MKn model in diversitree with deSolve and custom initial conditions

mktest.Rmd

---
title: "mkn test"
author: "Simon D.W. Frost"
date: "18 August 2016"
output: html_document
---

```{r}
library(ape)
library(diversitree)
```

```{r}
set.seed(4)
tr <- rtree(2,br=1)
```

```{r}
k <- 2
states <- c(2,1)
names(states) <- tr$tip.label
```


```{r}
derivs <- function(t, y, pars) {
  k <- length(y)
  Q <- matrix(pars, k, k)
  ret <- Q %*% y
  dim(ret) <- NULL
  list(ret)
}
control <- diversitree:::check.control.mkn(list(),k)
control$method <- "ode"
control$backend <- "deSolve"
cache <- diversitree:::make.cache.mkn(tr,states,2,FALSE,control)
cache$info$derivs <- derivs
initial.conditions <- function (init, pars, t, idx) 
{
    init[, 1] * init[, 2]
}
all.branches <- diversitree:::make.all.branches.dtlik(cache, control, initial.conditions)
rootfunc <- diversitree:::rootfunc.mkn
f.pars <- diversitree:::make.pars.mkn(k)
ll <- function(pars, root = ROOT.OBS, root.p = NULL, intermediates = FALSE) {
        qmat <- f.pars(pars)
        ans <- all.branches(qmat, intermediates)
        rootfunc(ans, qmat, root, root.p, intermediates)
}
class(ll) <- c("mkn", "dtlik", "function")
ll(c(1,0),root=ROOT.GIVEN,root.p=c(1,0),intermediates=TRUE)
```