BIO Lab 2: TWO-LEVEL NORMAL MODELS with school children popularity data

Transcription

1 Lab : TWO-LEVEL NORMAL MODELS wth school chldren popularty data Purpose: Introduce basc two-level models for normally dstrbuted responses usng STATA. In partcular, we dscuss Random ntercept models wthout covarates Random ntercept models wth covarates Random ntercept models wth covarates and random slopes Cross-level nteractons We wll use the followng 5 varables n the popular.dta dataset: pupl: pupl dentfcaton number school: school dentfcaton number popular: the outcome varable popularty (Y), measured by a self-ratng scale that range from 0 (very unpopular) to 10 (very popular). sex: the pupl sex, 0 boy 1 grl texp: teacher experence n years The data are from 000 pupls from 100 classes (each at a dfferent school), the average number of students per school (class) s 0. Therefore, we have pupls nested wthn schools, and we need to account for the possble correlaton between pupls n the same school n our model. Intal EDA: Our outcome varable of nterest s self-reported popularty score:. hst popular, freq (bn=33, start=, wdth=.1111) Frequency popularty accordng to socometrc score 1

2 Q1. What s the average self-ratng score? Two-stage model of the popularty score of pupl (j) n school () MODEL 1: The ntercept-only (varance components) model: popular j U β + U + ε = 0 ε ~ N(0, σ ) j U ~ N(0, τ ) j Interpretatons of model parameters: β 0 + U : average score for pupls n school β : average score for pupls n a typcal school ( U =0) 0 U : school-level random ntercept (random effect). Represents the dfference between the average popularty score for a specfc school() and the average popularty score of a typcal (U =0) school. τ : varance of the random ntercept. Represents the varablty (or amount of dsperson) n specfc schools average scores around the average score of the typcal school. ε j : dfference between the popularty score for chld(j) and the average popularty score n school() σ : varance of the error. Represents the varablty of ndvdual chldren s scores n school() around the average score for school().

3 (At least) three ways to ft ths multlevel model for a contnuous outcome usng STATA, n order of generalty: 1. xtreg, re mle - estmates model parameters by fndng the maxmum of a closed form soluton for the lkelhood (fast) - can only do two level models - can only do a random ntercept, not random slopes - only for contnuous outcomes - usng the pa opton for xtreg s equvalent to usng xtgee, so wth xtreg you can easly swtch from dong a cluster-specfc random ntercept model to dong a margnal GEE model - automatcally gves you the ICC (rho) n the output - by default, returns the sd of the random ntercept. xtmxed, mle - estmates model parameters by fndng the maxmum of a closed form soluton for the lkelhood (fast) - very close to beng equvalent to xtreg, re mle - as many levels as you want (wthn reason!!) - can do random ntercepts and slopes - only for contnuous outcomes - by default returns the sd of the random effects 3. gllamm - estmates model parameters usng quadrature methods to approxmate the lkelhood functon, and then fnds the maxmum of the approxmated lkelhood (slow!) - results won t be exactly the same as xtmxed, but they should be close. You can ncrease np() and use the adapt opton to get better estmates n gllamm (even slower!) - can do many levels - can do random ntercepts and slopes - for many types of outcomes (contnuous, bnary, posson, etc ) - by default returns the varance of the random effects For contnuous outcomes, xtmxed s preferred because t uses a closed form soluton for the lkelhood and hence produces accurate results relatvely quckly. 3

4 Syntax for fttng the ntercept-only model xtreg. xtreg popular, re (school) mle Random-effects ML regresson Number of obs = 000 Group varable: school Number of groups = 100 Random effects u_ ~ Gaussan Obs per group: mn = 16 avg = 0.0 max = 6 Wald ch(0) = 0.00 Log lkelhood = Prob > ch =. _cons /sgma_u /sgma_e rho Lkelhood-rato test of sgma_u=0: chbar(01)= Prob>=chbar = xtmxed. xtmxed popular school:, mle Mxed-effects ML regresson Number of obs = 000 Group varable: school Number of groups = 100 Obs per group: mn = 16 avg = 0.0 max = 6 Wald ch(0) =. Log lkelhood = Prob > ch =. _cons Random-effects Parameters Estmate Std. Err. [95% Conf. Interval] school: Identty sd(_cons) sd(resdual) LR test vs. lnear regresson: chbar(01) = Prob >= chbar =

