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RMST.ado
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*! version 1.0.1 25may2021
cap program drop RMST
program RMST, rclass
version 15
syntax [varname(default=none)] [if] [in] [, tmax(string) df(string) npar fpm pseudo Level(cilevel)]
st_is 2 analysis
marksample touse, novarlist
if "`df'"=="" {
local df 3
}
if "`dftvc'"=="" {
local dftvc 0
//proportional hazard
}
if "`npar'" == "" & "`fpm'" =="" & "`pseudo'" == "" {
local npar = 1
local fpm = 1
local pseudo = 1
}
if "`level'"!="" {
local alpha = (100 - `level')/100
}
else {
local alpha=0.05
}
local quant=1-`alpha'/2
if "`fpm'" != "" {
cap which stpm2
if _rc {
dis as error "stpm2 is required; type -ssc install stpm2- to obtain it"
exit 499
}
}
if "`pseudo'" != "" {
cap which stpmean
if _rc {
dis as error "rmst is required; type -net install rmst, from(http://www.homepages.ucl.ac.uk/~ucakjpr/stata)- to obtain it"
exit 499
}
}
*********************
*no group
*******************
if "`varlist'"=="" {
if "`tmax'"=="" {
qui sum _t if _d==1 & `touse'
local tmax=`r(max)'
dis as text "tmax missing, longest observed event time was used: `=string(`tmax',"%4.2f")'"
}
return scalar tmax=`tmax'
*1) non-parametric
**********************
if "`npar'" != "" {
preserve
qui stset _t, fail(_d) exit(time `tmax')
qui stci if `touse', rmean level(`level')
restore
local r= `r(rmean)'
local se= `r(se)'
local r_lci=`r(lb)'
local r_uci=`r(ub)'
local z=`r'/`se'
local p=2*(1-normal(abs(`z')))
return scalar rmst_npar=`r'
return scalar rmst_lci_npar=`r_lci'
return scalar rmst_uci_npar=`r_uci'
tempname A
matrix `A'= `r' \ `se' \ `z' \ ///
`p' \ `r_lci' \ `r_uci'
mat colnames `A'= ""
mat rownames `A' = b se t pvalue ll ul
return matrix table_npar `A'
}
*2) parametric
*******************
if "`fpm'" != "" {
tempvar rmst
tempvar rmst_se
qui stpm2 if `touse' , scale(hazard) df(`df')
qui predict `rmst', rmst tmax(`tmax') stdp
local rmst_lci=`rmst'[1]-invnormal(`quant')*`rmst'_se[1]
local rmst_uci=`rmst'[1]+invnormal(`quant')*`rmst'_se[1]
local rmst_z=`rmst'[1]/`rmst'_se[1]
local rmst_p=2*(1-normal(abs(`rmst_z')))
return scalar tmax_fpm=`tmax'
return scalar rmst_fpm=`rmst'[1]
return scalar rmst_lci_fpm=`rmst_lci'
return scalar rmst_uci_fpm=`rmst_uci'
tempname B
matrix `B'= `rmst'[1] \ `rmst'_se[1] \ ///
`rmst_z' \ `rmst_p' \ ///
`rmst_lci' \ `rmst_uci'
mat colnames `B'= ""
mat rownames `B' = b se t pvalue ll ul
return matrix table_fpm `B'
}
* 3) pseudovalues
*********************
if "`pseudo'" != "" {
tempvar pmean50
tempname P
local tmax_ = `tmax' - `tmax'/10^6
qui stpmean if `touse' , at(`tmax_') generate(`pmean50')
qui glm `pmean50' if `touse' , family(gaussian) link(id) vce(robust)
matrix `P' = r(table)
local r = `P'[1,1]
local se = `P'[2,1]
local r_lci = `P'[5,1]
local r_uci = `P'[6,1]
local z = `P'[3,1]
local p = `P'[4,1]
return scalar rmst_pseudo=`r'
return scalar rmst_lci_pseudo=`r_lci'
return scalar rmst_uci_pseudo=`r_uci'
tempname C
matrix `C'= `r' \ `se' \ `z' \ ///
`p' \ `r_lci' \ `r_uci'
mat colnames `C'= ""
mat rownames `C' = b se t pvalue ll ul
return matrix table_pseudo `C'
}
}
else {
*********************
*group
*******************
qui levelsof `varlist', local(lev)
local wc: word count `lev'
cap assert `wc'==2
if _rc {
dis as text "Group variable does not have two levels, difference is not calculated."
