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Update NyagaArbyn2022ArchPubHealth.do
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@VNyaga
VNyaga committed Jan 16, 2024
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Showing 1 changed file with 152 additions and 11 deletions.
163 changes: 152 additions & 11 deletions NyagaArbyn2022ArchPubHealth.do
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Original file line number Diff line number Diff line change
@@ -1,14 +1,28 @@
/*
Updates:
16.01.2024 - version 3.0.0 options
*/



cd "C:\DATA\WIV\Projects\Stata\Metadta\Graphs\" //Change this

set more off


use "http://fmwww.bc.edu/repec/bocode/t/telomerase.dta", clear
list, noobs clean
*EXAMPLE 1
/*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*/
*Example 1
/*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*/

*1 - Figure 1
set more off


*1 cov(unstructured)
*===================================================================
*Version 2.0.0
set more off
metadta tp fp fn tn, ///
studyid(study) model(random) dp(2) sumtable(all) ///
soptions(xtitle("False positive rate") ciopt(lpattern(dash_dot)) ///
Expand All @@ -25,9 +39,21 @@ metadta tp fp fn tn, ///
olineopt(color(red) lpattern(dash)))

estimates restore metadta_modest
estimates store unstructured

*2
estimates store unstructured

*Version 3.0.0
set more off
metadta tp fp fn tn, ///
studyid(study) smooth sumtable(all) ///
soptions(xtitle("False positive rate") ciopt(lpattern(dash_dot)) graphsave("s1.gph")) ///
foptions(xline(1) graphregion(color(white)) texts(2) xlabel(0, 0.5, 1) ysize(10) xsize(20) astext(70))

estimates restore metadta_modest
estimates store unstructured


*2 cov(independent)
*===================================================================
set more off
metadta tp fp fn tn, ///
studyid(study) model(random) cov(independe) dp(2) sumtable(all) ///
Expand All @@ -43,6 +69,18 @@ metadta tp fp fn tn, ///
foptions(graphregion(color(white)) texts(2.5) ///
xlabel(0, 0.5, 1) diamopt(color(red)) ///
olineopt(color(red) lpattern(dash)))

estimates restore metadta_modest
estimates store reduced

lrtest unstructured reduced, stats

*====Version 3.0.0
set more off
metadta tp fp fn tn, ///
studyid(study) smooth cov(independe) sumtable(all) ///
soptions(xtitle("False positive rate") graphsave("s2.gph")) ///
foptions(xline(1) graphregion(color(white)) texts(2) xlabel(0, 0.5, 1) ysize(10) xsize(20) astext(70))

estimates restore metadta_modest
estimates store reduced
Expand All @@ -51,15 +89,20 @@ lrtest unstructured reduced, stats

//Figure 2
gr combine s1.gph s2.gph, cols(2) graphregion(color(white)) xsize(8) ysize(4) iscale(1)

*Example 2

/*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*/
*Example 2
/*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*//*\*/


use "https://github.com/VNyaga/Metadta/blob/master/clinselfdemo.dta?raw=true", clear
list in 1/10, noobs clean


*1.
*===================================================================
gsort sample

*Version 2.0.0
set more off

metadta tp fp fn tn sample if ta=="SA" & setting=="follow-up", ///
Expand All @@ -70,10 +113,22 @@ metadta tp fp fn tn sample if ta=="SA" & setting=="follow-up",
graphregion(color(white)) texts(2) tit("SA, follow-up, by sample, CIN2+") ///
graphsave("f1.gph") ///
xlabel(0, .2, .4, .6, .8, 1) arrowopt(msize(1)))


*Version 3.0.0
set more off

metadta tp fp fn tn sample if ta=="SA" & setting=="follow-up", ///
studyid(study) sortby(year study) nooverall nowt ///
noitable sumtable(abs rr) nosroc ///
foptions( subline pointopt(msize(1.5)) fysize(35) ///
graphregion(color(white)) texts(2) tit("SA, follow-up, by sample, CIN2+") ///
graphsave("f1.gph") ///
xlabel(0, .2, .4, .6, .8, 1) arrowopt(msize(1)))


