Merge pull request #24 from lshtm-gigs/dev

gigs 0.4.1

_gclassify_sga.ado → _gclassify_sfga.ado

@@ -1,7 +1,7 @@
-capture program drop _gclassify_sga
+capture program drop _gclassify_sfga
 capture program drop SGA_Badsyntax
-*! version 0.3.2 (SJxx-x: dmxxxx)
-program define _gclassify_sga
+*! version 0.4.0 (SJxx-x: dmxxxx)
+program define _gclassify_sfga
 	version 16
 	preserve
 
@@ -22,7 +22,7 @@ program define _gclassify_sga
 		*/ [SEVere by(string)]
 
 	if `"`by'"' != "" {
-		_egennoby classify_sga() `"`by'"'
+		_egennoby classify_sfga() `"`by'"'
 		/* NOTREACHED */
 	}
 
@@ -62,19 +62,19 @@ program define _gclassify_sga
 	    replace `return' = 1 if float(`p_temp') > 0.9
 	    replace `return' = . if missing(`p_temp') | `touse' == 0
 	}
-	cap la de sga_labels -1 "SGA" 0 "AGA" 1 "LGA"
-	cap la de sev_sga_labels -2 "severely SGA" -1 "SGA" 0 "AGA" 1 "LGA"
+	cap la de sfga_labels -1 "SGA" 0 "AGA" 1 "LGA"
+	cap la de sev_sfga_labels -2 "severely SGA" -1 "SGA" 0 "AGA" 1 "LGA"
 	if "`severe'"=="" {
-		la val `return' sga_labels
+		la val `return' sfga_labels
 	}
 	else {
 		replace `return' = -2 if float(`p_temp') < 0.03
-	    la val `return' sev_sga_labels
+	    la val `return' sev_sfga_labels
 	}
 	restore, not
 end
 
 program SGA_Badsyntax
-	di as err "sexcode() option invalid: see {help classify_sga}"
+	di as err "sexcode() option invalid: see {help classify_sfga}"
 	exit 198
 end

_gclassify_stunting.ado

@@ -1,5 +1,5 @@
 capture program drop _gclassify_stunting
-*! version 0.3.2 (SJxx-x: dmxxxx)
+*! version 0.4.0 (SJxx-x: dmxxxx)
 program define _gclassify_stunting
 	version 16
 	preserve
@@ -74,9 +74,9 @@ program define _gclassify_stunting
 		replace `return' = 0 if float(`z') > -2
 		replace `return' = . if missing(`z') | `touse' == 0
 	}
-	cap la de stunting_labs -2 "severe stunting" -1 "stunting" 0 "normal"
-	cap la de stunting_labs_out -2 "severe stunting" -1 "stunting" 0 "normal" /*
-	    */ 999 "outlier"
+	cap la de stunting_labs -2 "severe stunting" -1 "stunting" 0 "not stunting"
+	cap la de stunting_labs_out -2 "severe stunting" -1 "stunting" 0 /*
+	    */ "not stunting" 999 "outlier"
 	if "`outliers'"=="" {
 		la val `return' stunting_labs
 	}

_gclassify_svn.ado

@@ -1,6 +1,6 @@
 capture program drop _gclassify_svn
 capture program drop SVN_Badsyntax
-*! version 0.3.2 (SJxx-x: dmxxxx)
+*! version 0.4.0 (SJxx-x: dmxxxx)
 program define _gclassify_svn
 	version 16
 	preserve
@@ -53,18 +53,18 @@ program define _gclassify_svn
 
     marksample touse
 
- 	tempvar sga is_term is_sga
+ 	tempvar sfga is_term is_sfga
 	qui {
-		egen double `sga' = classify_sga(`input'), ///
+		egen double `sfga' = classify_sfga(`input'), ///
 			gest_days(`gest_days') sex(`sex') sexcode(m="`male'", f="`female'")
 		gen `is_term' = `gest_days' >= 259 // 259 days = 37 weeks
 	    gen `type' `return' = .
-	    replace `return' = -4 if `is_term' == 0 & `sga' == -1
-	    replace `return' = -3 if `is_term' == 0 & `sga' == 0
-        replace `return' = -2 if `is_term' == 0 & `sga' == 1
-        replace `return' = -1 if `is_term' == 1 & `sga' == -1
-        replace `return' =  0 if `is_term' == 1 & `sga' == 0
-        replace `return' =  1 if `is_term' == 1 & `sga' == 1
+	    replace `return' = -4 if `is_term' == 0 & `sfga' == -1
+	    replace `return' = -3 if `is_term' == 0 & `sfga' == 0
+        replace `return' = -2 if `is_term' == 0 & `sfga' == 1
+        replace `return' = -1 if `is_term' == 1 & `sfga' == -1
+        replace `return' =  0 if `is_term' == 1 & `sfga' == 0
+        replace `return' =  1 if `is_term' == 1 & `sfga' == 1
         replace `return' =  . if missing(`sga') | `touse' == 0
 	}
 	cap la de svn_labels -4 "Preterm SGA" -3 "Preterm AGA" -2 "Preterm LGA" ///