}
if "`tmax'"=="" {
local counter=0
foreach l of local lev {
qui sum _t if `varlist'==`l' & _d==1 & `touse'
local m`counter'=`r(max)'
local counter=`counter'+1
}
local tmax=min(`m0',`m1')
dis as text ///
"tmax missing, minimum of the longest observed event times in both groups was used (`=string(`tmax',"%4.2f")')."
}
return scalar tmax=`tmax'
dis as result "Restricted mean survival time calculated at `=string(`tmax',"%4.2f")'"
*1) non-parametric approach
*************************
if "`npar'" != "" {
preserve
qui stset _t, fail(_d) exit(time `tmax')
local i=0
foreach l of local lev {
local lb`i': label (`varlist') `l'
qui stci if `varlist'==`l' & `touse', rmean level(`level')
local r`i'=r(rmean)
local se`i'=r(se)
local r`i'_lci=r(lb)
local r`i'_uci=r(ub)
local z`i'=`r`i''/`se`i''
local p`i'=2*(1-normal(abs(`z`i'')))
return scalar rmst`l'_npar=`r`i''
return scalar rmst`l'_lci_npar=`r`i'_lci'
return scalar rmst`l'_uci_npar=`r`i'_uci'
tempname I
matrix `I' = `r`i'' \ `se`i'' \ `z`i'' \ `p`i'' \ `r`i'_lci' \ `r`i'_uci'
mat colnames `I'= "`lb`i''"
mat rownames `I' = b se t pvalue ll ul
if `i'==0 {
tempname Ic
matrix `Ic' = `I'
}
else {
matrix `Ic' = `Ic' , `I'
}
local i=`i'+1
}
restore
if `wc'!=2 {
return matrix table_npar `Ic'
}
else {
local rD=`r1'-`r0'
local seD=sqrt(`se1'^2+`se0'^2)
local rD_lci=`rD'-invnorm(`quant')*`seD'
local rD_uci=`rD'+invnorm(`quant')*`seD'
local zD=`rD'/`seD'
local pD=2*(1-normal(abs(`zD')))
dis ""
dis as result " based on non-parametric method:"
dis as result string(`rD',"%4.3f") + " (" + string(`rD_lci',"%4.3f") + " to " + ///
string(`rD_uci',"%4.3f") + "), p = " + string(`pD',"%5.4f")
return scalar rmstd_npar=`rD'
return scalar rmstd_lci_npar=`rD_lci'
return scalar rmstd_uci_npar=`rD_uci'
return scalar rmstd_p_npar=`pD'
tempname A
matrix `A'= `r0', `r1', `rD' \ `se0' , `se1' , `seD' \ `z0' , `z1' , `zD' \ ///
`p0' , `p1' , `pD' \ `r0_lci', `r1_lci', `rD_lci' \ `r0_uci', `r1_uci', `rD_uci'
mat colnames `A'= "`lb0'" "`lb1'" "difference"
mat rownames `A' = b se t pvalue ll ul
return matrix table_npar `A'
}
}
*2) parametric approach
************************
if "`fpm'"!="" {
local i=0
foreach l of local lev {
local lb`i': label (`varlist') `l'
tempvar rmst`i'
tempvar rmst`i'_se
qui stpm2 if `varlist'==`l' & `touse' , scale(hazard) df(`df')
qui predict `rmst`i'', rmst tmax(`tmax') stdp
local rmst`i'_lci=`rmst`i''[1]-invnormal(`quant')*`rmst`i''_se[1]
local rmst`i'_uci=`rmst`i''[1]+invnormal(`quant')*`rmst`i''_se[1]
local rmst`i'_z=`rmst`i''[1]/`rmst`i''_se[1]
local rmst`i'_p=2*(1-normal(abs(`rmst`i'_z')))
return scalar rmst`l'_fpm=`rmst`i''[1]
