Merge pull request #18 from lshtm-gigs/dev

gigs 0.3.1
lshtm-gigs · Nov 22, 2023 · 97dbc42 · 97dbc42
2 parents 1db68ce + 153fd55
commit 97dbc42
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Showing 24 changed files with 163 additions and 120 deletions.
diff --git a/_gclassify_sga.ado b/_gclassify_sga.ado
@@ -1,6 +1,6 @@
 capture program drop _gclassify_sga
 capture program drop SGA_Badsyntax
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gclassify_sga
 	version 16
 	preserve

diff --git a/_gclassify_stunting.ado b/_gclassify_stunting.ado
@@ -1,5 +1,5 @@
 capture program drop _gclassify_stunting
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gclassify_stunting
 	version 16
 	preserve
@@ -50,18 +50,22 @@ program define _gclassify_stunting
 	else StuntingSex_Badsyntax	
 
 	marksample touse
-	tempvar pma_weeks z_PNG z_WHO z
+	tempvar pma_weeks pma_wks_floored z_NBS z_PNG z_WHO z
 	qui {
-		gen double `pma_weeks' = floor((`age_days' + `gest_days') / 7)
+		gen double `pma_weeks' = (`age_days' + `gest_days') / 7
+		gen double `pma_wks_floored' = floor(`pma_weeks')
+
+		egen double `z_NBS' = ig_nbs(`input', "lfga", "v2z"), ///
+			gest_days(`gest_days') sex(`sex') sexcode(m="`male'", f="`female'")
 		egen double `z_PNG' = ig_png(`input', "lfa", "v2z"), ///
-			xvar(`pma_weeks') sex(`sex') sexcode(m="`male'", f="`female'")
+			xvar(`pma_wks_floored') sex(`sex') sexcode(m="`male'", f="`female'")
 		egen double `z_WHO' = who_gs(`input', "lhfa", "v2z"), ///
 			xvar(`age_days') sex(`sex') sexcode(m="`male'", f="`female'")
-
-		gen double `z' = `z_PNG' if ///
-		    `gest_days' >= 182 & `gest_days' < 259 & ///
+		
+		gen double `z' = `z_NBS' if `age_days' == 0
+		replace `z' = `z_PNG' if `age_days' > 0 & `gest_days' < 259 & ///
 			`pma_weeks' >= 27 & `pma_weeks' <= 64
-		replace `z' = `z_WHO' if `gest_days' >= 259 | ///
+		replace `z' = `z_WHO' if `age_days' > 0 & `gest_days' >= 259 | ///
 		    (`gest_days' < 259 & `pma_weeks' > 64)
 
 		generate `type' `return' = .

diff --git a/_gclassify_svn.ado b/_gclassify_svn.ado
@@ -1,6 +1,6 @@
 capture program drop _gclassify_svn
 capture program drop SVN_Badsyntax
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gclassify_svn
 	version 16
 	preserve

diff --git a/_gclassify_wasting.ado b/_gclassify_wasting.ado
@@ -1,5 +1,5 @@
 capture program drop _gclassify_wasting
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gclassify_wasting
 	version 16
 	preserve
@@ -54,25 +54,22 @@ program define _gclassify_wasting
 
 	tempvar z z_WHO_wfh z_WHO_wfl z_png
 	qui {
+		egen double `z_png' = ig_png(`weight_kg', "wfl", "v2z"), ///
+			xvar(`lenht_cm') sex(`sex') sexcode(m="`male'", f="`female'")
 		egen double `z_WHO_wfl' = who_gs(`weight_kg', "wfl", "v2z"), ///
 			xvar(`lenht_cm') sex(`sex') sexcode(m="`male'", f="`female'")
 		egen double `z_WHO_wfh' = who_gs(`weight_kg', "wfh", "v2z"), ///
 			xvar(`lenht_cm') sex(`sex') sexcode(m="`male'", f="`female'")
-		egen double `z_png' = ig_png(`weight_kg', "wfl", "v2z"), ///
-			xvar(`lenht_cm') sex(`sex') sexcode(m="`male'", f="`female'")
 
 		tempvar pma_weeks use_png use_who
-		gen double `pma_weeks' = floor((`age_days' + `gest_days') / 7)
-		gen byte `use_png' = 1 if `gest_days' >= 182 & `gest_days' < 259 & ///
+		gen double `pma_weeks' = (`age_days' + `gest_days') / 7
+		gen byte `use_png' = 1 if `gest_days' < 259 & ///
 			`pma_weeks' >= 27 & `pma_weeks' <= 64
 
