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Re: st: Writing z-values to a dataset after metacum
Sebastian Baumeister wrote:
Dear Statalist users,
I am running a cumulative meta analysis and I am trying to write the estimates to a dataset. I tried parmest after the metacum command but Stata told me that it could not find any previous estimation command. Any suggestions how I can write the z-values to a Stata dataset?
metacum logrr selogrr if year<1995, effect(r) eform id(trnamyr)
Cumulative random-effects meta-analysis of 2 studies (exponential form)
------------------------------------------------------------------------
Cumulative 95% CI
Trial estimate Lower Upper z P value
4S(1994) 0.712 0.594 0.853 -3.691 0.000
MAAS(1994) 0.632 0.379 1.056 -1.752 0.080
. end of do-file
. do "C:\DOKUME~1\bau\LOKALE~1\Temp\STD00000000.tmp"
. parmest,format(estimate min95 max95 %8.2f p %8.1e) list(,)
last estimates not found
Thanks
Sebastian Baumeister
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Try this ado file. Just put it under ado/plus/m and run metacum2 instead
of metacum. This will give you variables that contain the cumulative
estimat, SE, low CI, upper CI, z score, and p value.
Hope it will be usefull,
Nikos
*! version 1.02 jacs January 1998 STB-42 sbe22
program define metacum2
version 7.0
local varlist "req ex min(2) max(4)"
local if "opt"
local in "opt"
local options "EFOrm ID(string) Level(integer $S_level)"
local options "`options' EFFect(string) YLABel(string) XLOG GRaph"
local options "`options' Var CI"
local options "`options' Symbol(string) FMult(real 1)"
local options "`options' CLine YTick GAP CSize(real 180)"
local options "`options' LTRunc(string) RTRunc(string) SAving(string) *"
parse "`*'"
if "`id'"~=""{
confirm variable `id'
}
if "`var'"~=""&"`ci'"~="" {
di in re "Do not use the var option and the ci option at the same time"
exit 198
}
if "`effect'"~="" {
capture assert "`effect'"=="r" | "`effect'"=="f"
if _rc~=0 {
di in re "Must specify effect(f) or effect(r)"
exit 198
}
}
else {
di in re "Must specify effect(f) or effect(r)"
exit 198
}
if "`ylabel'"~="" {
di in re "ylabel option not permitted"
exit 198
}
if "`xlog'"~="" {
di in re "xlog option not permitted (use eform option)"
exit 198
}
if "`symbol'"~="" {
di in re "symbol option not permitted"
exit 198
}
if "`ytick'"~="" {
di in re "ytick option not permitted"
exit 198
}
if "`gap'"~="" {
di in re "gap option not permitted"
exit 198
}
if "`fmult'"~="" {
capture assert `fmult'>0
if _rc~=0 {
di in re "Label font scaling factor must be >0"
exit 198
}
}
tempvar touse v zz cumpsi cumse lc uc z pvalue idlen
parse "`varlist'", parse(" ")
local psi `1'
local se `2'
capture assert `se'>0
if _rc~=0 {
di in re "Standard error/variance/confidence limit must be>0 or missing for all studies"
exit 198
}
quietly {
mark `touse' `if' `in'
markout `touse' `psi' `se'
if "`3'"~="" {
markout `touse' `3'
}
keep if `touse'
}
if "`var'" == "var" {qui replace `se'=sqrt(`se')}
if "`ci'" == "ci" {
capture confirm variable `4'
if _rc~=0 { qui gen `zz' = invnorm(.975) }
else {
qui replace `4' = `4' * 100 if `4' < 1
qui gen `zz' = -1 * invnorm((1- `4' / 100) / 2 )
qui replace `zz' = invnorm(.025) if `zz'==.
}
qui replace `se' = ( ln(`3') - ln(`2')) / 2 / `zz'
qui replace `psi' = ln(`psi')
}
quietly gen `v'=`se'^2
local obs=_N
capture assert `obs'>=2
if _rc~=0 {
di in re "Need at least two studies"
exit 198
}
quietly {
if "`id'"~="" {
gen `idlen'=length(`id')
quietly summarize `idlen'
local idleng=_result(6)
}
gen `cumpsi'=`psi' in 1
gen `cumse'=`se' in 1
local i 2
while `i'<=`obs' {
meta `psi' `se' in 1/`i'
if "`effect'"=="f" {
replace `cumpsi'=$S_1 in `i'
replace `cumse'=$S_2 in `i'
}
else if "`effect'"=="r" {
replace `cumpsi'=$S_7 in `i'
replace `cumse'=$S_8 in `i'
}
local i=`i'+1
}
gen `lc'=`cumpsi'-invnorm(`level'*0.005 + 0.5)*(`cumse')
gen `uc'=`cumpsi'+invnorm(`level'*0.005 + 0.5)*(`cumse')
gen `z'=`cumpsi'/`cumse'
gen `pvalue'=2*min((1-normprob(`z')),normprob(`z'))
if "`eform'"~="" {
replace `cumpsi'=exp(`cumpsi')
replace `lc'=exp(`lc')
replace `uc'=exp(`uc')
local ef=" (exponential form)"
local efu="-------------------"
}
}
if "`effect'"=="f" {
local et="fixed-effects "
local etu="--------------"
