Open richfitz opened 10 years ago
Reported by @dwbapst:
library(diversitree) pars <- c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01) set.seed(2) phy <- tree.bisse(pars, max.t=60, x0=0) lik <- make.bisse(phy, phy$tip.state) lik.2 <- constrain(lik, lambda0 ~ lambda1, lambda0 ~ mu0)
last line generates warning:
Warning message: In rels[i] <- res[[2]] : (symbol) object cannot be coerced to type 'list'
but the likelihood function doubly constrains lambda0:
lambda0
BiSSE likelihood function: * Parameter vector takes 5 elements: - lambda1, mu0, mu1, q01, q10 * Function constrained (original took 6 elements): - lambda0 ~ lambda1 - lambda0 ~ mu0 * Function takes arguments (with defaults) - pars: Parameter vector - ...: Additional arguments to underlying function - pars.only [FALSE]: Return full parameter vector? * Phylogeny with 203 tips and 202 nodes - Taxa: sp1, sp27, sp29, sp31, sp41, sp43, sp46, sp47, sp48, ... * References: - Maddison et al. (2007) doi:10.1080/10635150701607033 - FitzJohn et al. (2009) doi:10.1093/sysbio/syp067 R definition: function (pars, ..., pars.only = FALSE)
lik.2(2:6, pars.only=TRUE)
gives
lambda0 lambda1 mu0 mu1 q01 q10 3 2 3 4 5 6
Reported by @dwbapst:
last line generates warning:
but the likelihood function doubly constrains
lambda0
:gives