corentinchoisy/simul_these
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

File restructure #1

Browse Source
This commit is contained in:
Corentin Choisy
2024-04-19 16:46:33 +02:00
parent a8a94ddc10
commit ecac05b9c4
703 changed files with 10 additions and 272568 deletions
Download Patch File Download Diff File Expand all files Collapse all files

637
Modules/ado/plus/h/hotdeck6.ado
View File

@ -1,637 +0,0 @@
*! Date : 1 Aug 2005
*! Version : 1.64
*! Authors : Adrian Mander/David Clayton
*! Email : adrian.mander@mrc-hnr.cam.ac.uk
*! Description : Hotdeck imputation
program define hotdeck6
version 6.0
syntax [varlist] [if] [in] [using/], [BY(varlist) IMPute(integer 1) STORE GENerate(string) COMmand(string) PARMS(string) REPlace NOISE KEEP(varlist) SEED(string) QUIET INFILES(string) ]
tokenize "`varlist'"
local z "`1'"
preserve
if "`if'"~="" {
qui keep `if'
}
/* Check the seed option */
if "`seed'"=="1" { local seed 2}
if "`seed'"=="" { local seed 1 }
confirm number `seed'
/* To generate a seed from the time */
if `seed'==1 {
local time = "$S_TIME"
local date = "$S_DATE"
tokenize "`time'", parse(":")
local seed1 "`1'`3'`5'"
tokenize "`date'", parse(" ")
local dat "`1'`2'`3'"
local dat1 = date("`dat'","dmy")
local seed1 "`seed1'`dat1'"
di
local l_seed "2^31-1"
local seed1 = mod(`seed1',`l_seed')
di in green "Seed is `seed1'"
set seed `seed1'
}
estimates clear
tempfile olddata
/*NOT SURE if I must implement no strings in BY() option
tokenize "`by'"
while "`1'"~="" {
confirm numeric variable `1'
mac shift 1
}
*/
tempvar touse
mark `touse' `if' `in'
markout `touse' `by', strok
di in green "DELETING all matrices...."
mat drop _all
if "`infiles'"=="" {
if "`by'"=="" { _misspat `varlist' `if' `in' }
else { _misspat `varlist' `if' `in', by(`by') }
local nfill=r(nmiss)
}
qui save "`olddata'"
if "`infiles'"=="" {
global allpat = r(allpat)
count if `touse'
local miss = (r(N)-`nfill')/r(N)
}
if "`command'"=="" {
di in red "WARNING: When the <command> option is not selected "
di in red "then no analysis is performed on the imputed datasets"
di
if "`store'"=="" {
di "ALSO STORE isnt selected so hotdeck will appear to do nothing"
exit(198)
}
}
if `impute'<1 {
di in red "The number of imputations must be more than 0 not `impute'"
exit(198)
}
if `impute'==1 & "`infiles'"=="" {
if "`store'"=="" | "`command'"~="" {
di in red "If one imputation is made then command option should NOT be used"
di in red "AND the store option must be specified"
exit(198)
}
}
if "`using'"~="" {
if "`store'"=="" {
di in red "To save datasets you must specify the STORE option"
exit(198)
}
}
if "`keep'"~="" {
if "`store'"=="" {
di in red "If you use the KEEP option you must specify the STORE option"
exit(198)
}
}
if "`noise'"~="" & "`command'"=="" {
di in red "When specifying noise you must also specify the command option"
exit(198)
}
if "`command'"~="" {
if "`parms'"=="" {
di in red "To obtain any output from the command option you must also specify "
di in red "the parameters of interest using the parms() option"
exit(198)
}
}
/************************************************
* Loop over the number of imputed data sets
* required
************************************************/
if "`seed'"~="1" {set seed `seed'}
/* This is the if statement that allows the input of imputed datafiles */
if "`infiles'"~="" {
local i 1
tokenize "`infiles'"
while "`1'"~="" {
use "`1'",replace
mac shift 1
if "`command'"=="" {
di in red "You must use the command option when using INFILES"
exit(198)
}
if "`noise'"~="" { `command' }
else { qui `command' } /* Do the analysis */
_parms, parms(`parms') command(`command') iter(`i') /* Select Parameters of interest*/
local i =`i'+1
}
local impute=`i'-1
}
else {
local i 1
while `i'<= `impute' {
use "`olddata'",clear /* Use original dataset */
qui keep if `touse'
if "`by'"~="" { _hotdeck `varlist', by(`by') }
else { _hotdeck `varlist' } /* Impute values */
if "`store'"~="" { /* Save imputed datasets */
if "`using'"=="" {
local using "imp"
}
if "`keep'"=="" {
qui keep `varlist' `by'
qui save `using'`i',replace
}
else {
mkvlist `varlist' `by', vlist(`keep')
qui keep `r(vlist)'
qui save `using'`i',replace
}
}
if "`command'"~="" {
if "`noise'"~="" { `command' }
else { qui `command' } /* Do the analysis */
_parms, parms(`parms') command(`command') iter(`i') /* Select Parameters of interest*/
}
local i=`i'+1
}
}
if "`command'"~="" {
/********************************************************
* Loop to calculate the estimates needed
*
* First get the dimensions of the parameter matrices
********************************************************/
local dim= rowsof(impV1)
mat Qbar = J(1,`dim',0)
mat Ubar = J(`dim',`dim',0)
/* calc the averaging factor */
local inv = 1/`impute'
/* calc the average coef and variance qbar and ubar */
local i 1
while `i'<= `impute' {
mat Qbar= `inv'*impb`i'+ Qbar
mat Ubar= `inv'*impV`i'+ Ubar
local i=`i'+1
}
/* calc between variances */
mat B=J(`dim',`dim',0)
local inv1 = 1/(`impute'-1)
local i 1
while `i'<= `impute' {
mat B= B + `inv1'*(impb`i' - Qbar)'*(impb`i' - Qbar)
local i=`i'+1
}
/* Calc total variance */
mat T = Ubar+(1+1/`impute')*B
cap mat tempmt=B*inv(Ubar)
if _rc==504 {
di as error "WARNING: Trying to invert variance matrix with zero elements?"
