inst/examples/parrotfish/parrotfish_power_knit_.md

In cboettig/wrightscape: wrightscape

• Author: Carl Boettiger [e-mail]
• License: BSD

``` {r } require(wrightscape) require(snowfall) require(ggplot2) require(reshape) data(parrotfish) traits <- c("bodymass", "close", "open", "kt", "gape.y", "prot.y", "AM.y", "SH.y", "LP.y") regimes <- intramandibular

``` {r }
fits <- lapply(traits, function(trait){
    multi <- function(modelspec){ 
     multiTypeOU(data = dat[[trait]], tree = tree, regimes = regimes, 
                model_spec = modelspec, control = list(maxit=8000))
    }
    bm <- multi(list(alpha = "fixed", sigma = "global", theta = "global")) 
    ou <- multi(list(alpha = "global", sigma = "global", theta = "global")) 
    bm2 <- multi(list(alpha = "fixed", sigma = "indep", theta = "global")) 
    a2  <- multi(list(alpha = "indep", sigma = "global", theta = "global")) 
    t2  <- multi(list(alpha = "global", sigma = "global", theta = "indep")) 
  mc <- montecarlotest(bm2,a2)
  bm2_a2 <- list(null=mc$null_dist, test=mc$test_dist, lr=-2*(mc$null$loglik-mc$test$loglik))
  mc <- montecarlotest(bm,ou)
  bm_ou <- list(null=mc$null_dist, test=mc$test_dist, lr=-2*(mc$null$loglik-mc$test$loglik))
  mc <- montecarlotest(bm,bm2)
  bm_bm2 <- list(null=mc$null_dist, test=mc$test_dist, lr=-2*(mc$null$loglik-mc$test$loglik))
  mc <- montecarlotest(ou,bm2)
  ou_bm2 <- list(null=mc$null_dist, test=mc$test_dist, lr=-2*(mc$null$loglik-mc$test$loglik))
  mc <- montecarlotest(t2,a2)
  t2_a2 <- list(null=mc$null_dist, test=mc$test_dist, lr=-2*(mc$null$loglik-mc$test$loglik))
  mc <- montecarlotest(bm2,t2)
  bm2_t2 <- list(null=mc$null_dist, test=mc$test_dist, lr=-2*(mc$null$loglik-mc$test$loglik))
  list(brownie_vs_alphas=bm2_a2, brownie_vs_thetas=bm2_t2, thetas_vs_alphas=t2_a2,
       bm_vs_brownie=bm_bm2,  bm_vs_ou=bm_ou, ou_vs_brownie=ou_bm2)
})

``` {r } names(fits) <- traits dat <- melt(fits) names(dat) <- c("value", "type", "comparison", "trait")

``` {r fig.height=26 }
require(ggplot2)
r <- cast(dat, comparison ~ trait, function(x) quantile(x, c(.10,.90)))
subdat <- subset(dat, abs(value) < max(abs(as.matrix(r))))
ggplot(subdat) + 
      geom_boxplot(aes(type, value)) +
      facet_grid(trait ~ comparison, scales="free_y") 

``` {r } save(list=ls(), file="~/public_html/data/parrotfish_power.rda") ````

cboettig/wrightscape documentation built on May 13, 2019, 2:12 p.m.