covariate} meta-regressions"
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`bsest'" == "" {
|
||
|
|
local bsest "mm" /* mm is default for permutation test */
|
||
|
|
}
|
||
|
|
if "`bsest'" == "mm" {
|
||
|
|
di as res _n "Moment-based " _c
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
di as res _n "REML " _c
|
||
|
|
}
|
||
|
|
di as txt "estimate of between-study variance"
|
||
|
|
|
||
|
|
if "`knapphartung'" == "" {
|
||
|
|
local z "z" /* z is default for for permutation test */
|
||
|
|
di as res "Without " _c
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
di as res "With " _c
|
||
|
|
}
|
||
|
|
di as txt "Knapp & Hartung modification to standard errors"
|
||
|
|
|
||
|
|
|
||
|
|
if "`noconstant'" != "" {
|
||
|
|
di as error "Permutation test inappropriate with no constant"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
|
||
|
|
local permopts `univariable' `noconstant' `bsest' `knapphartung' `z'
|
||
|
|
|
||
|
|
preserve
|
||
|
|
qui keep if `touse'
|
||
|
|
|
||
|
|
foreach x of varlist `xvars' {
|
||
|
|
local explist "`explist' `x'=r(z_`x')"
|
||
|
|
local xlist "`xlist' `x'"
|
||
|
|
}
|
||
|
|
|
||
|
|
/* parse varlists in joint() option separated by \ / or | */
|
||
|
|
local jt `joint'
|
||
|
|
local nj 0
|
||
|
|
while "`jt'" != "" {
|
||
|
|
gettoken tmp jt : jt, parse("\/|")
|
||
|
|
if strpos("\/|", "`tmp'") {
|
||
|
|
continue
|
||
|
|
}
|
||
|
|
local 0 `tmp'
|
||
|
|
syntax varlist
|
||
|
|
local nj = `nj' + 1
|
||
|
|
local joint`nj' `varlist'
|
||
|
|
di as txt "joint`nj' : " as res "`joint`nj''"
|
||
|
|
local explistj "`explistj' joint`nj'=r(chi2`nj')"
|
||
|
|
local jlist "`jlist' joint`nj'"
|
||
|
|
}
|
||
|
|
|
||
|
|
tempvar n
|
||
|
|
qui gen `n' = _n if `touse'
|
||
|
|
|
||
|
|
tempfile pm pmadj
|
||
|
|
if "`noisily'" =="" {
|
||
|
|
local quietly quietly
|
||
|
|
/* quietly permute then replay (if detail specified)
|
||
|
|
to suppress full -permute- header */
|
||
|
|
}
|
||
|
|
`quietly' permute `n' /*
|
||
|
|
*/ "metareg_pm `y' `wsvar' `n', xvars(`xvars') joint(`joint') `permopts'" /*
|
||
|
|
*/ `explist' `explistj', /*
|
||
|
|
*/ reps(`reps') saving(`pm') replace `options'
|
||
|
|
|
||
|
|
|
||
|
|
tempname R C P B
|
||
|
|
matrix `R' = r(reps)
|
||
|
|
matrix `C' = r(c)
|
||
|
|
matrix `P' = `C' * inv(diag(`R'))
|
||
|
|
|
||
|
|
local nx : word count `xvars'
|
||
|
|
forvalues i = 1/`nx' {
|
||
|
|
local minreps = min(`reps',`R'[1,`i'])
|
||
|
|
}
|
||
|
|
if `minreps' != `reps' {
|
||
|
|
di as txt "WARNING: some permutations returned missing values" _c