local ter = rowsof(Ubar)
mat temp = J(`ter',1,1)
mat temp2 = Ubar*temp
local tei 1
local names: colfullnames(impb1)
matrix rownames temp2 = `names'
while `tei'<=`ter' {
if temp2[`tei',1]==0 {
local var:word `tei' of "`names'"
di as txt "Variance for covariate `tei' is 0 !!"
}
local tei=`tei'+1
}
mat tempmt=B*inv(Ubar)
}
local trace=trace(tempmt)
local r1 = 1-((1+1/`impute')*`trace'/`dim')
local names: rowfullnames(impb1)
matrix rownames Qbar = `names'
local names: colfullnames(impb1)
matrix colnames Qbar = `names'
local names: rowfullnames(impV1)
matrix rownames T = `names'
matrix rownames B = `names'
matrix rownames Ubar = `names'
local names: colfullnames(impV1)
matrix colnames T = `names'
matrix colnames B = `names'
matrix colnames Ubar = `names'
mat Tsurr= `r1'*T
mat D = Qbar*inv(Tsurr)*Qbar'
local D1 = D[1,1]/`dim'
local t=`dim'*(`impute'-1)
local v1= 4+(`t'-4)*(1+(1-2/`t')*1/`r1')^2
local ftest= fprob(`dim',`v1',`D1')
/********************************************************
* The next will output the main results in Stata style
* if the normal approximation is good then you could
* use the matrix post command
********************************************************/
if "`quiet'"=="" {
if `r1'<0 {
di in red "WARNING: between se larger than within se in one or more "
di in red "parameters invalidating the global F test"
}
if `t'<4 {
di in red "WARNING: t less than 4 invalid global test increase "
di in red "parameters OR imputations"
}
}
di
di in gr _col(1) "Number of Obs.", _col(45) " = ", _N
di in gr _col(1) "No. of Imputations", _col(48) "= ", `impute'
if "`infiles'"=="" {
di in gr _col(1) "% Lines of Missing Data", _col(45) " = ", `miss'*100,"%"
}
di in gr _col(1) "F(",%6.3f `v1',",`dim')", _col(45) " = ", %9.4f `D1'
di in gr _col(1) "Prob > F " , _col(45) " = ", %9.4f `ftest'
di in gr _dup(83) "-"
local names: colfullnames(impb1)
local name : word 1 of `names'
local i 1
di in gr _continue "Variable |",_col(12) "Average",_col(21) "Between", _col(30) "Within", _col(40) "Total", _col(50) "df", _col(59) "t", _col(65) "p-value"
di
di in gr _continue" |",_col(12) "Coef.",_col(21) "Imp. SE", _col(30) "Imp. SE", _col(39) " SE", _col(50) "", _col(59) "", _col(65) ""
di
di in gr _continue "-------------+---------------------------------------------------------------------"
while "`name'"~="" {
di
mat qhat=Qbar[1,"`name'"]
mat b=B["`name'","`name'"]
mat u=Ubar["`name'","`name'"]
mat t=T["`name'","`name'"]
local df = (`impute'-1)*(1+(u[1,1])/((1+1/`impute')*b[1,1]))^2
local ttest= qhat[1,1]/sqrt(t[1,1])
di _continue "`name'",_col(9) "|", _col(10) %7.4f qhat[1,1],_col(17) %9.3f sqrt(b[1,1]), _col(25) %9.3f sqrt(u[1,1]), _col(34) %9.3f sqrt(t[1,1]), _col(44) %9.1f `df', _col(53) %9.3f `ttest', _col(62) %9.3f tprob(`df',`ttest')
local i=`i'+1
local name : word `i' of `names'
}
di
di in gr _continue "-------------+---------------------------------------------------------------------"
di
local name : word 1 of `names'
local i 1
di in gr _continue "Variable |",_col(12) "[$S_level% Conf. Interval]"
di
di in gr _continue "-------------+---------------------------------------------------------------------"
while "`name'"~="" {
di
mat qhat=Qbar[1,"`name'"]
mat b=B["`name'","`name'"]
mat u=Ubar["`name'","`name'"]
mat t=T["`name'","`name'"]
local df = (`impute'-1)*(1+(u[1,1])/((1+1/`impute')*b[1,1]))^2
local ttest= qhat[1,1]/sqrt(t[1,1])
local prob = 1-((100-$S_level)/2)/100
local tvalue = invt(`df',`prob')
local left = qhat[1,1]-`tvalue'*sqrt(t[1,1])
