[1] 30622
Error in eval(expr, envir, enclos): could not find function "qplot"
Error in eval(expr, envir, enclos): could not find function "familySearch"
Error in eval(expr, envir, enclos): could not find function "familySearch"
Error in eval(expr, envir, enclos): could not find function "habitatSearch"
Error in eval(expr, envir, enclos): object 'labrid.reef' not found
Error in eval(expr, envir, enclos): could not find function "habitatSearch"
Error in getSize(fish.data[habitatSearch("freshwater", fish.data)], "length"): could not find function "habitatSearch"
Error in getSize(fish.data[habitatSearch("marine", fish.data)], "length"): could not find function "habitatSearch"
Error in eval(expr, envir, enclos): could not find function "habitatSearch"
Error in gsub("_", " ", tree$tip.label): object 'tree' not found
tip.labels <- tree$tip.label
Error in eval(expr, envir, enclos): object 'tree' not found
Error in gsub("_", " ", species): object 'tip.labels' not found
Error in lapply(X = X, FUN = FUN, ...): object 'myfish' not found
Error in getQuantTraits(fish.data[myfish]): object 'myfish' not found
Error in eval(expr, envir, enclos): object 'species.names' not found
Error in getDepth(fish.data[myfish]): object 'myfish' not found
Error in eval(expr, envir, enclos): object 'species.names' not found
Error in getSize(fish.data[myfish], "length"): object 'myfish' not found
Error in eval(expr, envir, enclos): object 'species.names' not found
missing<-tip.labels[! tip.labels %in% species.names ]
Error in eval(expr, envir, enclos): object 'tip.labels' not found
Error in inherits(phy, "phylo"): object 'tree' not found
depth <- depths[,2]
Error in eval(expr, envir, enclos): object 'depths' not found
Error in eval(expr, envir, enclos): object 'depth' not found
Error in inherits(phy, "phylo"): object 'tr' not found
Error in eval(expr, envir, enclos): object 'size' not found
Error in inherits(phy, "phylo"): object 'tr' not found
pruned.names <- tr$tip.label
Error in eval(expr, envir, enclos): object 'tr' not found
size <- size[pruned.names]
Error in eval(expr, envir, enclos): object 'size' not found
depth <- depth[pruned.names]
Error in eval(expr, envir, enclos): object 'depth' not found
Error in inherits(phy, "phylo"): object 'tr' not found
Error in inherits(phy, "phylo"): object 'tr' not found
Enter a frame number, or 0 to exit
1: build_package(".", "inst/doc/html")
2: build_demos(package)
3: evaluate(demo_code, new.env(parent = globalenv()))
4: unlist(mapply(eval.with.details, parsed$expr, parsed$src, MoreArgs = list(e
5: mapply(eval.with.details, parsed$expr, parsed$src, MoreArgs = list(envir =
6: function (expr, envir = parent.frame(), enclos = NULL, src = NULL, debug =
7: try(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warni
8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatchOne(expr, names, parentenv, handlers[[1]])
11: doTryCatch(return(expr), name, parentenv, handler)
12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHand
13: withVisible(eval(expr, envir, enclos))
14: eval(expr, envir, enclos)
15: eval(expr, envir, enclos)
16: summary(lm(y ~ x - 1))
17: lm(y ~ x - 1)
18: eval(mf, parent.frame())
19: eval(expr, envir, enclos)
20: model.frame(formula = y ~ x - 1, drop.unused.levels = TRUE)
21: model.frame.default(formula = y ~ x - 1, drop.unused.levels = TRUE)
22: eval(predvars, data, env)
23: eval(expr, envir, enclos)
Error in summary(lm(y ~ x - 1)): error in evaluating the argument 'object' in selecting a method for function 'summary': Error in eval(expr, envir, enclos) : object 'y' not found
Error in is.vector(data): object 'depth' not found
Error in is.vector(data): object 'depth' not found


Loading required package: rtreebase
Warning message:
there is no package called 'rtreebase'
## Need to find an example of a fish tree on treebase that has branchlengths
#trees <- search_treebase("Scarus", by="taxon", branch=TRUE)
#str <- trees[[1]]$tip.label
#gsub("(\\w+)_(\\w+)_.*", "\\1 \\2", str)
#myfish <- findSpecies(species, fish.data)
#getQuantTraits(fish.data[myfish])