Dan's Thesis Analyses - Chair Stands 2
load(file="/Users/meganwilliams/Desktop/UMBC 2016/Dan's Thesis/DanThesisFinal.rdata")
library(lmerTest)
library(zStat)
library(zUtil)
Chair Stands - Model 1 (Main Effects)
mm1 = lmer(PhyPerfStands10~Age + Sex + EF + Race + BMI + PovStat + WRATtotal + (1|HNDid), data=DanThesisFinal,REML=F)
summary(mm1)
## Linear mixed model fit by maximum likelihood t-tests use Satterthwaite
## approximations to degrees of freedom [lmerMod]
## Formula:
## PhyPerfStands10 ~ Age + Sex + EF + Race + BMI + PovStat + WRATtotal +
## (1 | HNDid)
## Data: DanThesisFinal
##
## AIC BIC logLik deviance df.resid
## 14258.4 14314.8 -7119.2 14238.4 2061
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.5538262 -0.5197994 -0.0973399 0.4012000 8.4270475
##
## Random effects:
## Groups Name Variance Std.Dev.
## HNDid (Intercept) 25.15292 5.015269
## Residual 35.34888 5.945492
## Number of obs: 2071, groups: HNDid, 1372
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 34.49467829 1.58812704 1399.61340000 21.72035 < 2.22e-16
## Age 0.20342633 0.02042201 1528.62650000 9.96113 < 2.22e-16
## SexMen -1.34088867 0.39461590 1294.51950000 -3.39796 0.00069953
## EF -0.18558824 0.08364409 1924.79810000 -2.21878 0.02661762
## RaceAfrAm -0.30818030 0.40658467 1298.14800000 -0.75797 0.44860458
## BMI 0.02912362 0.02630433 1477.02000000 1.10718 0.26839663
## PovStatBelow 1.57167567 0.41506197 1312.89580000 3.78660 0.00015962
## WRATtotal -0.02731604 0.02884370 1407.75850000 -0.94704 0.34378272
##
## Correlation of Fixed Effects:
## (Intr) Age SexMen EF RcAfrA BMI PvSttB
## Age -0.017
## SexMen -0.212 0.004
## EF 0.256 0.091 -0.011
## RaceAfrAm -0.286 0.023 -0.012 0.110
## BMI -0.518 -0.016 0.185 0.041 -0.009
## PovStatBelw -0.274 0.103 0.032 0.056 -0.046 0.077
## WRATtotal -0.821 0.005 0.020 -0.395 0.185 -0.003 0.185
Chair Stands - Model 2 (Two-Way Interactions)
mm2 = lmer(PhyPerfStands10~(Age + Sex + EF + Race)^2 + BMI + PovStat + WRATtotal + (1|HNDid), data=DanThesisFinal,REML=F)
summary(mm2)
## Linear mixed model fit by maximum likelihood t-tests use Satterthwaite
## approximations to degrees of freedom [lmerMod]
## Formula: PhyPerfStands10 ~ (Age + Sex + EF + Race)^2 + BMI + PovStat +
## WRATtotal + (1 | HNDid)
## Data: DanThesisFinal
##
## AIC BIC logLik deviance df.resid
## 14258.5 14348.7 -7113.2 14226.5 2055
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.5906007 -0.5186639 -0.0901796 0.4012207 8.4470589
