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32 changes: 0 additions & 32 deletions input/InitialPopulations/compile/02_create_UKHLS_variables.do
Original file line number Diff line number Diff line change
Expand Up @@ -381,38 +381,6 @@ gen dhm_ghq_flag = missing(dhm_ghq)
replace dhm_ghq = round(dhm_ghq_prediction) if missing(dhm_ghq)
bys dhm_ghq_flag : sum dhm_ghq

/* Alternative method of GHQ caseness - binary cutoff at scghq2_dv <4
/**************************Subjective wellbeing (GHQ): Caseness ******************************
0: not psychologically distressed, scghq2_dv < 4
1: psychologically distressed, scghq2_dv >= 4
This measure converts valid answers to 12 questions of the General Health Questionnaire (GHQ) to a single scale by recoding 1 and 2 values
on individual variables to 0, and 3 and 4 values to 1, and then summing, giving a scale running from 0 (the least distressed) to 12
(the most distressed). A binary indicator is then created, equal to 1 for values >= 4.*/
// fre scghq2_dv
recode scghq2_dv (-9/-1 . = .)
gen scghq2_dv_miss_flag = (scghq2_dv == .)

*imputation for all
preserve
drop if dgn < 0 | dag<0 | dhe<0
eststo predict_scghq2: reg scghq2_dv c.dag i.dgn i.swv i.dhe if scghq2_dv>=0, vce(robust)
restore

estimates restore predict_scghq2
predict scghq2_prediction
fre scghq2_prediction

cap gen scghq2_dv_flag=missing(scghq2_dv)
replace scghq2_dv = round(scghq2_prediction) if missing(scghq2_dv)
bys scghq2_dv_flag: fre scghq2_dv
recode scghq2_dv(-1=0)

*create a dummy var
cap gen dhm_ghq = .
replace dhm_ghq = 0 if scghq2_dv>=0 & scghq2_dv<4
replace dhm_ghq = 1 if scghq2_dv>=4
lab var dhm_ghq "DEMOGRAPHIC: Subjective wellbeing (GHQ): Caseness"
//fre dhm_ghq


/****************************Self-rated health health - mental and physical component summary scores SF12 ***************************/
Expand Down
15 changes: 7 additions & 8 deletions input/InitialPopulations/compile/09_finalise_input_data.do
Original file line number Diff line number Diff line change
Expand Up @@ -161,16 +161,15 @@ rename der eduReturnFlag
rename dehm_c3 eduHighestMotherC3
rename dehf_c3 eduHighestFatherC3
rename stm statInterviewYear
rename dhm healthWbScore0to36
rename scghq2_dv demWbScore0to12
rename dhh_owned wealthPrptyFlag
rename lhw labHrsWorkWeek
rename l1_lhw labHrsWorkWeekL1
rename drgn1 demRgn
rename les_c4 labC4
rename dhm_ghq healthPsyDstrssFlag
rename adultchildflag demAdultChildFlag
rename dwt wgtHhCross
rename dot demEthnC4
rename dot01 demEthnC6

* --- Income, labour, wealth ---
rename potential_earnings_hourly labWageHrly
Expand Down Expand Up @@ -201,13 +200,13 @@ rename formal_socare_cost careCareFormal
rename careHoursProvidedWeekly careHrsProvidedWeek

* --- Health & wellbeing ---
rename dhm healthWbScore0to36
rename dhm_ghq healthPsyDstrss0to12
rename dhe_mcs healthMentalMcs
rename dhe_pcs healthPhysicalPcs
rename dhe_mcssp healthMentalPartnerMcs
rename dhe_pcssp healthPhysicalPartnerPcs
rename dls demLifeSatScore0to10
rename dot demEthnC4
rename dot01 demEthnC6
rename financial_distress yFinDstrssFlag