|
||
|
|
di as txt "See detail below:"
|
||
|
|
local detail detail
|
||
|
|
}
|
||
|
|
|
||
|
|
/* to get adjusted p-values from -permute-,
|
||
|
|
replace z-statistics by their largest absolute values
|
||
|
|
for each permutation */
|
||
|
|
quietly {
|
||
|
|
use `pm', clear
|
||
|
|
tempvar max
|
||
|
|
gen `max' = 0
|
||
|
|
foreach v of varlist `xlist' {
|
||
|
|
replace `max' = abs(`v') if abs(`v') > `max'
|
||
|
|
}
|
||
|
|
foreach v of varlist `xlist' {
|
||
|
|
replace `v' = `max'
|
||
|
|
}
|
||
|
|
drop `max'
|
||
|
|
save `pmadj', replace
|
||
|
|
permute `xlist' `jlist' using `pmadj', `level'
|
||
|
|
} // end quietly
|
||
|
|
|
||
|
|
matrix `B' = r(b)
|
||
|
|
matrix `R' = `R' \ r(reps)
|
||
|
|
matrix `C' = `C' \ r(c)
|
||
|
|
matrix `P' = `P' \ r(c) * inv(diag(r(reps)))
|
||
|
|
foreach M in `R' `C' `P' {
|
||
|
|
matrix rownames `M' = unadj multadj
|
||
|
|
if "`joint'" != "" {
|
||
|
|
/* set matrix entries for adjusted joint tests (N/A) to missing */
|
||
|
|
matrix `M'[2, colnumb(`M',"joint1")] = J(1,`nj',.)
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
/* clear results from last permutation so not available to user */
|
||
|
|
estimates clear
|
||
|
|
restore
|
||
|
|
|
||
|
|
/*** Display results of permutation test ****/
|
||
|
|
|
||
|
|
if `nx' == 1 { /* only one xvar */
|
||
|
|
local sep = sqrt(`P'[1,1]*(1-`P'[1,1])/`reps')
|
||
|
|
if `sep' == 0 {
|
||
|
|
local sep .
|
||
|
|
}
|
||
|
|
di as txt _n _col(9) "Number of obs =" as res %8.0f _N
|
||
|
|
di as txt _col(9) "Permutations =" as res %8.0f `reps'
|
||
|
|
di in smcl as txt "{hline 13}{c TT}{hline 17}"
|
||
|
|
di in smcl as txt /*
|
||
|
|
*/ %12s "`y'" " {c |}" _s(1) /*
|
||
|
|
*/ %6s "p" _s(4) /*
|
||
|
|
*/ %6s "SE(p)"
|
||
|
|
|
||
|
|
di in smcl as txt "{hline 13}{c +}{hline 17}"
|
||
|
|
di in smcl as txt /*
|
||
|
|
*/ %12s abbrev(`"`xvars'"',10) /*
|
||
|
|
*/ " {c |}" _s(2) /*
|
||
|
|
*/ as result %7.3f `P'[1,1] _s(1) /*
|
||
|
|
*/ as result %7.4f `sep'
|
||
|
|
di in smcl as txt "{hline 13}{c BT}{hline 17}"
|
||
|
|
}
|
||
|
|
|
||
|
|
else { /* more than one xvar */
|
||
|
|
|
||
|
|
/* Table Head */
|
||
|
|
di as txt _n "P-values unadjusted and adjusted for multiple testing"
|
||
|
|
di as txt _n _col(14) "Number of obs =" as res %8.0f `nobs'
|
||
|
|
di as txt _col(14) "Permutations =" as res %8.0f `reps'
|
||
|
|
di in smcl as txt "{hline 13}{c TT}{hline 22}"
|
||
|
|
di in smcl as txt _s(13) "{c |}" _s(12) "P"
|
||
|
|
di in smcl as txt /*
|
||
|
|
*/ %12s abbrev("`y'",10) " {c |}" /*
|
||
|
|