}
if "`effect'"=="r" {
local et="random-effects "
local etu="---------------"
}
di in gr _n "Cumulative " "`et'" "meta-analysis of `obs' studies `ef'"
di in ye "----------" "`etu'" "----------------------------`efu'"
di " "
if "`id'"=="" {
di in gr "Cumulative `level'% CI"
di in gr " estimate Lower Upper z P value"
}
else {
local idleng1=max((`idleng'+1), 8)
di in gr _column(`idleng1') " Cumulative `level'% CI"
di in gr "Trial" _column(`idleng1') " estimate Lower Upper z P value"
local col1=`idleng1'+5
local col2=`idleng1'+14
local col3=`idleng1'+21
local col4=`idleng1'+31
local col5=`idleng1'+40
}
local i 1
while `i'<=`obs' {
if "`id'"=="" {
di in ye _column(5) %6.3f `cumpsi'[`i'] _column(14) %6.3f `lc'[`i'] /*
*/ _column(21) %6.3f `uc'[`i'] _column(31) %6.3f `z'[`i'] /*
*/ _column(40) %6.3f `pvalue'[`i']
}
else {
di in ye `id'[`i'] /*
*/ _column(`col1') %6.3f `cumpsi'[`i'] _column(`col2') %6.3f `lc'[`i'] /*
*/ _column(`col3') %6.3f `uc'[`i'] _column(`col4') %6.3f `z'[`i'] /*
*/ _column(`col5') %6.3f `pvalue'[`i']
}
local i=`i'+1
}
capture drop _cumpsi
capture drop _cumse
capture drop _lc
capture drop _uc
capture drop _z
capture drop _pvalue
gen _cumpsi=`cumpsi'
label var _cumpsi "Cumulative estimate"
gen _cumse=`cumse'
label var _cumse "SE of cumulative estimate"
gen _lc=`lc'
label var _lc "Lower 95% CI"
gen _uc=`uc'
label var _uc "Upper 95% CI"
gen _z=`z'
label var _z "z score"
gen _pvalue=`pvalue'
label var _pvalue "p value"
* list `psi' `se' `cumpsi' `cumse'
*****************************
* draw graph *
*****************************
if "`graph'"~="" {
tempvar obsno
tempname obslab k
gen `obsno'=_n
gsort -`obsno'
quietly replace `obsno'=_n
if _N>20 {
local fdiv1=20/_N
}
else {
local fdiv1=1
}
local fdiv=`fdiv1'
local k=_N
quietly {
if "`eform'"~="" {
local xlog "xlog"
}
if "`ltrunc'"~="" {
summ `cumpsi'
if `ltrunc'>_result(5) {
di in re "Left truncation must be less than all effect estimates"
exit 198
}
replace `lc'=`ltrunc' if `lc'<`ltrunc'
}
if "`rtrunc'"~="" {
summ `cumpsi'
if `rtrunc'<_result(6) {
di in re "Right truncation must be greater than all effect estimates"
exit 198
}
replace `uc'=`rtrunc' if `uc'>`rtrunc'
}
if "`saving'"~="" {
local saving "saving(`saving')"
}
local i 1
local ylab="1"
local ytick="1"
while `i'<=_N {
if `i'>=2 {
local ytick "`ytick',`i'"
}
local i=`i'+1
}
if _N<26 {
local ytick "ytick(`ytick')"
}
else {
local ytick ""
}
label define `obslab' 1 " "
label values `obsno' `obslab'
replace `psi'=`cumpsi'
summ `lc'
replace `psi'=_result(5) in 1
summ `uc'
replace `psi'=_result(6) in 2
}
label var `obsno' " "
graph `obsno' `psi', ylab(`ylab') `ytick' s(i) gap(10) `xlog' `options'
parse "$S_G1", parse(",")
* noi display "* `*'"
local leftgph `3'
local dr `9'
local dc `11'
parse "$S_G2", parse(",")
local leftdat `3'
local rgttext=(`leftdat'-`leftgph')*.75
local imax=_N
local i=1
if "`id'"~="" {
if `idleng'>8 {
local fdiv2=8/`idleng'
}
else {
local fdiv2=1
}
local fdiv=min(`fdiv1',`fdiv2')
}
local dr=`dr'*.7*`fdiv'*`fmult'
local dc=`dc'*.7*`fdiv'*`fmult'
gph open, `saving'
graph
local ay=_result(5)
local by=_result(6)
local ax=_result(7)
local bx=_result(8)
gph font `dr' `dc'
while `i'<=`imax' {
* row value
local st=`obsno'[`i']
local row=(`st'*`ay') + `by'
* label y axis
if "`id'"~="" {
local textrow=`row'+(`dc'/2)
local chari=`id'[`i']
gph text `textrow' `rgttext' 0 1 `chari'
}
local mu=`cumpsi'[`i']
if "`eform'"~="" {
local col=(log(`mu')*`ax') + `bx'
}
else {
local col=(`mu'*`ax') + `bx'
}
gph point `row' `col' `csize' 1
* confidence interval
local l=`lc'[`i']
local u=`uc'[`i']
if "`eform'"~="" {
local cleft=(log(`l')*`ax') + `bx'
local cright=(log(`u')*`ax') + `bx'
}
else {
local cleft=(`l'*`ax') + `bx'
local cright=(`u'*`ax') + `bx'
}
gph line `row' `cleft' `row' `cright'
local i=`i'+1
}
* dotted line at the combined estimate
if "`cline'"~="" {
if "`eform'"~="" {
local cmiddle=(log(`cumpsi'[1])*`ax') + `bx'
}
else {
local cmiddle=(`cumpsi'[1]*`ax') + `bx'
}
local top=`obsno'[1]
local rowup=(`top'*`ay') + `by'
local incr=(`rowup'-`row')/100
local j 0
while `j'<50 {
local i=2*`j'
local lower=`row'+(`i'*`incr')
local upper=`row'+((`i'+1)*`incr')
gph line `lower' `cmiddle' `upper' `cmiddle'
local j=`j'+1
}
}
gph close
}
end