Expand Down Expand Up @@ -267,7 +266,7 @@ forvalues yy = $firstSimYear/$lastSimYear {
keep idHh idBu idPers idPartner idMother idFather statCollectionWave demMaleFlag demAge demNChild0to2 demNChild eduSpellFlag ///
eduHighestC3 eduExitSampleFlag healthDsblLongtermFlag healthSelfRated yHhQuintilesMonthC5 yEmpPersGrossMonth yNonBenPersGrossMonth ///
yMiscPersGrossMonth demPartnerNYear demAgePartnerDiff yPersAndPartnerGrossDiffMonth eduReturnFlag eduHighestMotherC3 eduHighestFatherC3 ///
statInterviewYear healthWbScore0to36 demWbScore0to12 wealthPrptyFlag labHrsWorkWeek labHrsWorkWeekL1 demRgn labC4 healthPsyDstrssFlag ///
statInterviewYear healthWbScore0to36 wealthPrptyFlag labHrsWorkWeek labHrsWorkWeekL1 demRgn labC4 healthPsyDstrss0to12 ///
demAdultChildFlag wgtHhCross labWageHrly labWageHrlyL1 wealthTotValue wealthPensValue wealthPrptyValue wealthMortgageDebtValue careNeedFlag ///
careHrsFormal careHrsFromPartner careHrsFromDaughter careHrsFromSon careHrsFromOther careCareFormal careHrsProvidedWeek yBenReceivedFlag ///
yBenNonUCReceivedFlag yBenUCReceivedFlag yDispMonth yCapitalPersMonth yPensPersGrossMonth aidhrs careWho healthMentalMcs healthPhysicalPcs ///
Expand All @@ -276,7 +275,7 @@ forvalues yy = $firstSimYear/$lastSimYear {
order idHh idBu idPers idPartner idMother idFather statCollectionWave demMaleFlag demAge demNChild0to2 demNChild eduSpellFlag ///
eduHighestC3 eduExitSampleFlag healthDsblLongtermFlag healthSelfRated yHhQuintilesMonthC5 yEmpPersGrossMonth yNonBenPersGrossMonth ///
yMiscPersGrossMonth demPartnerNYear demAgePartnerDiff yPersAndPartnerGrossDiffMonth eduReturnFlag eduHighestMotherC3 eduHighestFatherC3 ///
statInterviewYear healthWbScore0to36 demWbScore0to12 wealthPrptyFlag labHrsWorkWeek labHrsWorkWeekL1 demRgn labC4 healthPsyDstrssFlag ///
statInterviewYear healthWbScore0to36 wealthPrptyFlag labHrsWorkWeek labHrsWorkWeekL1 demRgn labC4 healthPsyDstrss0to12 ///
demAdultChildFlag wgtHhCross labWageHrly labWageHrlyL1 wealthTotValue wealthPensValue wealthPrptyValue wealthMortgageDebtValue careNeedFlag ///
careHrsFormal careHrsFromPartner careHrsFromDaughter careHrsFromSon careHrsFromOther careCareFormal careHrsProvidedWeek yBenReceivedFlag ///
yBenNonUCReceivedFlag yBenUCReceivedFlag yDispMonth yCapitalPersMonth yPensPersGrossMonth aidhrs careWho healthMentalMcs healthPhysicalPcs ///
Expand All @@ -285,7 +284,7 @@ forvalues yy = $firstSimYear/$lastSimYear {
recode idHh idBu idPers idPartner idMother idFather statCollectionWave demMaleFlag demAge demNChild0to2 demNChild eduSpellFlag ///
eduHighestC3 eduExitSampleFlag healthDsblLongtermFlag healthSelfRated yHhQuintilesMonthC5 yEmpPersGrossMonth yNonBenPersGrossMonth ///
yMiscPersGrossMonth demPartnerNYear demAgePartnerDiff yPersAndPartnerGrossDiffMonth eduReturnFlag eduHighestMotherC3 eduHighestFatherC3 ///
statInterviewYear healthWbScore0to36 demWbScore0to12 wealthPrptyFlag labHrsWorkWeek labHrsWorkWeekL1 demRgn labC4 healthPsyDstrssFlag ///
statInterviewYear healthWbScore0to36 wealthPrptyFlag labHrsWorkWeek labHrsWorkWeekL1 demRgn labC4 healthPsyDstrss0to12 ///
demAdultChildFlag wgtHhCross labWageHrly labWageHrlyL1 wealthTotValue wealthPensValue wealthPrptyValue wealthMortgageDebtValue careNeedFlag ///
careHrsFormal careHrsFromPartner careHrsFromDaughter careHrsFromSon careHrsFromOther careCareFormal careHrsProvidedWeek yBenReceivedFlag ///
yBenNonUCReceivedFlag yBenUCReceivedFlag yDispMonth yCapitalPersMonth yPensPersGrossMonth aidhrs careWho healthMentalMcs healthPhysicalPcs ///
Expand Down
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
idHh,idBu,idPers,idPartner,idMother,idFather,statCollectionWave,demMaleFlag,demAge,demNChild0to2,demNChild,eduSpellFlag,eduHighestC3,eduExitSampleFlag,healthDsblLongtermFlag,healthSelfRated,yEmpPersGrossMonth,yNonBenPersGrossMonth,yMiscPersGrossMonth,demPartnerNYear,demAgePartnerDiff,yPersAndPartnerGrossDiffMonth,eduReturnFlag,eduHighestMotherC3,eduHighestFatherC3,statInterviewYear,healthWbScore0to36,demWbScore0to12,labHrsWorkWeek,labHrsWorkWeekL1,labC4,healthPsyDstrssFlag,demAdultChildFlag,labWageHrly,labWageHrlyL1,careNeedFlag,careHrsFormal,careHrsFromPartner,careHrsFromDaughter,careHrsFromSon,careHrsFromOther,careCareFormal,careHrsProvidedWeek,yBenReceivedFlag,yBenNonUCReceivedFlag,yBenUCReceivedFlag,yCapitalPersMonth,yPensPersGrossMonth,aidhrs,careWho,healthMentalMcs,healthPhysicalPcs,healthMentalPartnerMcs,healthPhysicalPartnerPcs,demLifeSatScore0to10,demEthnC4,demEthnC6,labUnempFlag,yFinDstrssFlag,labEmpNyear,demRgn,yHhQuintilesMonthC5,wealthPrptyFlag,wgtHhCross,wealthTotValue,wealthPensValue,wealthPrptyValue,wealthMortgageDebtValue,yDispMonth