##
## Random effects:
## Groups Name Variance Std.Dev.
## HNDid (Intercept) 24.76362 4.976306
## Residual 35.31655 5.942773
## Number of obs: 2071, groups: HNDid, 1372
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.442297e+01 1.600982e+00 1.401060e+03 21.50116
## Age 1.824803e-01 3.706361e-02 1.542325e+03 4.92344
## SexMen -1.081207e+00 6.203975e-01 1.305032e+03 -1.74277
## EF -7.819774e-02 1.343822e-01 1.811013e+03 -0.58191
## RaceAfrAm 2.347422e-02 5.337844e-01 1.316583e+03 0.04398
## BMI 2.543874e-02 2.655379e-02 1.479166e+03 0.95801
## PovStatBelow 1.614083e+00 4.141984e-01 1.314277e+03 3.89688
## WRATtotal -2.874190e-02 2.886703e-02 1.406380e+03 -0.99567
## Age:SexMen 1.234215e-01 4.144850e-02 1.524531e+03 2.97771
## Age:EF -7.875954e-03 7.909287e-03 1.890310e+03 -0.99579
## Age:RaceAfrAm -4.072371e-02 4.258215e-02 1.528157e+03 -0.95636
## SexMen:EF -1.613917e-02 1.539461e-01 1.849014e+03 -0.10484
## SexMen:RaceAfrAm -5.584361e-01 8.083861e-01 1.315447e+03 -0.69080
## EF:RaceAfrAm -1.626703e-01 1.527044e-01 1.837062e+03 -1.06526
## Pr(>|t|)
## (Intercept) < 2.22e-16
## Age 9.4163e-07
## SexMen 0.08161018
## EF 0.56070271
## RaceAfrAm 0.96492944
## BMI 0.33821538
## PovStatBelow 0.00010235
## WRATtotal 0.31958414
## Age:SexMen 0.00294996
## Age:EF 0.31948178
## Age:RaceAfrAm 0.33904352
## SexMen:EF 0.91651694
## SexMen:RaceAfrAm 0.48981083
## EF:RaceAfrAm 0.28689723
Chair Stands - Model 3 (Three-Way Interactions)
mm3 = lmer(PhyPerfStands10~(Age + Sex + EF + Race)^3 + BMI + PovStat + WRATtotal + (1|HNDid), data=DanThesisFinal,REML=F)
summary(mm3)
## Linear mixed model fit by maximum likelihood t-tests use Satterthwaite
## approximations to degrees of freedom [lmerMod]
## Formula: PhyPerfStands10 ~ (Age + Sex + EF + Race)^3 + BMI + PovStat +
## WRATtotal + (1 | HNDid)
## Data: DanThesisFinal
##
## AIC BIC logLik deviance df.resid
## 14264.2 14376.9 -7112.1 14224.2 2051
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.5479911 -0.5197129 -0.0969140 0.4052429 8.4549308
##
## Random effects:
## Groups Name Variance Std.Dev.
## HNDid (Intercept) 24.63266 4.963130
## Residual 35.35022 5.945605
## Number of obs: 2071, groups: HNDid, 1372
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.437884e+01 1.604718e+00 1.401529e+03 21.42360
## Age 1.663225e-01 4.430560e-02 1.594322e+03 3.75398
## SexMen -1.076958e+00 6.402140e-01 1.331004e+03 -1.68218
## EF -3.495815e-02 1.508297e-01 1.771073e+03 -0.23177
## RaceAfrAm 3.492800e-02 5.359409e-01 1.315716e+03 0.06517
## BMI 2.618910e-02 2.654831e-02 1.475693e+03 0.98647
## PovStatBelow 1.622169e+00 4.139127e-01 1.312227e+03 3.91911
## WRATtotal -2.873741e-02 2.885779e-02 1.405725e+03 -0.99583
## Age:SexMen 1.570003e-01 6.852926e-02 1.550740e+03 2.29100
## Age:EF 9.286596e-04 1.373578e-02 1.875135e+03 0.06761
## Age:RaceAfrAm -1.808199e-02 5.582546e-02 1.563003e+03 -0.32390
## SexMen:EF -1.216055e-01 2.268939e-01 1.812554e+03 -0.53596
## SexMen:RaceAfrAm -5.737623e-01 8.177345e-01 