From 9edfeabe785a6be8e3ce5db137278695f29ea4cd Mon Sep 17 00:00:00 2001 From: Carl Boettiger Date: Thu, 5 May 2011 19:04:07 -0700 Subject: [PATCH] sim ann shows release in intramandibulars --- demos/loop_models_traits_regimes.R | 7 +++++-- demos/parrotfish.R | 5 ++++- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/demos/loop_models_traits_regimes.R b/demos/loop_models_traits_regimes.R index 264190d..6fbd7c8 100644 --- a/demos/loop_models_traits_regimes.R +++ b/demos/loop_models_traits_regimes.R @@ -37,16 +37,19 @@ fit_all <- function(models, traits, regimes, tree){ ## Reporting, optional # print(paste("model = ", models[[i]], "trait = ", names(traits[j]), # "regime=", names(regimes[k]))) + + ## use hansen to start with good parameters hansen <- try(fit("hansen", traits[j], regimes[[k]], tree=tree, maxit=5000)) - ## hansen will sometimes give very large or negative + ## Fit one of the generalized models using the initial guess from hansen out[[i]] <- try( fit(models[[i]], traits[j], regimes[[k]], tree=tree, alpha=c(0.1,5), #(min(10, hansen@sqrt.alpha^2)), - sigma=hansen@sigma, control=list(maxit=5000))) + sigma=hansen@sigma, method ="SANN" )) + ## If errors, attempt default starting conditions if(is(out[[i]], "try-error")){ out[[i]] <- try( fit(models[[i]], traits[j], regimes[[k]], diff --git a/demos/parrotfish.R b/demos/parrotfish.R index fd05fe3..e780c92 100644 --- a/demos/parrotfish.R +++ b/demos/parrotfish.R @@ -10,7 +10,10 @@ source("loop_models_traits_regimes.R") model_list <- list("brown", "hansen", "ouch", "brownie", "wright", "release_constraint") regime_list <- list(intramandibular=intramandibular) -test <- fit_all(model_list, labrid$data, regime_list, labrid$tree) +#test <- fit_all(model_list, labrid$data, regime_list, labrid$tree) + +test <- fit_all(model_list[c(4,5,6)], labrid$data[10:11], regime_list, labrid$tree) + conv(test)