idHh,idBu,idPers,idPartner,idMother,idFather,statCollectionWave,demMaleFlag,demAge,demNChild0to2,demNChild,eduSpellFlag,eduHighestC3,eduExitSampleFlag,healthDsblLongtermFlag,healthSelfRated,yEmpPersGrossMonth,yNonBenPersGrossMonth,yMiscPersGrossMonth,demPartnerNYear,demAgePartnerDiff,yPersAndPartnerGrossDiffMonth,eduReturnFlag,eduHighestMotherC3,eduHighestFatherC3,statInterviewYear,healthWbScore0to36,healthPsyDstrss0to12,labHrsWorkWeek,labHrsWorkWeekL1,labC4,healthPsyDstrssFlag,demAdultChildFlag,labWageHrly,labWageHrlyL1,careNeedFlag,careHrsFormal,careHrsFromPartner,careHrsFromDaughter,careHrsFromSon,careHrsFromOther,careCareFormal,careHrsProvidedWeek,yBenReceivedFlag,yBenNonUCReceivedFlag,yBenUCReceivedFlag,yCapitalPersMonth,yPensPersGrossMonth,aidhrs,careWho,healthMentalMcs,healthPhysicalPcs,healthMentalPartnerMcs,healthPhysicalPartnerPcs,demLifeSatScore0to10,demEthnC4,demEthnC6,labUnempFlag,yFinDstrssFlag,labEmpNyear,demRgn,yHhQuintilesMonthC5,wealthPrptyFlag,wgtHhCross,wealthTotValue,wealthPensValue,wealthPrptyValue,wealthMortgageDebtValue,yDispMonth
1,1,1,-9,-9,-9,1,0,61,0,0,0,2,-9,0,4,6.725114889498321,7.898206598471436,7.253384840698923,0,0,-1062.469215318536,0,2,2,2019,11,0,15,11,1,0,0,8.015179360993026,8.015179360993026,0,0,0,0,0,0,0,0,0,0,0,0,7.526514096434597,0,0,57.16,56.15,-9,-9,5,1,1,0,0,9,9,3,0,953,676131.0275408182,316456.4680975397,193683.8957471466,63936.64369794785,-377.4915825240205
2,2,2,3,-9,-9,1,1,68,0,0,0,1,-9,0,3,7.886993691667886,8.544583694034513,7.38271831749168,49,1,60.31366416029789,0,2,3,2019,6,0,25,30,1,0,0,11.51763815191938,11.51763815191938,0,0,0,0,0,0,0,0,1,1,0,6.387541206929813,7.104293718128605,0,0,51.41,56.15,42.24,58.9,6,1,1,0,0,9,9,4,1,715,2410787.41512763,1690222.068883574,706502.8913574461,104302.781800875,4909.79139019544
2,2,3,2,-9,-9,1,0,67,0,0,0,1,-9,0,4,7.710280110469539,8.041401738620744,6.862359188400778,49,-1,31.38179225666527,0,2,1,2019,18,7,15,25,1,1,0,17.98276105377562,17.98276105377562,0,0,0,0,0,0,0,0,1,1,0,4.429519137618809,7.08824878144737,0,0,42.24,58.9,51.41,56.15,6,1,1,0,0,7,9,4,1,715,2410787.41512763,1690222.068883574,706502.8913574461,104302.781800875,4909.79139019544
Expand Down
Binary file modified input/SimPaths_Variable_Codebook.xlsx
Binary file not shown.
3 changes: 1 addition & 2 deletions src/main/java/simpaths/data/Parameters.java
Original file line number Diff line number Diff line change
Expand Up @@ -129,8 +129,7 @@ public class Parameters {
"healthMentalPartnerMcs", //mental health - SF12 score MCS (partner)
"healthPhysicalPartnerPcs", //physical health - SF12 score PCS (partner)
"healthWbScore0to36", //mental health status
"demWbScore0to12", //mental health status case based
"healthPsyDstrssFlag", //mental health status case based dummy (1 = psychologically distressed)
"healthPsyDstrss0to12", // mental health status 0 to 12
"demLifeSatScore0to10", //life satisfaction
"yFinDstrssFlag", //financial distress
"demPartnerNYear", //years in partnership
Expand Down
3 changes: 1 addition & 2 deletions src/main/java/simpaths/data/startingpop/DataParser.java
Original file line number Diff line number Diff line change
Expand Up @@ -252,8 +252,7 @@ private static void parse(String inputFileLocation, String inputFileName, Connec
+ "ALTER TABLE " + personTable + " ALTER COLUMN HEALTHPHYSICALPARTNERPCS DECIMAL(4, 2);"
+ "ALTER TABLE " + personTable + " ALTER COLUMN DEMLIFESATSCORE0to10 DECIMAL(4, 2);"
+ "ALTER TABLE " + personTable + " ALTER COLUMN HEALTHWBSCORE0TO36 INT;"
+ "ALTER TABLE " + personTable + " ALTER COLUMN HEALTHPSYDSTRSSFLAG INT;"
+ "ALTER TABLE " + personTable + " ALTER COLUMN DEMWBSCORE0TO12 INT;"
+ "ALTER TABLE " + personTable + " ALTER COLUMN HEALTHPSYDSTRSS0to12 INT;"