1.319791e+03 -0.70165
## EF:RaceAfrAm -2.416239e-01 2.024517e-01 1.829361e+03 -1.19349
## Age:SexMen:EF -2.155013e-02 1.603998e-02 1.886370e+03 -1.34353
## Age:SexMen:RaceAfrAm -4.572386e-02 8.692281e-02 1.532483e+03 -0.52603
## Age:EF:RaceAfrAm 4.730243e-04 1.594279e-02 1.890399e+03 0.02967
## SexMen:EF:RaceAfrAm 1.832408e-01 3.074962e-01 1.840322e+03 0.59591
## Pr(>|t|)
## (Intercept) < 2.22e-16
## Age 0.00018029
## SexMen 0.09276771
## EF 0.81674162
## RaceAfrAm 0.94804746
## BMI 0.32406451
## PovStatBelow 9.3461e-05
## WRATtotal 0.31950478
## Age:SexMen 0.02209719
## Age:EF 0.94610425
## Age:RaceAfrAm 0.74605543
## SexMen:EF 0.59205373
## SexMen:RaceAfrAm 0.48302204
## EF:RaceAfrAm 0.23283260
## Age:SexMen:EF 0.17926323
## Age:SexMen:RaceAfrAm 0.59894467
## Age:EF:RaceAfrAm 0.97633328
## SexMen:EF:RaceAfrAm 0.55130712
Chair Stands - Model 4 (Four-Way Interactions)
mm4 = lmer(PhyPerfStands10~(Age + Sex + EF + Race)^4 + BMI + PovStat + WRATtotal + (1|HNDid), data=DanThesisFinal,REML=F)
summary(mm4)
## Linear mixed model fit by maximum likelihood t-tests use Satterthwaite
## approximations to degrees of freedom [lmerMod]
## Formula: PhyPerfStands10 ~ (Age + Sex + EF + Race)^4 + BMI + PovStat +
## WRATtotal + (1 | HNDid)
## Data: DanThesisFinal
##
## AIC BIC logLik deviance df.resid
## 14266.1 14384.4 -7112.0 14224.1 2050
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.5397401 -0.5239892 -0.0955580 0.4029609 8.4545476
##
## Random effects:
## Groups Name Variance Std.Dev.
## HNDid (Intercept) 24.63942 4.963811
## Residual 35.34270 5.944973
## Number of obs: 2071, groups: HNDid, 1372
##
## Fixed effects:
## Estimate Std. Error df t value
## (Intercept) 3.438098e+01 1.604750e+00 1.401442e+03 21.42450
## Age 1.692819e-01 4.520500e-02 1.616778e+03 3.74476
## SexMen -1.057383e+00 6.429648e-01 1.333370e+03 -1.64454
## EF -3.457100e-02 1.508338e-01 1.770269e+03 -0.22920
## RaceAfrAm 4.158341e-02 5.363313e-01 1.315040e+03 0.07753
## BMI 2.611459e-02 2.654948e-02 1.475708e+03 0.98362
## PovStatBelow 1.625666e+00 4.140549e-01 1.311967e+03 3.92621
## WRATtotal -2.887144e-02 2.886091e-02 1.406028e+03 -1.00036
## Age:SexMen 1.513806e-01 7.060835e-02 1.582927e+03 2.14395
## Age:EF -1.599174e-03 1.572611e-02 1.866253e+03 -0.10169
## Age:RaceAfrAm -2.056467e-02 5.632891e-02 1.579621e+03 -0.36508
## SexMen:EF -1.198865e-01 2.269521e-01 1.816601e+03 -0.52825
## SexMen:RaceAfrAm -6.023520e-01 8.223200e-01 1.324466e+03 -0.73250
## EF:RaceAfrAm -2.407989e-01 2.024651e-01 1.830666e+03 -1.18934
## Age:SexMen:EF -1.559465e-02 2.414495e-02 1.923677e+03 -0.64588
## Age:SexMen:RaceAfrAm -4.063156e-02 8.827775e-02 1.559522e+03 -0.46027
## Age:EF:RaceAfrAm 4.929954e-03 2.089872e-02 1.882088e+03 0.23590
## SexMen:EF:RaceAfrAm 1.792755e-01 3.077260e-01 1.847592e+03 0.58258
## Age:SexMen:EF:RaceAfrAm -1.066349e-02 3.231637e-02 1.895159e+03 -0.32997
## Pr(>|t|)
## (Intercept) < 2.22e-16
## Age 0.0001869
## SexMen 0.1003000
## EF 0.8187405
## RaceAfrAm 