_gclassify_wasting.ado

@@ -1,5 +1,5 @@
 capture program drop _gclassify_wasting
-*! version 0.3.2 (SJxx-x: dmxxxx)
+*! version 0.4.0 (SJxx-x: dmxxxx)
 program define _gclassify_wasting
 	version 16
 	preserve
@@ -80,9 +80,9 @@ program define _gclassify_wasting
 			*/ missing(`gest_days') 
 	}	
 	cap la def wasting_labs -2 "severe wasting"  -1 "wasting" ///
-	    0 "normal" 1 "overweight"
+	    0 "not wasting" 1 "overweight"
 	cap la def wasting_labs_out -2 "severe wasting"  -1 "wasting" ///
-	    0 "normal" 1 "overweight" 999 "outlier"
+	    0 "not wasting" 1 "overweight" 999 "outlier"
 
 	if "`outliers'"=="" {
 		la val `return' wasting_labs

_gclassify_wfa.ado

@@ -1,5 +1,5 @@
 capture program drop _gclassify_wfa
-*! version 0.3.2 (SJxx-x: dmxxxx)
+*! version 0.4.0 (SJxx-x: dmxxxx)
 program define _gclassify_wfa
 	version 16
 	preserve
@@ -77,9 +77,9 @@ program define _gclassify_wfa
 		replace `return' = . if missing(`z') | `touse' == 0
 	}
 	cap la def wfa_labs -2 "severely underweight" -1 "underweight" ///
-	    0 "normal" 1 "overweight"
+	    0 "normal weight" 1 "overweight"
 	cap la def wfa_labs_out -2 "severely underweight" -1 "underweight" ///
-	    0 "normal" 1 "overweight" 999 "outlier"
+	    0 "normal weight" 1 "overweight" 999 "outlier"
 
 	if "`outliers'"=="" {
 		la val `return' wfa_labs

classify_sga.sthlp → classify_sfga.sthlp

@@ -1,15 +1,15 @@
 {smcl}
-{* *! version 0.3.2 23 Nov 2023}{...}
+{* *! version 0.4.0 23 Jan 2023}{...}
 {vieweralsosee "" "--"}{...}
-{vieweralsosee "gigs: Classification functions" "help classify_sga"}{...}
-{viewerjumpto "Syntax" "classify_sga##syntax"}{...}
-{viewerjumpto "Description" "classify_sga##description"}{...}
-{viewerjumpto "Functions" "classify_sga##functions"}{...}
-{viewerjumpto "Options" "classify_sga##options"}{...}
-{viewerjumpto "Remarks" "classify_sga##remarks"}{...}
-{viewerjumpto "Examples" "classify_sga##examples"}{...}
-
-{hi:help classify_sga, help classify_svn, help classify_stunting, help classify_wasting, help classify_wfa}{right: ({browse "https://www.overleaf.com/project/641db63564edd62fb54c963b":SJXX-X: st0001})}
+{vieweralsosee "gigs: Classification functions" "help classify_sfga"}{...}
+{viewerjumpto "Syntax" "classify_sfga##syntax"}{...}
+{viewerjumpto "Description" "classify_sfga##description"}{...}
+{viewerjumpto "Functions" "classify_sfga##functions"}{...}
+{viewerjumpto "Options" "classify_sfga##options"}{...}
+{viewerjumpto "Remarks" "classify_sfga##remarks"}{...}
+{viewerjumpto "Examples" "classify_sfga##examples"}{...}
+
+{hi:help classify_sfga, help classify_svn, help classify_stunting, help classify_wasting, help classify_wfa}{right: ({browse "https://www.overleaf.com/project/641db63564edd62fb54c963b":SJXX-X: st0001})}
 {hline}
 
