Create phylolm.R

Author: florianhartig

Code/DHARMaPackageSupport/phylolm/phylolm.R

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+library(phylolm)
+
+
+
+set.seed(123456)
+tre = rcoal(60)
+taxa = sort(tre$tip.label)
+b0=0; b1=1;
+x <- rTrait(n=1, phy=tre,model="BM",
+            parameters=list(ancestral.state=0,sigma2=10))
+y <- b0 + b1*x + 
+  rTrait(n=1,phy=tre,model="lambda",parameters=list(
+    ancestral.state=0,sigma2=1,lambda=0.5))
+dat = data.frame(trait=y[taxa],pred=x[taxa])
+fit = phylolm(trait~pred,data=dat,phy=tre,model="lambda")
+summary(fit)
+
+# adding measurement errors and bootstrap
+z <- y + rnorm(60,0,1)
+dat = data.frame(trait=z[taxa],pred=x[taxa])
+fit = phylolm(trait~pred,data=dat,phy=tre,model="BM",measurement_error=TRUE,boot=100)
+summary(fit)
+
+
+
+phyloglm
+
+
+
+set.seed(123456)
+tre = rtree(50)
+x = rTrait(n=1,phy=tre)
+X = cbind(rep(1,50),x)
+y = rbinTrait(n=1,phy=tre, beta=c(-1,0.5), alpha=1 ,X=X)
+dat = data.frame(trait01 = y, predictor = x)
+fit = phyloglm(trait01~predictor,phy=tre,data=dat,boot=100)
+summary(fit)
+coef(fit)
+vcov(fit)
+
+predict(fit)
+simulate(fit)