*/ %11s "Unadjusted" %11s "Adjusted"
|
||
|
|
di in smcl as txt "{hline 13}{c +}{hline 22}"
|
||
|
|
|
||
|
|
foreach x of local xvars {
|
||
|
|
local i = `i' + 1
|
||
|
|
di in smcl as txt /*
|
||
|
|
*/ %12s abbrev(`"`x'"',10) /*
|
||
|
|
*/ " {c |}" _s(4) /*
|
||
|
|
*/ as result %7.3f `P'[1,`i'] _s(4) /*
|
||
|
|
*/ %7.3f `P'[2,`i']
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`joint'" != "" {
|
||
|
|
di in smcl as txt "{hline 13}{c +}{hline 22}"
|
||
|
|
forvalues j = 1/`nj' {
|
||
|
|
di in smcl as txt /*
|
||
|
|
*/ %12s "joint`j'" /*
|
||
|
|
*/ " {c |}" _s(4) /*
|
||
|
|
*/ as result %7.3f `P'[1,`nx'+`j']
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
/* Table Foot */
|
||
|
|
di in smcl as txt "{hline 13}{c BT}{hline 22}"
|
||
|
|
/* largest SE(p) = sqrt( max( p(1-p)/n ) ) */
|
||
|
|
local maxvarp 0
|
||
|
|
forvalues i = 1/2 {
|
||
|
|
forvalues j = 1/`=colsof(`P')'{
|
||
|
|
local maxvarp = max( `maxvarp', ///
|
||
|
|
`P'[`i',`j'] * (1 - `P'[`i',`j']) / `R'[`i',`j'] )
|
||
|
|
}
|
||
|
|
}
|
||
|
|
if `maxvarp' == 0 {
|
||
|
|
local maxvarp .
|
||
|
|
}
|
||
|
|
di as txt "largest Monte Carlo SE(P) =" /*
|
||
|
|
*/ as res %7.4f sqrt(`maxvarp')
|
||
|
|
}
|
||
|
|
|
||
|
|
/* Detailed results if requested, as displayed by -permute- */
|
||
|
|
if "`detail'" != "" {
|
||
|
|
di as txt in smcl _n(2) "{title:Unadjusted}"
|
||
|
|
permute `xlist' `jlist' using `pm', `level'
|
||
|
|
|
||
|
|
if `nx' > 1 {
|
||
|
|
di as txt in smcl _n(2) "{title:Adjusted for multiple testing}"
|
||
|
|
permute `xlist' using `pmadj', `level'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
di as txt _n "WARNING:"
|
||
|
|
di as txt "Monte Carlo methods use random numbers, so results may differ between runs."
|
||
|
|
di as txt "Ensure you specify enough permutations to obtain the desired precision."
|
||
|
|
|
||
|
|
return scalar N = `nobs'
|
||
|
|
return matrix reps = `R'
|
||
|
|
return matrix c = `C'
|
||
|
|
return matrix p = `P'
|
||
|
|
return matrix b = `B'
|
||
|
|
|
||
|
|
end
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
program define metareg_orig
|
||
|
|
*! v1.06 copyright Stephen Sharp January 1998 STB-42 sbe23
|
||
|
|
version 5.0
|
||
|
|
local varlist "req ex min(1)"
|
||
|
|
local if "opt"
|
||
|
|
local in "opt"
|
||
|
|
local options "WSSe(string) WSVar(string) BSest(string) TOLeran(integer 4) Level(integer $S_level)"
|
||
|
|
local options "`options' NOITer ORIGinal" /* original added by RMH */
|
||
|
|
|
||
|
|
parse "`*'"
|
||
|
|
if "`wsse'"=="" & "`wsvar'"=="" {
|
||
|
|