return scalar rmst`l'_lci_fpm=`rmst`i'_lci'
return scalar rmst`l'_uci_fpm=`rmst`i'_uci'
tempname I
matrix `I' = `rmst`i''[1] \ `rmst`i''_se[1] \ `rmst`i'_z' \ `rmst`i'_p' \ `rmst`i'_lci' \ `rmst`i'_uci'
mat colnames `I'= "`lb`i''"
mat rownames `I' = b se t pvalue ll ul
if `i'==0 {
tempname Ic
matrix `Ic' = `I'
}
else {
matrix `Ic' = `Ic' , `I'
}
local i=`i'+1
}
if `wc'!=2 {
return matrix table_fpm `Ic'
}
else {
local rmstd=`rmst1'[1]-`rmst0'[1]
local rmstd_se=sqrt(`rmst1'_se[1]^2 + `rmst0'_se[1]^2)
local rmstd_lci=`rmstd'-invnormal(`quant')*`rmstd_se'
local rmstd_uci=`rmstd'+invnormal(`quant')*`rmstd_se'
local rmstd_z=`rmstd'/`rmstd_se'
local rmstd_p=2*(1-normal(abs(`rmstd_z')))
dis ""
dis as result " based on flexible parametric survival models:"
dis as result string(`rmstd',"%4.3f") + " (" + string(`rmstd_lci',"%4.3f") + " to " + ///
string(`rmstd_uci',"%4.3f") + "), p = " + string(`rmstd_p',"%5.4f")
return scalar rmstd_fpm=`rmstd'
return scalar rmstd_lci_fpm=`rmstd_lci'
return scalar rmstd_uci_fpm=`rmstd_uci'
return scalar rmstd_p_fpm=`rmstd_p'
tempname B
matrix `B'= `rmst0'[1], `rmst1'[1], `rmstd' \ `rmst0'_se[1] , `rmst1'_se[1] , `rmstd_se' \ ///
`rmst0_z' , `rmst1_z' , `rmstd_z' \ `rmst0_p' , `rmst1_p' , `rmstd_p' \ ///
`rmst0_lci', `rmst1_lci', `rmstd_lci' \ `rmst0_uci', `rmst1_uci', `rmstd_uci'
mat colnames `B'= "`lb0'" "`lb1'" "difference"
mat rownames `B' = b se t pvalue ll ul
return matrix table_fpm `B'
}
}
*3) Pseudovalues
********************
if "`pseudo'" != "" {
tempname P M PM
tempvar pmean50
qui stpmean, at(`tmax') generate(`pmean50')
qui glm `pmean50' i.`varlist' if `touse', family(gaussian) link(id) vce(robust)
matrix `P' = r(table)
qui margins `varlist'
matrix `M' = r(table)
matrix `PM' = `M'[1..6,1...] , `P'[1..6,2]
local i=0
foreach l of local lev {
local i=`i'+1
local lb`i': label (`varlist') `l'
return scalar rmst`l'_pseudo=`M'[1,`i']
return scalar rmst`l'_lci_pseudo=`M'[5,`i']
return scalar rmst`l'_uci_pseudo=`M'[6,`i']
}
local rmstd = `P'[1,2]
local rmstd_lci = `P'[5,2]
local rmstd_uci = `P'[6,2]
local rmstd_p = `P'[4,2]
dis ""
dis as result " based on pseudovalues:"
dis as result string(`rmstd',"%4.3f") + " (" + string(`rmstd_lci',"%4.3f") + " to " + ///
string(`rmstd_uci',"%4.3f") + "), p = " + string(`rmstd_p',"%5.4f")
return scalar rmstd_pseudo=`rmstd'
return scalar rmstd_lci_pseudo=`rmstd_lci'
return scalar rmstd_uci_pseudo=`rmstd_uci'
return scalar rmstd_p_pseudo=`rmstd_p'
mat colnames `PM'= "`lb0'" "`lb1'" "difference"
mat rownames `PM' = b se t pvalue ll ul
return matrix table_pseudo `PM'
}
}
end