local right = qhat[1,1]+`tvalue'*sqrt(t[1,1])
di _continue "`name'",_col(9) "|", %9.4f `left', %9.4f `right'
local i=`i'+1
local name : word `i' of `names'
}
di ""
di in gr _dup(83) "-"
} /* end of command if statement */
restore
end
/****************************************************
* The approximate Bayesian Bootstrap hotdecking
****************************************************/
program define _hotdeck
version 6.0
syntax [varlist] [using], [BY(string)]
tokenize "`varlist'"
local z "ipattern"
if "`by'"!="" {
confirm ex var `by'
}
tempvar nobs bstrp b2strp temp temp2
qui {
local nold = _N
local nnew = _N
sort `by' `z' `varlist'
gen long `nobs' = (`z'!=.)
if "`by'"=="" {
replace `nobs' = sum(`nobs')
replace `nobs' = `nobs'[_N]
gen long `bstrp' = int(uniform()*`nobs'+1)
gen long `b2strp' = int(uniform()*`nobs'+1)
gen long `temp' = `bstrp'[`b2strp']
replace `bstrp' = `temp'
replace `bstrp' = _n if _n<=`nobs'
tokenize "`varlist'"
while "`1'"~="" {
gen `temp2' = `1'[`bstrp']
replace `1' = `temp2'
drop `temp2'
mac shift 1
}
}
else {
by `by': replace `nobs' = sum(`nobs')
by `by': replace `nobs' = `nobs'[_N]
by `by': gen long `bstrp' = int(uniform()*`nobs'+1)
by `by': gen long `b2strp' = int(uniform()*`nobs'+1)
by `by': gen long `temp' = `bstrp'[`b2strp']
by `by': replace `bstrp' = `temp'
by `by': replace `bstrp' = _n if _n<=`nobs'
tokenize "`varlist'"
while "`1'"~="" {
by `by': gen `temp2' = `1'[`bstrp']
by `by': replace `1' = `temp2'
mac shift 1
drop `temp2'
}
}
}
end
/*******************************************************************
* Get the parameters or a subset of them from the
* model and the subset
* the covariance variance matrix as well
* Note that this section can also handle non-regression commands
* and macro lists
*******************************************************************/
program define _parms
syntax [varlist], [PARMS(string) ITER(integer 1) COMMAND(string) GENerate(string) REPlace]
local 0 "`parms'"
while "`parms'"~="" {
gettoken 0 parms: parms , parse(" ,")
cap syntax [varlist]
if _rc~=0 {
if "`0'"=="_cons" { local vlist "`vlist' `0'" }
else { local plist "`plist' `0'" }
}
else { local vlist "`vlist' `varlist'" }
}
* if results were not part of a regression command
if "`e(cmd)'"=="" {
local names = ""
if `iter'==1 { di in red "Using Non Regression Parameters and Command" }
tokenize "`plist' `vlist'"
local np=0
while "`1'"~="" {
local names1 ="`names1' `1'"
local names2 ="`names2' `2'"
if "`2'"=="" { di in red "Must supply variance estimate of `1'"
exit(302)
}
mac shift 2
local np = `np'+1
}
mat impb`iter' = J(1,`np',0)
mat impV`iter' = J(`np',`np',0)
tokenize "`plist' `vlist'"
local np 1
while "`1'"~="" {
if "$`1'"=="" & "``1''"=="" {
di in red "Global = $`1' Local = ``1''"
di in red "Global/local macro `1' is missing "
exit(198)
}
if "``1''"~="" { mat impb`iter'[1,`np'] = ``1'' }
if "$`1'"~="" & "``1''"=="" { mat impb`iter'[1,`np'] = $`1' }
if "$`2'"=="" & "``2''"=="" {
di in red "Global = $`2' Local = ``2''"
di in red "Global/local macro `2' is missing "
exit(198)
}
if "``2''"~="" { mat impV`iter'[`np',`np'] = ``2'' }
if "$`2'"~="" & "``2''"=="" { mat impV`iter'[`np',`np'] = $`2' }
local np=`np'+1
mac shift 2
}
matrix colnames impb`iter'=`names1'
matrix colnames impV`iter'=`names1'
matrix rownames impV`iter'=`names1'
}
else {
matrix myb = get(_b)
matrix myV = get(VCE)
tokenize "`vlist' `plist'"
if "`2'"~="" {
cap mat impb`iter' = myb[.,"`1'"]
if _rc==111 {
di as error "Are you sure `1' is in the model??"