//Rename idBu to BU_ID
+ "ALTER TABLE " + personTable + " ALTER COLUMN idBu RENAME TO buid;"
Expand Down
60 changes: 30 additions & 30 deletions src/main/java/simpaths/model/Person.java
Original file line number Diff line number Diff line change
Expand Up @@ -130,8 +130,8 @@ public class Person implements EventListener, IDoubleSource, IIntSource, Weight,
@Transient private Boolean demAlignPartnerProcess;
@Transient private Boolean demLeavePartnerFlag; // Used in partnership alignment process. Indicates that this person has found partner in a test run of union matching.
@Column(name="wgt") private Double wgt;
@Column(name="healthPsyDstrss") private Double healthPsyDstrss; //Psychological distress GHQ-12 0-12 caseness score
@Transient private Double healthPsyDstrssL1;
@Column(name="healthPsyDstrss0to12") private Double healthPsyDstrss0to12; //Psychological distress GHQ-12 0-12 caseness score
@Transient private Double healthPsyDstrss0to12L1;
@Transient private Dhe healthSelfRatedL1;
@Enumerated(EnumType.STRING) private Dhe healthSelfRated;
private Double healthWbScore0to36; //Psychological distress GHQ-12 Likert scale
Expand Down Expand Up @@ -293,7 +293,7 @@ public Person(Gender gender, Person mother) {
wgt = mother.getWgt(); //Newborn has same weight as mother (the number of newborns will then be aligned in fertility alignment)
healthSelfRated = Dhe.VeryGood;
healthWbScore0to36 = 10.; //Set to median for under 18's as a placeholder
healthPsyDstrss = 0.;
healthPsyDstrss0to12 = 0.;
healthMentalMcs = 48.;
healthPhysicalPcs = 56.;
demLifeSatScore0to10 = 6.;
Expand Down Expand Up @@ -492,8 +492,8 @@ else if (demAge > Parameters.MAX_AGE_TO_LEAVE_CONTINUOUS_EDUCATION)
healthWbScore0to36L1 = originalPerson.healthWbScore0to36;
}