 {title:Title}
@@ -21,7 +21,7 @@
 {title:Syntax}
 
 {p 8 17 2}{cmd:egen} [{it:{help datatype:type}}] {newvar} {cmd:=}
-{cmd:classify_sga}{cmd:(}{varname}{cmd:)} 
+{cmd:classify_sfga}{cmd:(}{varname}{cmd:)}
 {ifin}{cmd:,} 
 {cmdab:gest:_days}{cmd:(}{varname}{cmd:)} {cmdab:sex}{cmd:(}{varname}{cmd:)}
 {cmdab:sexc:ode}{cmd:(}{cmdab:m:ale=}{it:code}{cmd:,} {cmdab:f:emale=}{it:code}{cmd:)}
@@ -79,7 +79,7 @@
 {marker functions}{...}
 {title:Functions for egen}
 
-{p 4 4 2}{hi:classify_sga(}{varname}{cmd:)} is used to classify size for 
+{p 4 4 2}{hi:classify_sfga(}{varname}{cmd:)} is used to classify size for
  gestational age in newborns according to INTERGROWTH-21st 
  weight-for-gestational age standards. It produces a variable with the
  following values and labels:
@@ -126,7 +126,7 @@
 {col 20}{hline 38}
 {col 21}{cmd: -2}{col 27}Severe stunting{col 45}-5 to -3
 {col 21}{cmd: -1}{col 27}Stunting       {col 45}-3 to -2
-{col 21}{cmd:  0}{col 27}Normal         {col 45}-2 to 5
+{col 21}{cmd:  0}{col 27}Not stunting   {col 45}-2 to 5
 {col 21}{cmd:999}{col 27}Outlier        {col 45}<-5 or >5
 
 {pmore}This function takes one argument:
@@ -146,7 +146,7 @@
 {col 20}{hline 38}
 {col 21}{cmd: -2}{col 27}Severe wasting{col 45}-5 to -3
 {col 21}{cmd: -1}{col 27}Wasting       {col 45}-3 to -2
-{col 21}{cmd:  0}{col 27}Normal        {col 45}-2 to 2
+{col 21}{cmd:  0}{col 27}Not wasting   {col 45}-2 to 2
 {col 21}{cmd:  1}{col 27}Overweight    {col 45}2 to 5
 {col 21}{cmd:999}{col 27}Outlier       {col 45}<-5 or >5
 
@@ -180,7 +180,7 @@
 {dlgtab:Non-specific}
 
 {phang}{opt gest:_days(varname numeric)} specifies gestational age in days for
- newborns. In {cmd:classify_sga()} and {cmd:classify_sga()},any value outside
+ newborns. In {cmd:classify_sfga()} and {cmd:classify_svn()},any value outside
  the range of valid gestational ages as specified in the
  {help ig_nbs##tab1:ig_nbs() documentation} will return a missing value. In the
  other classification functions, this variable is used to compute post-menstrual
@@ -229,11 +229,11 @@
 {marker examples}{...}
 {title:Examples}
 
-{pstd}Classifying SGA, where {cmd:sex} contains the codes {cmd:1} and {cmd:2}:{p_end}
-{phang2}{cmd:. egen sga = classify_sga(weight_kg), gest_days(ga_days) sex(sex) sexcode(male=1, female=2)}
+{pstd}Classifying size-for-GA, where {cmd:sex} contains the codes {cmd:1} and {cmd:2}:{p_end}
+{phang2}{cmd:. egen sfga = classify_sfga(weight_kg), gest_days(ga_days) sex(sex) sexcode(male=1, female=2)}
 
-{pstd}Include severe SGA classifications with the {opt:severe} option:{p_end}
-{phang2}{cmd:. egen sga = classify_sga(weight_kg), gest_days(ga_days) sex(sex) sexcode(male=1, female=2) severe}
+{pstd}Include severe size-for-GA classifications with the {opt:severe} option:{p_end}
+{phang2}{cmd:. egen sfga = classify_sfga(weight_kg), gest_days(ga_days) sex(sex) sexcode(male=1, female=2) severe}
 
 {pstd}Classifying stunting, where {cmd:sex} contains the codes {cmd:M} and {cmd:F}:{p_end}
 {phang2}{cmd:. egen stunting = classify_stunting(weight_kg), gest_days(ga_days) age_days(age) sex(sex) sexcode(male=M, female=F)}
@@ -244,7 +244,7 @@
 {pstd}You can use just the first letters of the {cmd:lenht_cm()}, {cmd:gest_days()}, and {cmd:sexcode()} arguments instead:{p_end}
 {phang2}{cmd:. egen wasting = classify_wasting(weight_kg), lenht(lenht_cm) gest(ga_days) age_days(age) sex(sex) sexc(m=Male, f=Female)}
 