di in re "Must specify a variable containing estimate of precision"
|
||
|
|
di in re "within each trial, using either wsse() or wsvar() option"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
if "`wsse'"~="" & "`wsvar'"~=""{
|
||
|
|
confirm variable `wsse'
|
||
|
|
confirm variable `wsvar'
|
||
|
|
local i=1
|
||
|
|
while `i'<=_N {
|
||
|
|
if abs(`wsse[`i']'^2-`wsvar[`i']')>0.00001 {
|
||
|
|
di in re "Within study variance should be square of within study standard error"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
local i=`i'+1
|
||
|
|
}
|
||
|
|
}
|
||
|
|
if "`wsvar'"~="" {
|
||
|
|
confirm variable `wsvar'
|
||
|
|
}
|
||
|
|
if "`wsse'"~="" {
|
||
|
|
confirm variable `wsse'
|
||
|
|
tempvar wsvar
|
||
|
|
qui gen `wsvar'=`wsse'^2
|
||
|
|
}
|
||
|
|
if "`bsest'"=="" {
|
||
|
|
local bsest "reml"
|
||
|
|
}
|
||
|
|
if "`bsest'"~="reml" & "`bsest'"~="ml" & "`bsest'"~="eb" & "`bsest'"~="mm" & "`bsest'"~="" {
|
||
|
|
di in re "Between study variance estimation method invalid:"
|
||
|
|
di in re "should be either reml, ml, eb or mm"
|
||
|
|
exit 198
|
||
|
|
}
|
||
|
|
if "`noiter'"~="" & "`bsest'"=="mm" {
|
||
|
|
di in bl "Warning: mm is a non-iterative method, noiter option ignored"
|
||
|
|
}
|
||
|
|
parse "`varlist'", parse(" ")
|
||
|
|
|
||
|
|
local y "`1'"
|
||
|
|
mac shift
|
||
|
|
local xvars "`*'"
|
||
|
|
|
||
|
|
tempvar touse
|
||
|
|
preserve
|
||
|
|
qui {
|
||
|
|
mark `touse' `if' `in'
|
||
|
|
markout `touse' `y' `xvars'
|
||
|
|
keep if `touse'
|
||
|
|
}
|
||
|
|
|
||
|
|
qui regress `y' `xvars'
|
||
|
|
local p=_result(3)
|
||
|
|
local N=_result(1)
|
||
|
|
|
||
|
|
if "`bsest'"=="mm" {
|
||
|
|
tempvar wt ypred numi one
|
||
|
|
qui {
|
||
|
|
gen `wt'=`wsvar'^-1
|
||
|
|
regress `y' `xvars' [aw=`wt']
|
||
|
|
predict `ypred'
|
||
|
|
gen `one'=1
|
||
|
|
tempname X C Xt C1 XtC1 A A1 A1XtC1 C1X B
|
||
|
|
mkmat `one' `xvars', matrix(`X')
|
||
|
|
matrix `C'=J(`N',`N',0)
|
||
|
|
local i=1
|
||
|
|
while `i'<=_N {
|
||
|
|
matrix `C'[`i',`i']=`wsvar'[`i']
|
||
|
|
local i=`i'+1
|
||
|
|
}
|
||
|
|
mat `Xt'=`X''
|
||
|
|
mat `C1'=inv(`C')
|
||
|
|
mat `XtC1'=`Xt'*`C1'
|
||
|
|
mat `A'=`XtC1'*`X'
|
||
|
|
mat `A1'=inv(`A')
|
||
|
|
mat `A1XtC1'=`A1'*`XtC1'
|
||
|
|
mat `C1X'=`C1'*`X'
|
||
|
|
mat `B'=`C1X'*`A1XtC1'
|
||
|
|
local trB=trace(`B')
|
||
|
|
summ `wt'
|
||
|
|
local denom=_result(18)-`trB'
|
||
|
|
gen `numi'=`wt'*((`y'-`ypred')^2)
|
||
|
|
summ `numi'
|
||
|
|
local num=max(_result(18)-(`N'-(`p'+1)),0)
|
||
|
|
local newtsq=`num'/`denom'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`bsest'"~="mm" {