 		gen double `z' = .
 		replace `z' = `z_png' if `use_png' == 1
-		replace `z' = `z_WHO_wfl' if `gest_days' >= 259 & ///
-			`age_days' < 731
-		replace `z' = `z_WHO_wfh' if `gest_days' >= 259 & ///
-			`age_days' >= 731
-
+		replace `z' = `z_WHO_wfl' if `use_png' != 1 & `age_days' < 731
+		replace `z' = `z_WHO_wfh' if `use_png' != 1 & `age_days' >= 731
 
 		gen `type' `return' = .
 		replace `return' = -1 if float(`z') <= -2

diff --git a/_gclassify_wfa.ado b/_gclassify_wfa.ado
@@ -1,5 +1,5 @@
 capture program drop _gclassify_wfa
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gclassify_wfa
 	version 16
 	preserve
@@ -17,7 +17,7 @@ program define _gclassify_wfa
 		error 198
 	}
 
-	syntax [if] [in], GEST_days(varname numeric) age_days(varname) /*
+	syntax [if] [in], GEST_days(varname numeric) age_days(varname numeric) /*
 		*/ sex(varname) SEXCode(string) [OUTliers BY(string)]
 
 	if `"`by'"' != "" {
@@ -36,7 +36,7 @@ program define _gclassify_wfa
  			WFASex_Badsyntax
  		}
  		local male "`3'"
-  		local female "`6'"
+  	local female "`6'"
 	} 
 	else if "`1'" == substr("female",1,length("`1'")) {
 	    if "`2'" ~= "=" | "`5'" ~= "=" | /*
@@ -51,21 +51,24 @@ program define _gclassify_wfa
 
 	marksample touse
 
-	tempvar pma_weeks acronym z_WHO z_PNG z standard 
+	tempvar pma_weeks pma_wks_floored z_NBS z_PNG z_WHO z
 	qui {
-		gen double `pma_weeks' = floor((`age_days' + `gest_days') / 7)
+		gen double `pma_weeks' = (`age_days' + `gest_days') / 7
+		gen double `pma_wks_floored' = floor(`pma_weeks')
+
+		egen double `z_NBS' = ig_nbs(`weight_kg', "wfga", "v2z"), ///
+			gest_days(`gest_days') sex(`sex') sexcode(m="`male'", f="`female'")
 		egen double `z_PNG' = ig_png(`weight_kg', "wfa", "v2z"), ///
-			xvar(`pma_weeks') sex(`sex') sexcode(m="`male'", f="`female'")
-		egen double `z_WHO' = who_gs(`weight_kg', "wfa", "v2z"), xvar(`age_days') ///
-			sex(`sex') sexcode(m="`male'", f="`female'")
-
-		gen double `z' = `z_PNG' if ///
-		    `gest_days' >= 182 & `gest_days' < 259 & ///
-			`pma_weeks' >= 27 & `pma_weeks' < 64 
-		replace `z' = `z_WHO' if ///
-			`gest_days' < 182 | `gest_days' >= 259 | `pma_weeks' < 27 | ///
-			`pma_weeks' >= 64
+			xvar(`pma_wks_floored') sex(`sex') sexcode(m="`male'", f="`female'")
+		egen double `z_WHO' = who_gs(`weight_kg', "wfa", "v2z"), ///
+		  xvar(`age_days') sex(`sex') sexcode(m="`male'", f="`female'")
 
+		gen double `z' = `z_NBS' if `age_days' == 0
+		replace `z' = `z_PNG' if `age_days' > 0 & `gest_days' < 259 & ///
+			`pma_weeks' >= 27 & `pma_weeks' <= 64
+		replace `z' = `z_WHO' if `age_days' > 0 & `gest_days' >= 259 | ///
+			(`gest_days' < 259 & `pma_weeks' > 64)
+
 		generate `type' `return' = .
 		replace `return' = -1 if float(`z') <= -2
 		replace `return' = -2 if float(`z') <= -3

diff --git a/_gig_nbs.ado b/_gig_nbs.ado
@@ -1,7 +1,7 @@
 capture program drop _gig_nbs
 capture program drop Badsexvar_nbs
 capture program drop Badsyntax_nbs
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gig_nbs
  	version 16
 	preserve

diff --git a/_gig_png.ado b/_gig_png.ado
@@ -1,7 +1,7 @@
 capture program drop _gig_png
 capture program drop Badsexvar_png
 capture program drop Badsyntax_png
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gig_png
  	version 16
 	preserve

diff --git a/_gwho_gs.ado b/_gwho_gs.ado
@@ -1,7 +1,7 @@
 capture program drop _gwho_gs
 capture program drop Badsexvar_who
 capture program drop Badsyntax_who
-*! version 0.3.0 (SJxx-x: dmxxxx)
+*! version 0.3.1 (SJxx-x: dmxxxx)
 program define _gwho_gs
 	version 16
 	preserve