-{pstd}Request that gigs classifies outlier/implasuible values with the {opt:outliers} option:{p_end}
+{pstd}Request that gigs classifies outlier/implasuible values with the {cmd:outliers} option:{p_end}
 {phang2}{cmd:. egen wasting = classify_wasting(weight_kg), lenht(lenht_cm) gest(ga_days) age_days(age) sex(sex) sexc(m=Male, f=Female) outliers}
 
 {marker authors}{...}

classify_stunting.sthlp

@@ -1 +1 @@
-.h classify_sga
+.h classify_sfga

classify_svn.sthlp

@@ -1 +1 @@
-.h classify_sga
+.h classify_sfga

classify_wasting.sthlp

@@ -1 +1 @@
-.h classify_sga
+.h classify_sfga

classify_wfa.sthlp

@@ -1 +1 @@
-.h classify_sga
+.h classify_sfga

gigs.pkg

@@ -1,12 +1,12 @@
-v 0.4.0
-d 'GIGS': Newborn and infant growth assessment using international growth standards
+v 0.4.1
+d 'GIGS': Fetal, neonatal, and infant growth assessment using international growth standards
 d 
 d gigs provides a single, simple interface for working with outputs from the INTERGROWTH-21st project and the WHO Child Growth standards. You will find functions for converting between anthropometric measures (e.g. weight or length) to z-scores and centiles, and the inverse. Also included are functions for classifying newborn and infant growth according to DHS guidelines.
 d 
 d Distribution-Date: 20240116
 d License: GNU General Public License v3.0
 d 
-F _gclassify_sga.ado
+F _gclassify_sfga.ado
 F _gclassify_stunting.ado
 F _gclassify_svn.ado
 F _gclassify_wasting.ado
@@ -16,7 +16,7 @@ F _gig_nbs.ado
 F _gig_png.ado
 F _gwho_gs.ado
 F gigs_ipolate_coeffs.mo
-F classify_sga.sthlp
+F classify_sfga.sthlp
 F classify_stunting.sthlp
 F classify_svn.sthlp
 F classify_wasting.sthlp
@@ -40,3 +40,4 @@ F whoLMS_wfl.dta
 F who_gs.sthlp
 f gigs_examples.do
 f life6mo.dta
+f life6mo.sthlp

gigs.sthlp

@@ -2,9 +2,9 @@
 {* *! version 0.4.0 07 Dec 2023}{...}
 {vieweralsosee "" "--"}{...}
 {vieweralsosee "gigs: Conversion functions" "help ig_nbs"}{...}
-{vieweralsosee "gigs: Classification functions" "help classify_sga"}{...}
+{vieweralsosee "gigs: Classification functions" "help classify_sfga"}{...}
 
-{hi: help ig_nbs, help classify_sga}{right: ({browse "https://www.overleaf.com/project/641db63564edd62fb54c963b":SJXX-X: st0001})}
+{hi: help ig_nbs, help classify_sfga}{right: ({browse "https://www.overleaf.com/project/641db63564edd62fb54c963b":SJXX-X: st0001})}
 {hline}
 
 {title:Title}
@@ -52,7 +52,7 @@
 
 {p 4 14 2}Conversion functions: {help ig_nbs:documentation}
 
-{p 4 14 2}Classification functions: {help classify_sga:documentation}
+{p 4 14 2}Classification functions: {help classify_sfga:documentation}
 
 {p 4 14 2}Article: {it:Stata Journal}, volume XX, number X: {browse "https://www.overleaf.com/project/641db63564edd62fb54c963b":st0001}
 

gigs_examples.do

@@ -1,34 +1,33 @@
-use life6mo
-gen agedays = pma - gestage
+use life6mo, clear
+keep id gestage sex visitweek pma age_days weight_g
 local 37weeks 7 * 37
-list in f/10, noobs abbreviate(10) sep(10)
+list in f/9, noobs abbreviate(10) sep(9)
 
-egen double waz_nbs = ig_nbs(meaninfwgt/1000, "wfga", "v2z") ///
-    if agedays == 0, ///
+egen double waz_nbs = ig_nbs(weight_g/1000, "wfga", "v2z") ///
+    if age_days == 0, ///
     gest_days(gestage) sex(sex) sexcode(m=1, f=2)
 