*2.
*2.
*===================================================================
*Version 2.0.0
metadta tp fp fn tn sample if ta=="SA" & setting=="screening" , ///
studyid(study) sortby(year study) nooverall ///
noitable sumtable(abs rr) nosroc nomc ///
Expand All @@ -82,11 +137,23 @@ metadta tp fp fn tn sample if ta=="SA" & setting=="screening" ,
graphregion(color(white)) texts(2) tit("SA, screening, by sample, CIN2+") graphsave("f2.gph") ///
xlabel(0, .2, .4, .6, .8, 1) arrowopt(msize(1)))

*Version 3.0.0
set more off
metadta tp fp fn tn sample if ta=="SA" & setting=="screening" , ///
studyid(study) sortby(year study) nooverall ///
noitable sumtable(abs rr) nosroc nomc nowt ///
foptions(subline ///
texts(2) tit("SA, screening, by sample, CIN2+") graphsave("f2.gph") ///
xlabel(0, .2, .4, .6, .8, 1))

gr combine f1.gph f2.gph, graphregion(color(white))

*graph save sa.gph, replace
*3.
gsort sample

*Version 2.0.0
set more off
metadta tp fp fn tn sample if ta=="TA" & setting=="follow-up", ///
studyid(study) sortby(year study) nooverall nomc ///
noitable sumtable(abs rr) nosroc ///
Expand All @@ -95,8 +162,17 @@ metadta tp fp fn tn sample if ta=="TA" & setting=="follow-up",
graphregion(color(white)) texts(2) tit("TA, follow-up, by sample, CIN2+") graphsave("f3.gph") ///
xlabel(0, .2, .4, .6, .8, 1) arrowopt(msize(1)))


*Version 3.0.0
set more off
metadta tp fp fn tn sample if ta=="TA" & setting=="follow-up", ///
studyid(study) sortby(year study) nooverall nomc ///
noitable sumtable(abs rr) nosroc nowt ///
foptions(subline texts(2) tit("TA, follow-up, by sample, CIN2+") graphsave("f3.gph") ///
xlabel(0, .2, .4, .6, .8, 1) )

*4.
*Version 2.0.0
metadta tp fp fn tn sample if ta=="TA" & setting=="screening", ///
studyid(study) sortby(year study) nooverall nomc ///
noitable sumtable(abs rr) nosroc ///
Expand All @@ -105,6 +181,16 @@ metadta tp fp fn tn sample if ta=="TA" & setting=="screening",
graphregion(color(white)) texts(2) tit("TA, screening, by sample, CIN2+") graphsave("f4.gph") ///
xlabel(0, .2, .4, .6, .8, 1) arrowopt(msize(1)))

*Version 3.0.0
set more off
set trace off
metadta tp fp fn tn sample if ta=="TA" & setting=="screening", ///
studyid(study) sortby(year study) nooverall nomc ///
noitable sumtable(abs rr) nosroc nowt ///
foptions(subline fysize(35) ///
texts(2) tit("TA, screening, by sample, CIN2+") graphsave("f4.gph") ///
xlabel(0, .2, .4, .6, .8, 1) )

gr combine f1.gph f3.gph, graphregion(color(white)) cols(1) imargin(0 0 0 0)
graph save 13.gph, replace

Expand All @@ -118,6 +204,8 @@ gr combine 13.gph 24.gph, cols(2) graphregion(color(white)) xsize(8) ysize(4) is
set more off

gsort ta -setting study sample

*Version 2.0.0
metadta tp fp fn tn sample setting if ta=="SA", ///
studyid(study) nomc ///
comparative noitable sumtable(rr) ///
Expand All @@ -126,7 +214,21 @@ metadta tp fp fn tn sample setting if ta=="SA", ///
graphregion(color(white)) texts(1.75) ///
xlabel(0.3, 0.5, 1, 2, 3) logscale arrowopt(msize(1)))