diff --git a/benchmarking/benchmark.do b/benchmarking/benchmark.do
@@ -13,39 +13,47 @@
   be checked out on the R package website in the benchmarking article
   (https://lshtm-gigs.github.io/gigs/)
 */
+clear all
+foreach file in "_gclassify_sga.ado" "_gclassify_svn.ado" ///
+				"_gclassify_stunting.ado" "_gclassify_wasting.ado" ///
+				"_gclassify_wfa.ado" ///
+				"_gig_nbs.ado" "_gig_png.ado" "_gwho_gs.ado" ///
+				"gigs_ipolate_coeffs.ado" {
+	run "`file'"
+}
 
-// gigs 0.3.0:
-// foreach i in 1 10 100 500 1000 5000 10000 25000 50000 75000 100000 {
-// 	use "benchmarking/bench_dataset.dta", clear
-// 	qui drop if _n > `i'
-// 	di "Number of inputs: `i'"
-// 	bench, reps(25) restore last: ///
-// 		qui egen double z_gigs = who_gs(y, "wfa", "v2z"), ///
-// 		xvar(x) sex(sex) sexcode(m=M, f=F)
-// }
+foreach i in 1 10 100 500 1000 5000 10000 25000 50000 75000 100000 {
+	use "benchmarking/bench_dataset.dta", clear
+	qui drop if _n > `i'
+	di "Number of inputs: `i'"
+	bench, reps(25) restore last: ///
+		qui egen double z_gigs = who_gs(y, "wfa", "v2z"), ///
+		xvar(x) sex(sex) sexcode(m=M, f=F)
+}
 
+// gigs 0.3.1:
 // Number of inputs: 1
 // Average over 25 runs: 0.008 seconds
 // Number of inputs: 10
-// Average over 25 runs: 0.010 seconds
+// Average over 25 runs: 0.009 seconds
 // Number of inputs: 100
-// Average over 25 runs: 0.010 seconds
+// Average over 25 runs: 0.009 seconds
 // Number of inputs: 500
-// Average over 25 runs: 0.011 seconds
+// Average over 25 runs: 0.010 seconds
 // Number of inputs: 1000
-// Average over 25 runs: 0.013 seconds
+// Average over 25 runs: 0.012 seconds
 // Number of inputs: 5000
 // Average over 25 runs: 0.028 seconds
 // Number of inputs: 10000
-// Average over 25 runs: 0.048 seconds
+// Average over 25 runs: 0.047 seconds
 // Number of inputs: 25000
-// Average over 25 runs: 0.107 seconds
+// Average over 25 runs: 0.106 seconds
 // Number of inputs: 50000
-// Average over 25 runs: 0.205 seconds
+// Average over 25 runs: 0.204 seconds
 // Number of inputs: 75000
-// Average over 25 runs: 0.313 seconds
+// Average over 25 runs: 0.310 seconds
 // Number of inputs: 100000
-// Average over 25 runs: 0.431 seconds
+// Average over 25 runs: 0.410 seconds
 
 // zanthro 1.0.2:
 // foreach i in 1 10 100 500 1000 5000 10000 25000 50000 75000 100000 {
@@ -90,6 +98,30 @@ egen z_anthro = zanthro(y, wa, WHO), xvar(x) gender(sex) ///
 // OLD VERSIONS OF GIGS --------------------------------------------------------
 // Kept to note how development is progressing
 
+// gigs 0.3.0:
+// Number of inputs: 1
+// Average over 25 runs: 0.008 seconds
+// Number of inputs: 10
+// Average over 25 runs: 0.010 seconds
+// Number of inputs: 100
+// Average over 25 runs: 0.010 seconds
+// Number of inputs: 500
+// Average over 25 runs: 0.011 seconds
+// Number of inputs: 1000
+// Average over 25 runs: 0.013 seconds
+// Number of inputs: 5000
+// Average over 25 runs: 0.028 seconds
+// Number of inputs: 10000
+// Average over 25 runs: 0.048 seconds
+// Number of inputs: 25000
+// Average over 25 runs: 0.107 seconds
+// Number of inputs: 50000
+// Average over 25 runs: 0.205 seconds
+// Number of inputs: 75000
+// Average over 25 runs: 0.313 seconds
+// Number of inputs: 100000
+// Average over 25 runs: 0.431 seconds
+
 // gigs 0.2.4:
 // Number of inputs: 1
 // Average over 25 runs: 0.016 seconds