|
||
|
|
|
||
|
|
local tsq=0.1
|
||
|
|
local newtsq=0
|
||
|
|
local j=1
|
||
|
|
|
||
|
|
while abs(`tsq'-`newtsq')>=10^(-`toleran') {
|
||
|
|
tempvar wt ypred wtsq numi
|
||
|
|
local tsq=`newtsq'
|
||
|
|
if "`noiter'"=="" {
|
||
|
|
di in gr "Iteration " `j' ": tau^2 = " in ye `tsq'
|
||
|
|
}
|
||
|
|
qui {
|
||
|
|
gen `wt'=(`wsvar'+`tsq')^-1
|
||
|
|
regress `y' `xvars' [aw=`wt']
|
||
|
|
predict `ypred'
|
||
|
|
gen `wtsq'=`wt'^2
|
||
|
|
}
|
||
|
|
if "`bsest'"=="reml" {
|
||
|
|
qui {
|
||
|
|
gen `numi'=(`wtsq')*(((`N'/(`N'-(`p'+1)))*((`y'-`ypred')^2))-`wsvar')
|
||
|
|
summ `numi'
|
||
|
|
local num=max(_result(18),0)
|
||
|
|
summ `wtsq'
|
||
|
|
local denom=_result(18)
|
||
|
|
local newtsq=`num'/`denom'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`bsest'"=="ml" {
|
||
|
|
qui {
|
||
|
|
gen `numi'=(`wtsq')*(((`y'-`ypred')^2)-`wsvar')
|
||
|
|
summ `numi'
|
||
|
|
local num=max(_result(18),0)
|
||
|
|
summ `wtsq'
|
||
|
|
local denom=_result(18)
|
||
|
|
local newtsq=`num'/`denom'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
if "`bsest'"=="eb" {
|
||
|
|
qui {
|
||
|
|
gen `numi'=(`wt')*(((`N'/(`N'-(`p'+1)))*((`y'-`ypred')^2))-`wsvar')
|
||
|
|
summ `numi'
|
||
|
|
local num=max(_result(18),0)
|
||
|
|
summ `wt'
|
||
|
|
local denom=_result(18)
|
||
|
|
local newtsq=`num'/`denom'
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
local j=`j'+1
|
||
|
|
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
tempvar wt
|
||
|
|
qui {
|
||
|
|
gen `wt'=(`wsvar'+`newtsq')^-1
|
||
|
|
summ `wt'
|
||
|
|
}
|
||
|
|
local sumwt=_result(18)
|
||
|
|
|
||
|
|
#delimit ;
|
||
|
|
di _n
|
||
|
|
in gr "Meta-analysis regression"
|
||
|
|
_col(56) "No of studies = " in ye `N' _n
|
||
|
|
in gr _col(56) "tau^2 method " in ye "`bsest'" _n
|
||
|
|
in gr _col(56) "tau^2 estimate = " in ye %6.5g `newtsq' _n ;
|
||
|
|
#delimit cr
|
||
|
|
if "`bsest'"=="ml" | "`bsest'"=="reml" | "`bsest'"=="eb" {
|
||
|
|
di in bl "Successive values of tau^2 differ by less than 10^-"`toleran' " :convergence achieved"
|
||
|
|
}
|
||
|
|
|
||
|
|
qui regress `y' `xvars' [aw=`wt']
|
||
|
|
|
||
|
|
local scpar=(`sumwt'*(_result(9)^2))/_result(1)
|
||
|
|
local scpar1=(1/`scpar')
|
||
|
|
|
||
|
|
matrix V=get(VCE)
|
||
|
|
matrix b=get(_b)
|
||
|
|
|
||
|
|
matrix v=`scpar1'*V
|
||
|
|
|
||
|
|
|
||
|
|
mat post b v
|
||
|
|
mat mlout, level(`level')
|
||
|
|
|
||
|
|
global S_1 = `N'
|
||
|
|
global S_2 = `newtsq'
|
||
|
|
|
||
|
|
restore
|
||
|
|
|
||
|
|
end
|
||
|
|
|
||
|
|
|
||
|
|
exit
|