di as error "Check the matrix of estimates and only include column names in the parameters NOT variable names"
exit(111)
}
mac shift 1
while "`1'"~="" {
mat temp=myb[.,"`1'"]
mat impb`iter'= impb`iter' , temp
mac shift 1
}
tokenize "`vlist' `plist'", parse(" ")
mat impVt`iter' = myV[.,"`1'"]
mac shift 1
while "`1'"~="" {
mat temp=myV[.,"`1'"]
mat impVt`iter'= impVt`iter' , temp
mac shift 1
}
tokenize "`vlist' `plist'", parse(" ")
mat impV`iter' = impVt`iter'["`1'",.]
mac shift 1
while "`1'"~="" {
mat temp=impVt`iter'["`1'",.]
mat impV`iter'= impV`iter' \ temp
mac shift 1
}
mat drop myb
mat drop myV
mat drop impVt`iter'
mat drop temp
}
else {
cap mat impb`iter' = myb[.,"`1'"]
if _rc==111 {
di as error "Are you sure `1' is in the model??"
exit(111)
}
mat impVt`iter'=myV[.,"`1'"]
mat impV`iter' = impVt`iter'["`1'",.]
}
}
end
/*************************************************
* Look at the missing pattern in the varlist
*************************************************/
program define _misspat,rclass
syntax varlist [if] [in] , [BY(string) ]
tokenize "`varlist'"
tempvar touse2
mark `touse2' `if' `in'
markout `touse2'
qui gen str40 pattern=""
local allstr ""
while "`1'"~="" {
qui replace pattern = cond(`1'==.,pattern+"*",pattern+"-") if `touse2'
local allstr="-`allstr'"
mac shift 1
}
qui compress pattern
sort pattern
lab var pattern "Missing pattern"
di
di in green "Missing Patterns"
di in green "----------------"
di
di in green "Table of the Missing data patterns "
di in green " * signifies missing and - is not missing"
di
di "Varlist order: `varlist'"
tab pattern if `touse2'
local n=r(N)
qui count if pattern=="`allstr'" & `touse2'
if r(N)==`n' {
di "There is no missing data in the varlist"
exit(198)
}
return scalar nmiss = `n'-r(N)
return local allpat = "`allstr'"
qui gen ipattern=cond(pattern=="`allstr'",1,.) if `touse2'
/*****************************************
* Calculate stratum missing numbers
*****************************************/
if "`by'"~="" {
di
di in green "STRATUM information"
di in green "-------------------"
di
di in green "Listing the number observed (No_obs) and "
di in green "the number missing (No_miss) in each stratum"
tempvar cnt mcnt
qui sort `by'
qui by `by':gen `cnt'=sum(ipattern)
qui by `by':gen `mcnt'=sum(ipattern==.)
qui by `by': replace `cnt'=cond( _n==_N,`cnt',.)
qui by `by': replace `mcnt'=cond( _n==_N,`mcnt',.)
rename `cnt' No_obs
rename `mcnt' No_miss
l `by' No_obs No_miss if No_obs~=., noobs
di
qui count if No_obs==0
if `r(N)'>0 { di in red "WARNING: `r(N)' strata with NO observed data" }
qui count if No_obs==1
if `r(N)'>0 { di in blue "`r(N)' strata with only 1 observed data"}
qui count if (No_obs>1 & No_obs<6)
if `r(N)'>0 { di in blue "`r(N)' strata with 2-5 observed data"}
di
}
end
/*************************************************
* Expand stata syntax
*************************************************/
program define mkvlist, rclass
syntax varlist, VLIST(string)
local o_vlist "`varlist'"
local keep "`vlist'"
local 0 "`keep'"
while "`keep'"~="" {
gettoken 0 keep: keep , parse(" ,")
cap syntax [varlist]
if _rc~=0 {
if "`0'"=="_cons" {
local vlist "`vlist' `0'"
}
else { local plist "`plist' `0'" }
}
else {
local vlist "`vlist' `varlist'"
}
}
return local vlist "`o_vlist' `vlist'"
end