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set more off
version 15

* INPUT AND OUTPUT DATA PATHS
* location where input data is stored.  Change to your directory
global in "\\duhs-vclin-nc1\dusom_biostats_fs\data\biostatscore\CRU\SHARE Child\1 - Projects\0 - Cross-sectional Projects\6 - PHQ9 reliability and validity\Data"
* location where results are stored
global res "\\duhs-vclin-nc1\dusom_biostats_fs\data\biostatscore\CRU\SHARE Child\1 - Projects\0 - Cross-sectional Projects\6 - PHQ9 reliability and validity\Results\PeerJ"

* read in input dataset
use "$in\phq9scid_anon.dta", clear

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*************************************************************************************************************/

*************************************************************************************************************/
/* |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||||||||| INFORMATION FOR FIGURE 1 |||||||||||||||||||||||||
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| */
roctab scid phqTotal, detail graph summary 

*NOTE: demographic information for table 1 is not provided, as it
*is summary data not essential to analysis
/* |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||||||||| INFORMATION FOR FIRST SENTENCE OF RESULTS ||||||||
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| */
summ phqTotal, detail

/* |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||||||||| INFORMATION FOR TABLE 2 ||||||||||||||||||||||||||
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| */
tab phqCat scid, col

/* |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||||||||| INFORMATION FOR TABLE 3 ||||||||||||||||||||||||||
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| */
*ssc install diagt
tempname cutoffs
postfile `cutoffs' str30 cutoff sens senslb sensub spec speclb specub ppv ppvlb ppvub npv npvlb npvub using "$res\Screening Cutoffs.dta", replace

forvalues i=5/20 {
	capture drop phqDichot`i' 
	gen phqDichot`i' = 1*(phqTotal >= `i' & phqTotal != .) + 0*(phqTotal < `i')
	diagt scid phqDichot`i' 
	
	foreach x in sens spec ppv npv {
		local `x': di %09.1f r(`x')
		scalar `x' = ``x''
		local `x'lb: di %09.1f r(`x'_lb)
		scalar `x'lb = ``x'lb'
		local `x'ub: di %09.1f r(`x'_ub)
		scalar `x'ub = ``x'ub'
	}

	scalar cutoff = "`i'"
	scalar list

	post `cutoffs' (cutoff) (sens) (senslb) (sensub) (spec) (speclb) (specub) (ppv) (ppvlb) (ppvub) (npv) (npvlb) (npvub)
}

postclose `cutoffs'

preserve
use "$res\Screening Cutoffs.dta", clear
export excel using "$res\Screening Cutoffs.xlsx", firstrow(varlabels) replace
restore

/* |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||||||||| INFORMATION FOR TABLE 4 ||||||||||||||||||||||||||
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| */
*Internal reliability
alpha phq1 - phq9, item std
matrix list r(Alpha)
putexcel set "$res\screening_alpha.xlsx", replace
putexcel A1= matrix(r(Alpha)')

putexcel B1=matrix(r(alpha))