healthPsyDstrss = Objects.requireNonNullElse(originalPerson.healthPsyDstrss, 0.);
healthPsyDstrssL1 = Objects.requireNonNullElse(originalPerson.healthPsyDstrssL1, healthPsyDstrss);
healthPsyDstrss0to12 = Objects.requireNonNullElse(originalPerson.healthPsyDstrss0to12, 0.);
healthPsyDstrss0to12L1 = Objects.requireNonNullElse(originalPerson.healthPsyDstrss0to12L1, healthPsyDstrss0to12);

demLifeSatScore0to10 = originalPerson.demLifeSatScore0to10;
healthMentalMcs = originalPerson.healthMentalMcs;
Expand Down Expand Up @@ -1064,44 +1064,44 @@ protected void healthMentalHM2Level() {
/**
* Health and wellbeing - GHQ-12 subjective wellbeing, Caseness scale 0-12 step 1
*
* <p>Calculates the 'baseline' yearly update to the GHQ-12 Caseness (cases) score ({@code healthPsyDstrss}) based on demographic variables.
* <p>Calculates the 'baseline' yearly update to the GHQ-12 Caseness (cases) score ({@code healthPsyDstrss0to12}) based on demographic variables.
* Runs <b>before</b> {@link #healthMentalHM2Case()}.</p>
*
* @filter Age 16+
* @updates {@code Person.healthPsyDstrss}
* @updates {@code Person.healthPsyDstrss0to12}
* @see <a href="https://www.understandingsociety.ac.uk/documentation/mainstage/variables/scghq2_dv/">scghq2_dv</a>
*/
protected void healthMentalHM1Case() {
if (demAge >= 16) {
Map<DhmGhq,Double> probs = ManagerRegressions.getProbabilities(this, RegressionName.HealthHM1Case);
MultiValEvent event = new MultiValEvent(probs, statInnovations.getDoubleDraw(36));
healthPsyDstrss = Double.valueOf(event.eval().getValue());
healthPsyDstrss0to12 = Double.valueOf(event.eval().getValue());
}
}

/**
* Health and wellbeing - GHQ-12 subjective wellbeing, Caseness scale 0-12 step 2
*
* <p>Updates GHQ-12 Caseness (cases) score ({@code healthPsyDstrss}) from the causal effects of economic transitions.
* <p>Updates GHQ-12 Caseness (cases) score ({@code healthPsyDstrss0to12}) from the causal effects of economic transitions.
* Applies separate estimates for Male and Female Persons.
* Runs <b>after</b> {@link #healthMentalHM1Case()}</p>
*
* @filter Age 25-64
* @updates {@code Person.healthPsyDstrss}
* @updates {@code Person.healthPsyDstrss0to12}
* @see <a href="https://www.understandingsociety.ac.uk/documentation/mainstage/variables/scghq2_dv/">scghq2_dv</a>
*/
protected void healthMentalHM2Case() {
double dhmGhqPrediction;
if (demAge >= 25 && demAge <= 64) {
if (Gender.Male.equals(getDemMaleFlag())) {
dhmGhqPrediction = Parameters.getRegHealthHM2CaseMales().getScore(this, Person.DoublesVariables.class);
healthPsyDstrss = constrainhealthPsyDstrssEstimate(dhmGhqPrediction+ healthPsyDstrss);
healthPsyDstrss0to12 = constrainhealthPsyDstrssEstimate(dhmGhqPrediction+ healthPsyDstrss0to12);
} else if (Gender.Female.equals(getDemMaleFlag())) {
dhmGhqPrediction = Parameters.getRegHealthHM2CaseFemales().getScore(this, Person.DoublesVariables.class);
healthPsyDstrss = constrainhealthPsyDstrssEstimate(dhmGhqPrediction+ healthPsyDstrss);
healthPsyDstrss0to12 = constrainhealthPsyDstrssEstimate(dhmGhqPrediction+ healthPsyDstrss0to12);
} else System.out.println("healthMentalHM2 method in Person class: Person has no gender!");
} else if (healthPsyDstrss != null) {
healthPsyDstrss = constrainhealthPsyDstrssEstimate(healthPsyDstrss);
} else if (healthPsyDstrss0to12 != null) {
healthPsyDstrss0to12 = constrainhealthPsyDstrssEstimate(healthPsyDstrss0to12);
}
}

