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Merge pull request #21 from lshtm-gigs/dev
gigs 0.3.2: README change + sga silencing
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‎README.md

+42-49
Original file line numberDiff line numberDiff line change
@@ -197,7 +197,6 @@ contains weight measurements for term and preterm infants from birth
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```stata
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. use life6mo
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. local 40weeks 7 * 40
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. local 37weeks 7 * 37
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. list in f/10, noobs abbreviate(10) sep(10)
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___________________________________________________________
@@ -224,24 +223,24 @@ INTERGROWTH-21<sup>st</sup> Newborn Size Standards, WHO/INTERGROWTH Postnatal
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standards after birth).
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```stata
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. egen waz_nbs = ig_nbs(meaninfwgt/1000, "wfga", "v2z") ///
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> if visitweek == 0, ///
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> gest_age(gestage) sex(sex) sexcode(m=1, f=2)
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(7,308 missing values generated)
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. gen agedays = pma - gestage
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. egen waz_who = who_gs(meaninfwgt/1000, "wfa", "v2z") ///
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> if gestage > `37weeks´ & visitweek > 0, ///
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. egen double waz_nbs = ig_nbs(meaninfwgt/1000, "wfga", "v2z") ///
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> if agedays == 0, ///
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> gest_days(gestage) sex(sex) sexcode(m=1, f=2)
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(8,228 missing values generated)
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. egen double waz_who = who_gs(meaninfwgt/1000, "wfa", "v2z") ///
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> if agedays > 0 & gestage >= `37weeks', ///
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> xvar(agedays) sex(sex) sexcode(m=1, f=2)
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(4,657 missing values generated)
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. drop agedays
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(4,073 missing values generated)
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. gen pma_weeks = round(pma/7, 1)
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. egen waz_png = ig_png(meaninfwgt/1000, "wfa", "v2z") ///
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> if gestage < `37weeks´ & visitweek > 0 & visitweek <= 18, ///
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> pma_weeks(pma_weeks) sex(sex) sexcode(m=1, f=2)
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(5,391 missing values generated)
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. drop pma_weeks
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. gen pma_weeks = pma / 7
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. gen pma_weeks_floored = floor(pma / 7)
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. egen double waz_png = ig_png(meaninfwgt/1000, "wfa", "v2z") ///
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> if gestage < `37weeks' & agedays > 0, ///
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> xvar(pma_weeks_floored) sex(sex) sexcode(m=1, f=2)
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(4,659 missing values generated)
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. drop pma_weeks pma_weeks_floored
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. gen age_corrected = pma - `40weeks´
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. egen waz_whocorr = who_gs(meaninfwgt/1000, "wfa", "v2z") ///
@@ -254,33 +253,28 @@ standards after birth).
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We can then combine these WAZs into one overall `waz` variable:
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```stata
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. gen waz = waz_who if gestage > `37weeks´
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(4,657 missing values generated)
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. replace waz = waz_nbs if visitweek == 0
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(1,112 real changes made, 4 to missing)
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. replace waz = waz_png if gestage < `37weeks´ & visitweek > 0 & visitweek <= 18
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(3,025 real changes made)
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. replace waz = waz_whocorr if gestage < `37weeks´ & visitweek == 26
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(420 real changes made)
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. list gestage pma visitweek waz_* waz in f/10, noobs
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__________________________________________________________________________
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| gestage pma week waz_who waz_nbs waz_png waz_whocorr waz |
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|--------------------------------------------------------------------------|
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| 132 133 0 . . . . . |
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| 132 139 1 . . . . . |
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| 132 146 2 . . . . . |
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| 132 162 4 . . . . . |
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| 132 174 6 . . . . . |
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| 132 203 10 . . 7.859 . 7.859 |
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| 132 230 14 . . 6.699 . 6.699 |
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| 132 258 18 . . 5.612 . 5.612 |
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| 132 317 26 . . . 3.512 3.512 |
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| 237 238 0 . -.712 . . -.712 |
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|--------------------------------------------------------------------------|
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. gen double waz = waz_who if gestage > `37weeks'
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(4,749 missing values generated)
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. replace waz = waz_png if gestage < `37weeks'
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(3,757 real changes made)
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. replace waz = waz_nbs if agedays == 0
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(188 real changes made)
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. list visitweek gestage pma waz_* waz in f/10, noobs sep(10)
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+------------------------------------------------------------------------+
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| visitw~k gestage pma waz_nbs waz_who waz_png waz |
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|------------------------------------------------------------------------|
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| 0 132 133 . . . . |
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| 1 132 139 . . . . |
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| 2 132 146 . . . . |
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| 4 132 162 . . . . |
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| 6 132 174 . . . . |
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| 10 132 203 . . 7.8594946 7.8594946 |
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| 14 132 230 . . 7.2548282 7.2548282 |
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| 18 132 258 . . 6.0985216 6.0985216 |
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| 26 132 317 . . 3.8344571 3.8344571 |
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| 0 237 238 . . -.43606208 -.43606208 |
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+------------------------------------------------------------------------+
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```
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This `waz` variable can then be used to determine whether infants are
@@ -294,13 +288,12 @@ remove any observations which were not made at birth. We then use the
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`classify_sga()` command to give us our classifications:
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```stata
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. use life6mo, clear
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. drop if visitweek != 0
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. keep if (gestage - pma) == 0
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(7,303 observations deleted)
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```
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```
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. egen sga = classify_sga(meaninfwgt/1000), ///
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> gest_age(gestage) sex(sex) sexcode(m=1, f=2)
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(5 missing values generated)
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> gest_days(gestage) sex(sex) sexcode(m=1, f=2)
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(2 missing values generated)
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```
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## Known issues and bug reporting

‎_gclassify_sga.ado

+3-3
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@@ -54,9 +54,9 @@ program define _gclassify_sga
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marksample touse
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tempvar p_temp
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egen double `p_temp' = ig_nbs(`input', "wfga", "v2c"), ///
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gest_days(`gest_days') sex(`sex') sexcode(m="`male'", f="`female'")
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qui {
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qui {
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egen double `p_temp' = ig_nbs(`input', "wfga", "v2c"), ///
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gest_days(`gest_days') sex(`sex') sexcode(m="`male'", f="`female'")
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generate `type' `return' = 0
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replace `return' = -1 if float(`p_temp') < 0.1
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replace `return' = 1 if float(`p_temp') > 0.9

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