5 gllamm. gllamm popular, (school) adapt Runnng adaptve quadrature Iteraton 0: log lkelhood = Iteraton 1: log lkelhood = Iteraton : log lkelhood = Iteraton 3: log lkelhood = Iteraton 4: log lkelhood = Adaptve quadrature has converged, runnng Newton-Raphson Iteraton 0: log lkelhood = Iteraton 1: log lkelhood = (backed up) Iteraton : log lkelhood = number of level 1 unts = 000 number of level unts = 100 Condton Number = gllamm model log lkelhood = _cons Varance at level ( ) Varances and covarances of random effects ***level (school) var(1): ( ) xtmxed can gve you the varance of the error and the random ntercept, not the sd. xtmxed popular school:, mle var _cons Random-effects Parameters Estmate Std. Err. [95% Conf. Interval] school: Identty var(_cons) var(resdual) LR test vs. lnear regresson: chbar(01) = Prob >= chbar =

6 Q. Do gender and teachng experence affect the self-ratng score? Gender s a level-l covarate (t vares for each chld (j) nested n school ()). Teachng experence s a level- covarate snce t s fxed for all students n a gven class (school). Exploratory analyss of the relatonshp between texp and popularty gnorng clusterng. lowess popular texp, bw(0.5) jtter(3) Lowess smoother popularty accordng to socometrc score teacher experence n years bandwdth =.5 But what we ll really be modelng s how the average popularty scores of chldren n a gven school vary accordng to the covarate values of student gender and teacher s experence snce we have the model: MODEL : popular j = β β β texp + ε U,grlj, texp ( 0 + U ) + 1grlj + j Or, n other words, E ( popularj U, grlj, texp ) = ( β 0 + U ) + β1grlj + β texp A more nformatve plot mght look at the relatonshp between the mean popularty score at each school and teacher experence.. sort school. by school: egen mscore_sch=mean(popular). lowess mscore_sch texp, yttle("school Average Popularty score") xttle("teacher Experence") bw(0>.5) 6

7 Lowess smoother School Average Popularty score Teacher Experence bandwdth =.5 We fnd a postve assocaton between the teachers experence and the average popularty score for each school. Next we explore the relatonshp between the mean popularty score at each school for grls versus boys.. sort school grl. by school grl: egen mscore_sch_grl = mean(popular). sort grl. graph box mscore_sch_grl, over(grl) yttle("school Average Score") School Average Score boy grl We fnd the average reported scores for grls are hgher than for boys. 7

8 Do we see evdence of an nteracton?. lowess mscore_sch_grl texp, by(grl) boy Lowess smoother grl mscore_sch_grl teacher experence n years bandwdth =.8 The slopes are relatvely smlar, but the two curves defntely start at dfferent ponts, so for ths example we ll contnue by just ncludng a lnear term for teacher s experence and an ndcator varable for pupl gender, but not an nteracton term (an nteracton term would allow the slope on the relaton between average popularty score and texp to vary accordng gender). Random ntercept model wth fxed effects for texp and grl. xtmxed popular texp grl school:, mle Mxed-effects ML regresson Number of obs = 000 Group varable: school Number of groups = 100 Obs per group: mn = 16 avg = 0.0 max = 6 Wald ch() = Log lkelhood = Prob > ch = texp grl _cons