*Version 3.0.0
set more off

gsort ta -setting study sample
metadta tp fp fn tn sample setting if ta=="SA", ///
studyid(study) nomc ///
comparative noitable sumtable(rr) ///
foptions(outplot(rr) tit("SA, self- vs clin-samples, by setting, CIN2+") graphsave("f5.gph") ///
texts(1.75) ///
xlabel(0.3, 0.5, 1, 2, 3) logscale )

*RELATIVE ACCURACY SELF VS CLIN BY SETTING WITH TA
*Version 2.0.0
set more off

sort ta setting study sample
metadta tp fp fn tn sample setting if ta=="TA", ///
studyid(study) nomc ///
Expand All @@ -136,20 +238,48 @@ metadta tp fp fn tn sample setting if ta=="TA", ///
graphregion(color(white)) texts(1.75) ///
xlabel(0.3, 0.5, 1, 2, 3) logscale arrowopt(msize(1)))

*Version 3.0.0
set more off

sort ta setting study sample
metadta tp fp fn tn sample setting if ta=="TA", progress ///
studyid(study) nomc cov(unstructured, independent) ///
comparative noitable sumtable(rr) smooth ///
foptions( outplot(rr) tit("TA, self- vs clin-samples, by setting, CIN2+") graphsave("f6.gph") ///
texts(1.75) ///
xlabel(0.3, 0.5, 1, 2, 3) logscale arrowopt(msize(1)) astext(70) xsize(20) ysize(10))

//Figure 4
gr combine f5.gph f6.gph, col(1) graphregion(color(white))

*RELATIVE ACCURACY SELF VS CLIN interaction(sesp)
set more off
set trace off

sort ta setting study sample
*Version 2.0.0
metadta tp fp fn tn sample ta setting, ///
studyid(study) interaction(sesp) nomc ///
comparative noitable sumtable(rr) nooverall ///
foptions(subline pointopt(msize(1.3)) diamopt(color(red)) olineopt(color(red) ///
lpattern(dash)) outplot(rr) tit("self- vs clin-samples - interaction(sesp)") ///
graphregion(color(white)) texts(1.7) lcol(setting) graphsave("f7.gph") ///
xlabel(0.3, 0.5, 1, 2, 3) logscale arrowopt(msize(1)))




sort ta setting study sample

set more off


*Version 3.0.0
metadta tp fp fn tn sample ta setting, ///
studyid(study) interaction(sesp) nomc smooth ///
comparative noitable sumtable(rr) nooverall ///
foptions(subline outplot(rr) tit("self- vs clin-samples - interaction(sesp)") ///
texts(1.7) lcol(setting) graphsave("f7.gph") ///
xlabel(0.3, 0.5, 1, 2, 3) logscale astext(70) xsize(20) ysize(10))

estimates restore metadta_modest
estimates store full
Expand All @@ -158,13 +288,24 @@ estimates store full
*RELATIVE ACCURACY SELF VS CLIN interaction(sesp)
set more off
sort ta setting study sample
*Version 2.0.0
metadta tp fp fn tn sample ta setting, ///
studyid(study) interaction(se) ///
comparative noitable sumtable(rr) nooverall ///
foptions(subline pointopt(msize(1.3)) diamopt(color(red)) olineopt(color(red) ///
lpattern(dash)) outplot(rr) tit("self- vs clin-samples - interaction(se)") ///
graphregion(color(white)) texts(1.7) lcol(setting) graphsave("f8.gph") ///
xlabel(0.3, 0.5, 1, 2, 3) logscale arrowopt(msize(1)))

set more off
sort ta setting study sample
*Version 3.0.0
metadta tp fp fn tn sample ta setting, ///
studyid(study) interaction(se) ///
comparative noitable sumtable(rr) nooverall smooth gof ///
foptions(subline pointopt(msize(1.3)) outplot(rr) tit("self- vs clin-samples - interaction(se)") ///
texts(1.7) lcol(setting) graphsave("f8.gph") ///
xlabel(0.3, 0.5, 1, 2, 3) logscale astext(70) xsize(20) ysize(10))
//Figure 5
gr combine f7.gph f8.gph, row(1) graphregion(color(white)) xsize(8)

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