dat1 <-read.table("lecture4ex1.csv", sep=",", header=TRUE) dat1$lengthx <- dat1$length/10 dat1$avelengthx <- ave(dat1$lengthx, dat1$groupid) dat1$difflengthx <- dat1$lengthx - dat1$avelengthx dat1$avegold <- ave(dat1$goldcolor, dat1$groupid) dat1$diffgold <- dat1$goldcolor - dat1$avegold library(lme4) out1b0 <- lmer(consume ~ 1 + (1|groupid), data=dat1, REML=FALSE) out1b1 <- lmer(consume ~ 1 + difflengthx + (1|groupid), data=dat1, REML=FALSE) out1b2 <- lmer(consume ~ 1 + diffgold + (1|groupid), data=dat1, REML=FALSE) anova(out1b0, out1b1) anova(out1b0, out1b2) out1b3 <- lmer(consume ~ 1 + difflengthx + diffgold + (1|groupid), data=dat1, REML=FALSE) out1b4 <- lmer(consume ~ 1 + difflengthx + diffgold + difflengthx:diffgold + (1|groupid), data=dat1, REML=FALSE) anova(out1b3, out1b4) # Use out1b1 out1b5 <- lmer(consume ~ 1 + difflengthx + volume + (1|groupid), data=dat1, REML=FALSE) out1b6 <- lmer(consume ~ 1 + difflengthx + nfish + (1|groupid), data=dat1, REML=FALSE) out1b7 <- lmer(consume ~ 1 + difflengthx + avelengthx + (1|groupid), data=dat1, REML=FALSE) out1b8 <- lmer(consume ~ 1 + difflengthx + avegold + (1|groupid), data=dat1, REML=FALSE) anova(out1b1, out1b5) anova(out1b1, out1b6) anova(out1b1, out1b7) anova(out1b1, out1b8) out1b9 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + (1|groupid), data=dat1, REML=FALSE) out1b10 <- lmer(consume ~ 1 + difflengthx + avelengthx*volume + (1|groupid), data=dat1, REML=FALSE) anova(out1b9, out1b10) out1b11 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + nfish + (1|groupid), data=dat1, REML=FALSE) out1b12 <- lmer(consume ~ 1 + difflengthx + volume + avelengthx*nfish + (1|groupid), data=dat1, REML=FALSE) out1b13 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume*nfish + (1|groupid), data=dat1, REML=FALSE) anova(out1b11, out1b12) anova(out1b11, out1b13) out1b14 <- lmer(consume ~ 1 + difflengthx + volume + avelengthx + avegold + (1|groupid), data=dat1, REML=FALSE) out1b15 <- lmer(consume ~ 1 + difflengthx + volume + avelengthx*avegold + (1|groupid), data=dat1, REML=FALSE) out1b16 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume*avegold + (1|groupid), data=dat1, REML=FALSE) anova(out1b14, out1b15) anova(out1b14, out1b16) out1b17 <- lmer(consume ~ 1 + difflengthx + diffgold + volume + avelengthx + avegold + nfish + (1|groupid), data=dat1, REML=FALSE) out1b18 <- lmer(consume ~ 1 + difflengthx + diffgold + volume + avelengthx + avegold*nfish + (1|groupid), data=dat1, REML=FALSE) anova(out1b17, out1b18) # Random slope then out1b9 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + (1|groupid), data=dat1, REML=FALSE) out1b19 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + (1 + difflengthx|groupid), data=dat1, REML=FALSE) anova(out1b9, out1b19) out1b20 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + volume + (1|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1b21 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + volume + (1 + goldcolor|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out1b20, out1b21) # Use out1b19 out1b22 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + difflengthx:avelengthx + (1 + difflengthx|groupid), data=dat1, REML=FALSE) out1b23 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + difflengthx:volume + (1 + difflengthx|groupid), data=dat1, REML=FALSE) anova(out1b19, out1b22) anova(out1b19, out1b23) out1b24 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) out1b25 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + nfish + difflengthx:nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) anova(out1b24, out1b25) out1b26 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + avegold + (1 + difflengthx|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1b27 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + avegold + difflengthx:avegold + (1 + difflengthx|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out1b26, out1b27) # Use out1b23 # Tear-down strategy out1t0 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) dat1a <- dat1 dat1a$difflengthx <- dat1a$difflengthx * 10 dat1a$avelength <- dat1a$avelength * 10 out1t1a <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1a, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t0a <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1a, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t2 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t3 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t4 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + diffgold:avelengthx + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t5 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avegold + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t6 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:volume + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t7 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out1t8 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + difflengthx:avelengthx + difflengthx:avegold + difflengthx:volume + difflengthx:nfish + diffgold:avelengthx + diffgold:avegold + diffgold:volume + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out1t1a, out1t0a) anova(out1t2, out1t0) anova(out1t3, out1t0) anova(out1t4, out1t0) anova(out1t5, out1t0) anova(out1t6, out1t0) anova(out1t7, out1t0) anova(out1t8, out1t0) out1t9 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + (1 + difflengthx + diffgold|groupid), data=dat1, REML=FALSE) out1t10 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + (1 + diffgold|groupid), data=dat1, REML=FALSE) out1t11 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) anova(out1t10, out1t9) anova(out1t11, out1t9) # Use out1t11 out1t12 <- lmer(consume ~ 1 + difflengthx + avelengthx + avegold + volume + nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) out1t13 <- lmer(consume ~ 1 + difflengthx + diffgold + avegold + volume + nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) out1t14 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + volume + nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) out1t15 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + nfish + (1 + difflengthx|groupid), data=dat1, REML=FALSE) out1t16 <- lmer(consume ~ 1 + difflengthx + diffgold + avelengthx + avegold + volume + (1 + difflengthx|groupid), data=dat1, REML=FALSE) anova(out1t12, out1t11) anova(out1t13, out1t11) anova(out1t14, out1t11) anova(out1t15, out1t11) anova(out1t16, out1t11) dat2 <-read.table("lecture7ex1.csv", sep=",", header=TRUE) # dat2$eeiq <- dat2$eeiq/100 # dat2$eeworkexp <- dat2$eeworkexp/10 # dat2$erexp <- dat2$erexp/10 library(lme4) out2m0 <- lmer(score ~ 1 + eesex + eesalary + eeworkexp + I(eeiq - 100) + ersex + erexp + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE) summary(out2m0) out2m1 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + ersex + erexp + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out2m2 <- lmer(score ~ 1 + eesex + eesalary + I(eeiq - 100) + ersex + erexp + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE) out2m3 <- lmer(score ~ 1 + eesex + eesalary + eeworkexp + ersex + erexp + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE) out2m4 <- lmer(score ~ 1 + eesex + eesalary + eeworkexp + I(eeiq - 100) + ersex + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out2m1, out2m0) anova(out2m2, out2m0) anova(out2m3, out2m0) anova(out2m4, out2m0) out2m5 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + ersex + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out2m6 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + ersex + eesex:ersex + (1 + eesex + eeworkexp|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out2m7 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq/10 - 10) + ersex + eesex:ersex + (1 + eesex + I(eeiq/10 - 10)|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out2m5, out2m6) anova(out2m5, out2m7) out2m8 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + eesalary + ersex + eesex:ersex + (1 + eesex|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out2m9 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + eesalary + ersex + eesex:ersex + (1 + eesex + eesalary|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out2m8, out2m9) # out2b9 out2m10 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + eesalary + ersex + eesex:ersex + eesalary:ersex + (1 + eesex + eesalary|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out2m9, out2m10) out2m11 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + eesalary + ersex + erexp + eesex:ersex + (1 + eesex + eesalary|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out2m12 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + eesalary + ersex + erexp + eesex:ersex + eesex:erexp + (1 + eesex + eesalary|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) out2m13 <- lmer(score ~ 1 + eesex + eeworkexp + I(eeiq - 100) + eesalary + ersex + erexp + eesex:ersex + eesalary:erexp + (1 + eesex + eesalary|erid), data=dat2, REML=FALSE, control = lmerControl(optimizer ="Nelder_Mead")) anova(out2m11, out2m12) anova(out2m11, out2m13) # Keey out2b9 summary(out2m9) #################################################### dat1 <-read.table("lecture4ex1.csv", sep=",", header=TRUE) dat1$lengthx <- dat1$length/10 dat1$avelengthx <- ave(dat1$lengthx, dat1$groupid) dat1$difflengthx <- dat1$lengthx - dat1$avelengthx dat1$avegold <- ave(dat1$goldcolor, dat1$groupid) dat1$diffgold <- dat1$goldcolor - dat1$avegold library(lme4) out1b0 <- lmer(consume ~ 1 + (1|groupid), data=dat1, REML=FALSE) summary(out1b0) out1b9 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + (1|groupid), data=dat1, REML=FALSE) summary(out1b9) out1b19 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + (1 + difflengthx|groupid), data=dat1, REML=FALSE) summary(out1b19) out1b91 <- lmer(consume ~ 1 + difflengthx + avelengthx + (1|groupid), data=dat1, REML=FALSE) summary(out1b91) out1b92 <- lmer(consume ~ 1 + volume + (1|groupid), data=dat1, REML=FALSE) summary(out1b92) out1b23 <- lmer(consume ~ 1 + difflengthx + avelengthx + volume + difflengthx:volume + (1 + difflengthx|groupid), data=dat1, REML=FALSE) summary(out1b23) out1i0 <- lmer(consume ~ 1 + (1|groupid), data=dat1, REML=FALSE) summary(out1i0) out1i1 <- lmer(consume ~ 1 + difflengthx + (1|groupid), data=dat1, REML=FALSE) summary(out1i1) out1i2 <- lmer(consume ~ 1 + avelengthx + (1|groupid), data=dat1, REML=FALSE) summary(out1i2) out1i12 <- lmer(consume ~ 1 + difflengthx + avelengthx + (1|groupid), data=dat1, REML=FALSE) summary(out1i12) out1n1 <- lmer(consume ~ 1 + lengthx + (1|groupid), data=dat1, REML=FALSE) summary(out1n1) out1n12 <- lmer(consume ~ 1 + lengthx + avelengthx + (1|groupid), data=dat1, REML=FALSE) summary(out1n12) alln <- table(dat1$groupid) bign <- sum(alln) k <- length(alln) ntilde <- (bign^2 - sum(alln^2))/(bign * (k-1)) ntilde dat1$zconsume <- scale(dat1$consume) dat1$zlength <- scale(dat1$length) dat1$avezlength <- ave(dat1$zlength, dat1$groupid) dat1$diffzlength <- dat1$zlength - dat1$avezlength volume <- dat1[!duplicated(dat1$groupid), "volume"] mvolume <- mean(volume) sdvolume <- sd(volume) dat1$zvolume <- (dat1$volume - mvolume) / sd(volume) out1z23 <- lmer(zconsume ~ 1 + diffzlength + avezlength + zvolume + diffzlength:zvolume + (1 + diffzlength|groupid), data=dat1, REML=FALSE) summary(out1z23) out1zb23 <- lmer(consume ~ 1 + diffzlength + avezlength + zvolume + diffzlength:zvolume + (1 + diffzlength|groupid), data=dat1, REML=FALSE) summary(out1zb23) out1bz23 <- lmer(zconsume ~ 1 + difflengthx + avelengthx + volume + difflengthx:volume + (1 + difflengthx|groupid), data=dat1, REML=FALSE) summary(out1bz23)