9 Random-effects Parameters Estmate Std. Err. [95% Conf. Interval] school: Identty sd(_cons) sd(resdual) LR test vs. lnear regresson: chbar(01) = Prob >= chbar = Interpretaton of the coeffcent on texp : For a gven school, we estmate that ncreasng the teacher s experence by one year would result n average popularty scores that are.09 ponts hgher for both male and female students. Interpretaton of the coeffcent on grl : Wthn a school, we estmate that the average popularty scores are.845 ponts hgher for grls than for boys, controllng for teacher s experence. Q3. Does the dfference n average self-ratng score between female and male students vary across schools? To address ths queston usng EDA, we ll frst create a varable that contans the mean scores for boys for each school and then another varable that contans the mean score for grls for each school.. sort school grl. by school: gen meanpop_boys = mscore_sch_grl[1]. gen boy = 1-grl. sort school boy. by school: gen meanpop_grls = mscore_sch_grl[1] We ll subtract the average boys score from the average females score to get the dfference n scores across genders for each school.. gen genddff = meanpop_grls - meanpop_boys. replace genddff =. f pupl!=1 We then make a hstogram of the gender dfferences for each school to see how much heterogenety (or varablty) we have between schools n our gender dfference.. hst genddff, norm freq xttle(school-specfc dfference between female and male average scores) 9

10 Frequency School-specfc dfference between female and male average scores We do see qute a bt of heterogenety n the gender dfferences across the dfferent school. We can buld the heterogenety of the gender effect nto our model: Random ntercept model wth fxed effects for texp and grl and a random coeffcent on pupl gender MODEL 3: popular j U 0, U1, grlj, texp ( 0 + U 0 ) + ( β1 + U1 )grlj + β = β texp + ε U U ε ~ N(0, σ ) j 0 1 ~ MVN (0, Σ) j In the above model, popularty score s functon of pupl gender and teachng experence. We allow for dfferent baselne scores for dfferent schools by usng a random ntercept, and we allow dfferent gender effects for dfferent schools by usng a random slope for gender. Note: We could NOT ft a model that ncludes a random slope on teachng experence because teachng experence does not vary wthn school. 10

11 . xtmxed popular texp grl school: grl, cov(unstr) mle Mxed-effects ML regresson Number of obs = 000 Group varable: school Number of groups = 100 Obs per group: mn = 16 avg = 0.0 max = 6 Wald ch() = Log lkelhood = Prob > ch = texp grl _cons Random-effects Parameters Estmate Std. Err. [95% Conf. Interval] school: Unstructured sd(grl) sd(_cons) corr(grl,_cons) sd(resdual) LR test vs. lnear regresson: ch(3) = Prob > ch = Note: LR test s conservatve and provded only for reference. Important! Always allow the random slope and random ntercept to be correlated Q4. Does teachng experence explan the between-school heterogenety n the gender effect? MODEL 4: popular j U 0, U1, grlj, texp ( 0 + U 0 ) + ( β1 + β3texp + U1 )grlj + β = β texp + ε U U ε ~ N(0, σ ) j 0 1 ~ MVN (0, Σ) j We can answer ths queston by fttng the above model that ncludes a cross-level nteracton of the varables sex and texp. It s called cross-level snce gender s a level- 1 covarate (vares at the pupl level) whle teacher s experence s a level- unt (vares at the class (school) level). 11

12 . gen grlxtexp = grl*texp. xtmxed popular texp grl grlxtexp school: grl, cov(unstr) mle Mxed-effects ML regresson Number of obs = 000 Group varable: school Number of groups = 100 Obs per group: mn = 16 avg = 0.0 max = 6 Wald ch(3) = Log lkelhood = Prob > ch = texp grl grlxtexp _cons Random-effects Parameters Estmate Std. Err. [95% Conf. Interval] school: Unstructured sd(grl) sd(_cons) corr(grl,_cons) sd(resdual) LR test vs. lnear regresson: ch(3) = Prob > ch = Note: LR test s conservatve and provded only for reference. The estmate of fxed coeffcent on teacher s experence s smlar for both model 3 and model 4. However, the regresson slope for pupl gender s consderable larger n model 4 (the model wth the cross-level nteracton between gender and teacher s experence) and ths coeffcent now has the nterpretaton of beng the school-specfc dfference n average scores between genders when the teacher s experence s zero for a typcal school. The coeffcent on the nteracton between gender and teacher experence s estmated as -0.03, whch s statstcally sgnfcant. The negatve value means the dfference between grls and boys s smaller wth more experenced teachers. The standard devaton of the random slope on gender decreases from 0.5 to 0.47, whch means that the varaton n teacher experence between schools explans some of the varablty between schools n the estmated gender dfference n self-reported popularty scores. 1