Description Usage Arguments Value Note Examples

Logikelihood calculation for the SecSSE model given a set of parameters and data

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ```
secsse_loglik(
parameter,
phy,
traits,
num_concealed_states,
use_fortran = TRUE,
methode = "ode45",
cond = "proper_cond",
root_state_weight = "proper_weights",
sampling_fraction,
run_parallel = FALSE,
setting_calculation = NULL,
setting_parallel = NULL,
see_ancestral_states = FALSE,
loglik_penalty = 0,
is_complete_tree = FALSE,
func = ifelse(is_complete_tree, "secsse_runmod_ct", ifelse(use_fortran == FALSE,
secsse_loglik_rhs, "secsse_runmod2")),
reltol = 1e-12,
abstol = 1e-16
)
``` |

`parameter` |
list where first vector represents lambdas, the second mus and the third transition rates. |

`phy` |
phylogenetic tree of class phylo, ultrametric, fully-resolved, rooted and with branch lengths. |

`traits` |
vector with trait states, order of states must be the same as tree tips, for help, see vignette. |

`num_concealed_states` |
number of concealed states, generally equivalent to number of examined states. |

`use_fortran` |
Should the Fortran code for numerical integration be called? Default is TRUE. |

`methode` |
Solver for the set of equations, default is "ode45". |

`cond` |
condition on the existence of a node root: "maddison_cond","proper_cond"(default). For details, see vignette. |

`root_state_weight` |
the method to weigh the states:"maddison_weights","proper_weights"(default) or "equal_weights". It can also be specified the root state:the vector c(1,0,0) indicates state 1 was the root state. |

`sampling_fraction` |
vector that states the sampling proportion per trait state. It must have as many elements as trait states. |

`run_parallel` |
should the routine to run in parallel be called? |

`setting_calculation` |
argument used internally to speed up calculation. It should be left blank (default : setting_calculation = NULL) |

`setting_parallel` |
argument used internally to set a parallel calculation. It should be left blank (default : setting_parallel = NULL) |

`see_ancestral_states` |
should the ancestral states be shown? Deafault FALSE |

`loglik_penalty` |
the size of the penalty for all parameters; default is 0 (no penalty) |

`is_complete_tree` |
whether or not a tree with all its extinct species is provided |

`func` |
function to be used in solving the ODE system Currently only for testing purposes. |

`reltol` |
relative tolerance in integration |

`abstol` |
absolute tolerance in integration |

The loglikelihood of the data given the parameters

To run in parallel it is needed to load the following libraries when windows: apTreeshape, doparallel and foreach. When unix, it requires: apTreeshape, doparallel, foreach and doMC

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ```
rm(list = ls(all = TRUE))
library(secsse)
library(DDD)
library(deSolve)
library(apTreeshape)
library(foreach)
set.seed(13)
phylotree <- ape::rcoal(31, tip.label = 1:31)
traits <- sample(c(0,1,2),ape::Ntip(phylotree),replace = TRUE)
num_concealed_states <- 2
use_fortran <- TRUE
cond <- "proper_cond"
methode <- "ode45"
root_state_weight <- "proper_weights"
sampling_fraction <- c(1,1,1)
run_parallel <- FALSE
drill <- id_paramPos(traits,num_concealed_states)
drill[[1]][] <- c(0.12,0.01,0.2,0.21,0.31,0.23)
drill[[2]][] <- 0
drill[[3]][,] <- 0.1
diag(drill[[3]]) <- NA
secsse_loglik(parameter = drill,phylotree,traits,num_concealed_states,
use_fortran,methode,cond,root_state_weight,sampling_fraction,see_ancestral_states = FALSE)
#[1] -113.1018
``` |

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