-egen double waz_who = who_gs(meaninfwgt/1000, "wfa", "v2z") ///
-    if agedays > 0 & gestage >= `37weeks', ///
-    xvar(agedays) sex(sex) sexcode(m=1, f=2)
+egen double waz_who = who_gs(weight_g/1000, "wfa", "v2z") ///
+    if age_days > 0 & gestage >= `37weeks', ///
+    xvar(age_days) sex(sex) sexcode(m=1, f=2)
 
 gen pma_weeks = pma / 7
-gen pma_weeks_floored = floor(pma / 7)
-egen double waz_png = ig_png(meaninfwgt/1000, "wfa", "v2z") ///
-    if gestage < `37weeks' & agedays > 0, ///
-    xvar(pma_weeks_floored) sex(sex) sexcode(m=1, f=2)
-drop pma_weeks pma_weeks_floored
+egen double waz_png = ig_png(weight_g/1000, "wfa", "v2z") ///
+    if age_days > 0 & gestage < `37weeks', ///
+    xvar(pma_weeks) sex(sex) sexcode(m=1, f=2)
+drop pma_weeks
 
 gen double waz = waz_who if gestage > `37weeks'
 replace waz = waz_png if gestage < `37weeks'
-replace waz = waz_nbs if agedays == 0
+replace waz = waz_nbs if age_days == 0
 
-list visitweek gestage pma waz_* waz in f/10, noobs sep(10)
+list visitweek gestage pma waz_* waz in f/9, noobs sep(9)
 drop waz_*
 
 gen preterm = gestage < `37weeks'
 collapse waz, by(visitweek preterm)
 line waz visitweek if preterm == 0 || line waz visitweek if preterm == 1 ||, ///
-    title("WAZ in term/preterm infants in the LIFE study") ///
+    title("WAZ in 300 infants from the LIFE data extract") ///
     xtitle("Visit week") ///
     ytitle("Weight-for-age z-score (WAZ)") ///
     xlabel(0 1 2 4 6 10 14 18 26) ///
@@ -37,14 +36,22 @@ line waz visitweek if preterm == 0 || line waz visitweek if preterm == 1 ||, ///
 graph export "gigs_fig1.pdf"
 
 use life6mo, clear
-keep if (gestage - pma) == 0
-egen sga = classify_sga(meaninfwgt/1000), ///
+keep if (age_days) == 0
+egen sfga = classify_sfga(weight_g/1000), ///
+    gest_days(gestage) sex(sex) sexcode(m=1, f=2)
+graph bar, over(sfga) ///
+    title("Size-for-GA categorisations in the LIFE data extract") ///
+    note("") ///
+    ytitle("Percentage") ///
+    scheme(sj)
+graph export "gigs_fig2.pdf"
+
+
+egen svn = classify_svn(weight_g/1000), ///
     gest_days(gestage) sex(sex) sexcode(m=1, f=2)
-gen term_status = "Preterm" if gestage < `37weeks'
-replace term_status = "Term" if gestage >= `37weeks'
-graph bar, over(sga) by(term_status, ///
-    title("Percentage of each size-for-GA category by term status") ///
-    note("")) ///
+graph bar, over(svn) ///
+    title("SVN categorisations in the LIFE data extract") ///
+    note("") ///
     ytitle("Percentage") ///
     scheme(sj)
-graph export "gigs_fig2.pdf"
+graph export "gigs_fig3.pdf"

ig_nbs.sthlp

@@ -1,7 +1,7 @@
 {smcl}
 {* *! version 0.4.0 07 Dec 2023}{...}
 {vieweralsosee "" "--"}{...}
-{vieweralsosee "gigs: Classification functions" "help classify_sga"}{...}
+{vieweralsosee "gigs: Classification functions" "help classify_sfga"}{...}
 {viewerjumpto "Syntax" "ig_nbs##syntax"}{...}
 {viewerjumpto "Description" "ig_nbs##description"}{...}
 {viewerjumpto "Functions" "ig_nbs##functions"}{...}
@@ -310,7 +310,7 @@ also {it:fcn} dependent.
 
 {title:Also see}
 
-{p 4 14 2}Classification functions: {help classify_sga:documentation}
+{p 4 14 2}Classification functions: {help classify_sfga:documentation}
 
 {p 4 14 2}Article: {it:Stata Journal}, volume XX, number X: {browse "https://www.overleaf.com/project/641db63564edd62fb54c963b":st0001}