CTFSworkshop(data=TRUE)
grwfull300$dbhctr=(grwfull300$dbh1-mean(grwfull300$dbh1))
mod=lmer(LnGrowth~1+dbhctr+(1+dbhctr|Species),data=grwfull300)
xyplot(LnGrowth~dbhctr|Species,data=grwfull300)
dotplot(ranef(mod),postVar=TRUE)
dotplot(ranef(mod,postVar=TRUE))
xyplot(ht~dbh|species,data=treeht)
xyplot(lht~ldb|species,data=treeht)
xyplot(lht~ldb|species,data=treeht,
panel = function(x,y)
 {
panel.xyplot(x,y)
panel.abline(lm(y~x))
 }
)
head(treemass)
options(width=75)
head(treemass)
colnames(treemass)
mod=lmer(logagb~1+logdbh+(1+logdbh|Latin)+(1+logagb|ForestType),data=treemass)
treemass$ldbhctr=treemass$logdbh-mean(treemass$logdbh)
mod=lmer(logagb~1+ldbhctr+(1+ldbhctr|Latin)+(1+ldbhctr|ForestType),data=treemass)
fixef(mod)
coef(mod)$ForestType
head(coef(mod)$Latin)
colnames(treemass)
table(treemass$Locality)
mod=lmer(logagb~1+ldbhctr+(1+ldbhctr|Latin)+(1+ldbhctr|Locality),data=treemass)
display(mod)
head(coef(mod)$Local)
xyplot(logagb~logdbh|Locality,data=treemass)
xyplot(logagb~logddbh|ForestType,data=treemass)
xyplot(logagb~logdbh|ForestType,data=treemass)
xyplot(logagb~logdbh|ForestType,data=treemass,
   panel = function(x,y)
 {
panel.xyplot(x,y)
panel.abline(lm(y~x))
 }  
)
colnames(grwfull300)
options(width=60)
colnames(grwfull300)
mod=lmer(LnGrowth=1+dbhctr+(1+dbhctr|Species),data=grwfull300)
mod=lmer(LnGrowth~1+dbhctr+(1+dbhctr|Species),data=grwfull300)
fixef(mod)
dotplot(ranef(mod,postVar=TRUE))
dotplot(ranef(mod))
dotplot(ranef(mod,postVar=TRUE))
display(mod,digits=5)
dotplot(ranef(mod,postVar=TRUE),xlim=c(-.005,.005))
xyplot(LnGrowth~dbhctr|Species,data=grwfull300)
xyplot(ht~dbh|species,treeht)
xyplot(lht~ldb|species,treeht)
xyplot(lht~ldb|species,data=treeht, 
   panel = function(x,y)
 {
panel.xyplot(x,y)
panel.abline(lm(y~x))
 }  
   )
mod2=lmer(LnGrowth~1+dbhctr+(1+dbhctr|Species)+(1+dbhctr|census),data=grwfull300)
mod3=lmer(LnGrowth~1+dbhctr+(1|Species)+(1|census),data=grwfull300)
display(mod2,digits=5)
dotplot(ranef(mod2,postVar=TRUE))
dotplot(ranef(mod2,postVar=TRUE),xlim=c(-.005,.005))
dotplot(ranef(mod2,postVar=TRUE),xlim=c(-.001,.001))
coef(mod2)$census
dotplot(ranef(mod2,postVar=TRUE))
lm(LnGrowth~census,data=grwfull300)$coef
coef(mod2)$census
head(coef(mod2)$Species)
mod2=lmer(LnGrowth~1+dbhctr+(1+dbhctr|Species)+(1+dbhctr|census),data=grwfull300)
str(sleepstudy)
xyplot(Reaction~Days|Subject,data=sleepstudy)
plot(Reaction~Days,data=sleepstudy)
modslp=lmer(Reaction~1+Days+(1+Days|Subject),data=sleepstudy)
coef(modslp)$Sub
display(modslp)
colnames(treemass)
fit=lm(ldbhctr~logdbh,data=treemass)
aic(fit)
AIC(fit)
fit=lm(ldbhctr~1+logdbh,data=treemass)
AIC(fit)
fit=lm(ldbhctr~1+ldbhctr,data=treemass)
fit=lm(logagb~1+ldbhctr,data=treemass)
AIC(fit)
fit=lm(logagb~1+logdbh,data=treemass)
AIC(fit)
