Nothing
## ----include=FALSE-------------------------------------------------------
knitr::opts_chunk$set(eval = FALSE)
## ----install, eval=FALSE-------------------------------------------------
# install.packages('treebase')
## ----loadpkg-------------------------------------------------------------
# library(treebase)
## ----search1, eval=FALSE, message=FALSE, warning=FALSE-------------------
# both <- search_treebase("Ronquist or Hulesenbeck", by=c("author", "author"))
# dolphins <- search_treebase('"Delphinus"', by="taxon", max_trees=5)
# studies <- search_treebase("2377", by="id.study")
## ----search2, message=FALSE, warning=FALSE-------------------------------
# Near <- search_treebase("Near", "author", branch_lengths=TRUE, max_trees=3)
# Near[1]
## ----metadata, eval=FALSE, message=FALSE, warning=FALSE------------------
# all <- download_metadata("", by="all")
# dates <- sapply(all, function(x) as.numeric(x$date))
# library(ggplot2)
# qplot(dates, main="Treebase growth", xlab="Year", binwidth=.5)
## ----eval=FALSE, message=FALSE, warning=FALSE----------------------------
# nature <- sapply(all, function(x) length(grep("Nature", x$publisher))>0)
# science <- sapply(all, function(x) length(grep("^Science$", x$publisher))>0)
# sum(nature)
# sum(science)
## ----message=FALSE, warning=FALSE----------------------------------------
# search_treebase("Derryberry", "author")[[1]] -> tree
# plot(tree)
## ----message=FALSE, warning=FALSE, eval = FALSE--------------------------
# library(laser)
# tt <- branching.times(tree)
# models <- list(pb = pureBirth(tt),
# bdfit = bd(tt),
# y2r = yule2rate(tt), # yule model with single shift pt
# ddl = DDL(tt), # linear, diversity-dependent
# ddx = DDX(tt), #exponential diversity-dendent
# sv = fitSPVAR(tt), # vary speciation in time
# ev = fitEXVAR(tt), # vary extinction in time
# bv = fitBOTHVAR(tt)# vary both
# )
# names(models[[3]])[5] <- "aic"
# aics <- sapply(models, "[[", "aic")
# # show the winning model
# models[which.min(aics)]
#
#
## ----eval=FALSE, message=FALSE, warning=FALSE----------------------------
# timetree <- function(tree){
# check.na <- try(sum(is.na(tree$edge.length))>0)
# if(is(check.na, "try-error") | check.na)
# NULL
# else
# try( chronoMPL(multi2di(tree)) )
# }
# drop_errors <- function(tr){
# tt <- tr[!sapply(tr, is.null)]
# tt <- tt[!sapply(tt, function(x) is(x, "try-error"))]
# print(paste("dropped", length(tr)-length(tt), "trees"))
# tt
# }
# require(laser)
# pick_branching_model <- function(tree){
# m1 <- try(pureBirth(branching.times(tree)))
# m2 <- try(bd(branching.times(tree)))
# as.logical(try(m2$aic < m1$aic))
# }
## ----eval=FALSE, message=FALSE, warning=FALSE----------------------------
# all <- search_treebase("Consensus", "type.tree", branch_lengths=TRUE)
# tt <- drop_errors(sapply(all, timetree))
# is_yule <- sapply(tt, pick_branching_model)
# table(is_yule)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.