0.9382113
## BMI 0.3254639
## PovStatBelow 9.0779e-05
## WRATtotal 0.3173062
## Age:SexMen 0.0321891
## Age:EF 0.9190144
## Age:RaceAfrAm 0.7150991
## SexMen:EF 0.5973932
## SexMen:RaceAfrAm 0.4639911
## EF:RaceAfrAm 0.2344619
## Age:SexMen:EF 0.5184364
## Age:SexMen:RaceAfrAm 0.6453869
## Age:EF:RaceAfrAm 0.8135380
## SexMen:EF:RaceAfrAm 0.5602462
## Age:SexMen:EF:RaceAfrAm 0.7414578
Chair Stands - Model 5 (Retaining significant higher-order terms)
mm5 = lmer(PhyPerfStands10~Age + Sex + EF + Race + BMI + PovStat + WRATtotal + (1|HNDid) + Age*Sex, data=DanThesisFinal,REML=F)
summary(mm5)
## Linear mixed model fit by maximum likelihood t-tests use Satterthwaite
## approximations to degrees of freedom [lmerMod]
## Formula:
## PhyPerfStands10 ~ Age + Sex + EF + Race + BMI + PovStat + WRATtotal +
## (1 | HNDid) + Age * Sex
## Data: DanThesisFinal
##
## AIC BIC logLik deviance df.resid
## 14251.5 14313.5 -7114.8 14229.5 2060
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6544423 -0.5132560 -0.0918566 0.4131548 8.4477156
##
## Random effects:
## Groups Name Variance Std.Dev.
## HNDid (Intercept) 24.76960 4.976907
## Residual 35.38981 5.948934
## Number of obs: 2071, groups: HNDid, 1372
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 34.52286333 1.58260591 1398.08530000 21.81394 < 2.22e-16
## Age 0.15481810 0.02607154 1519.40810000 5.93820 3.5651e-09
## SexMen -1.40316188 0.39371543 1289.31860000 -3.56390 0.00037873
## EF -0.17556260 0.08349284 1922.73050000 -2.10273 0.03561939
## RaceAfrAm -0.28791847 0.40515146 1297.74930000 -0.71064 0.47743254
## BMI 0.02770173 0.02621991 1475.41010000 1.05651 0.29090598
## PovStatBelow 1.59436113 0.41362515 1312.67920000 3.85460 0.00012152
## WRATtotal -0.02684736 0.02874327 1406.11060000 -0.93404 0.35044368
## Age:SexMen 0.12339987 0.04123546 1516.21640000 2.99257 0.00281113
##
## Correlation of Fixed Effects:
## (Intr) Age SexMen EF RcAfrA BMI PvSttB WRATtt
## Age -0.018
## SexMen -0.212 0.036
## EF 0.256 0.045 -0.013
## RaceAfrAm -0.286 0.008 -0.013 0.110
## BMI -0.518 0.000 0.185 0.040 -0.009
## PovStatBelw -0.274 0.069 0.031 0.057 -0.046 0.077
## WRATtotal -0.821 0.001 0.020 -0.395 0.185 -0.003 0.185
## Age:SexMen 0.007 -0.625 -0.053 0.042 0.016 -0.019 0.019 0.004
Plot Final Model (mm5)
pAge = seq(-19,20)
hatEFchair1 = zMixHat(DanThesisFinal, mm5, vary = "Age=pAge, Sex=zQ(Women,Men)",fixedCov=c("BMI","Race","EF","PovStat","WRATtotal"))
par(mar=c(4,4,.5,2),las = 1, lwd = 2)
HNDcolors = HNDpltColors()
## Error in eval(expr, envir, enclos): could not find function "HNDpltColors"
with(hatEFchair1[hatEFchair1$Sex == "Women",],plot(pAge,hat, lty = 1, col = "black", type = "l",ylim = c(20,40), ylab = "Time(Sec)", xlab = "Age",xaxt = "n" ))
with(hatEFchair1[hatEFchair1$Sex == "Men",], lines(pAge,hat, lty = 2, col = "black"))
axis(1,at=c(-20,-15,-10,-5,0,5,10,15,20),labels = c("30","35","40","45","50","55","60","65","70"))
legend(-20,40, zQ(Women,Men), lty = 1:2, col = "black",cex=.75,bty="n")