fit=lm(logagb~1+ldbhctr+I(ldbhctr^2),data=treemass)
fit=lm(logagb~1+ldbhctr,data=treemass)
fitq=lm(logagb~1+ldbhctr+I(ldbhctr^2),data=treemass)
AIC(fit,fitq)
mod=lmer(logagb~1+ldbhctr+I(ldbhctr^2)+(1+ldbhctr+I(ldbhctr^2)|Species),data=treemass)
mod=lmer(logagb~1+ldbhctr+I(ldbhctr^2)+(1+ldbhctr+I(ldbhctr^2)|species),data=treemass)
mod=lmer(logagb~1+ldbhctr+I(ldbhctr^2)+(1+ldbhctr+I(ldbhctr^2)|Latin),data=treemass)
AIC(fit,fitq,mod)
dim(subset(treemass,is.na(Latin)))
dim(subset(treemass,!is.na(Latin)))
mod=lmer(logagb~1+ldbhctr+(1+ldbhctr|Latin),data=treemass)
AIC(mod,fit)
fit=lm(logagb~1+ldbhctr,data=treemass)
mod=lmer(logagb~1+logdbh+(1+logdbh|Latin),data=treemass)
fit=lm(logagb~1+logdbh,data=treemass)
AIC(mod,fit)
fit=lm(logagb~1+ldbhctr,data=treemass)
mod=lmer(logagb~1+logdbh+(1+logdbh|Latin),data=treemass)
AIC(mod,fit)
treemassSp=subset(treemass,!is.na(Latin))
dim(treemass)
dim(treemassSp
)
fit=lm(logagb~1+logdbh,data=treemassSp)
mod=lmer(logagb~1+logdbh+(1+logdbh|Latin),data=treemassSp)
AIC(fit,mod)
plot(logagb~lodbh,data=treemassSp)
plot(logagb~logdbh,data=treemassSp)
modLoc=lmer(logagb~1+logdbh+(1+logdbh|Latin)+(1+logdbh|Locality),data=treemassSp)
anova(mod,modLoc)
fitFT=lm(logagb~1+logdbh+ForestType,data=treemassSp)
coef(fitFT)
fitFT=lm(logagb~1+logdbh+ForestType+logdbh*ForestType,data=treemassSp)
fitFT=lm(logagb~1+logdbh+ForestType,data=treemassSp)
fitFTInt=lm(logagb~1+logdbh+ForestType+logdbh*ForestType,data=treemassSp)
coef(fitFTInt)
cfdry=coef(fitFTInt)[1:2]
cfdr
cfdry
cfmoist=cfdry+coef(fitFTInt)[c(3,5)]
cfmoist
cfwet=cfdry+coef(fitFTInt)[c(4,6)]
plot(logagb~logdbh,data=treemassSp,cex=.3)
abline(cfdry,col='red',lwd=2)
abline(cfmoist,col='green',lwd=2)
abline(cfwet,col='blue',lwd=2)
modFT=lmer(logagb~1+logdbh+(1+logdbh|ForestType),data=treemassSp)
coef(modFT)
cfdry
cfmoist
cfwet
table(treemassSp$ForestType)
AIC(modFT,fitFTInt)
modmej=lmer(logagb~1+logdbh+ForestType+ForestType*logdbh+
(1+logdbh|Latin)+(1+logdbh|Locality),data=treemassSp)
(1+logdbh|Latin)+(1+logdbh|Locality),data=treemassSp,verbose=TRUE)
modmej=lmer(logagb~1+logdbh+ForestType+ForestType*logdbh+
(1+logdbh|Latin)+(1+logdbh|Locality),data=treemassSp,verbose=TRUE)
display(modmej)
hmod6=lmer(lht ~ ldb + I(ldb^2) + (1+ldb+I(ldb^2)|species), data=treeht)
str(treeht)
treeht$species=as.factor(treeht$species)
xyplot(lht~ldb|species, data=treeht, subset=species%in%levels(species)[1:25], ran=coef(hmod6)$species, fix = fixef(hmod6),
   panel = function(x, y, ran, fix)
 {
panel.xyplot(x,y)
x1 = seq(-3,3,0.5)
i=packet.number()
x2 = ran[i,1] * 1 + ran[i,2]*x1 + ran[i,3]*x1^2
x3 = fix[1] * 1 + fix[2]*x1 + fix[3]*x1^2
panel.lines(x2~x1, col='red')
panel.lines(x3~x1, lty=3)
     }  
  )
treemassSp=subset(treemass,!is.na(Latin))
savehistory('~/meetings_workshops/Rmodeling/Cenpat/history12OctAM.txt')