Expand Down Expand Up @@ -1300,16 +1300,16 @@ protected Double constrainDhmEstimate(Double healthWbScore0to36) {
/**
* Constrains GHQ12 Caseness estimates to valid range, 0-12
*
* @param healthPsyDstrssFlag predicted GHQ12 Caseness score
* @return {@code Person.healthPsyDstrss} Caseness score constrained to 0-12
* @param healthPsyDstrss0to12 predicted GHQ12 Caseness score
* @return {@code Person.healthPsyDstrss0to12} Caseness score constrained to 0-12
*/
protected Double constrainhealthPsyDstrssEstimate(Double healthPsyDstrssFlag) {
if (healthPsyDstrssFlag < 0.) {
healthPsyDstrssFlag = 0.;
} else if (healthPsyDstrssFlag > 12.) {
healthPsyDstrssFlag = 12.;
protected Double constrainhealthPsyDstrssEstimate(Double healthPsyDstrss0to12) {
if (healthPsyDstrss0to12 < 0.) {
healthPsyDstrss0to12 = 0.;
} else if (healthPsyDstrss0to12 > 12.) {
healthPsyDstrss0to12 = 12.;
}
return healthPsyDstrssFlag;
return healthPsyDstrss0to12;
}


Expand Down Expand Up @@ -2197,7 +2197,7 @@ private void updateLaggedVariables(boolean initialUpdate) {
demStatusHhL1 = getHouseholdStatus();
healthSelfRatedL1 = healthSelfRated; //Update lag(1) of health
healthWbScore0to36L1 = healthWbScore0to36; //Update lag(1) of mental health
healthPsyDstrssL1 = healthPsyDstrss;
healthPsyDstrss0to12L1 = healthPsyDstrss0to12;
demLifeSatScore0to10L1 = demLifeSatScore0to10;
healthMentalMcsL1 = healthMentalMcs;
healthPhysicalPcsL1 = healthPhysicalPcs;
Expand Down Expand Up @@ -2470,7 +2470,7 @@ public int getIntValue(Enum<?> variableID) {
return (isToBePartnered())? 1 : 0;

case isPsychologicallyDistressed:
return (healthPsyDstrss >= 4)? 1 : 0;
return (healthPsyDstrss0to12 >= 4)? 1 : 0;

case isNeedSocialCare:
return (Indicator.True.equals(careNeedFlag)) ? 1 : 0;
Expand Down Expand Up @@ -4891,12 +4891,12 @@ public void setHealthWbScore0to36L1(Double dhm) {
this.healthWbScore0to36L1 = dhm;
}

public Double getHealthPsyDstrss() {
return healthPsyDstrss;
public Double getHealthPsyDstrss0to12() {
return healthPsyDstrss0to12;
}

public void setHealthPsyDstrss(Double dhm_ghq) {
this.healthPsyDstrss = dhm_ghq;
public void setHealthPsyDstrss0to12(Double dhm_ghq) {
this.healthPsyDstrss0to12 = dhm_ghq;
}

public Ethnicity getDot01() {
Expand Down Expand Up @@ -5847,9 +5847,9 @@ public void setProcessedId(long id) {
public long getSeed() {return (statSeed !=null) ? statSeed : 0L;}

private Double gethealthPsyDstrss_lag1() {
if (healthPsyDstrssL1 == null)
if (healthPsyDstrss0to12L1 == null)
throw new RuntimeException("attempt to access dhmGhq_lag1 before it has been initialised");
return healthPsyDstrssL1;
return healthPsyDstrss0to12L1;
}

public Double getYnbcpdf_dv() {
Expand Down