This function computes the maximum likelihood estimates of the parameters of the relationships between parameters of the DAISIE model (with clade-specific diversity-dependence) and island area and distance of the island to the mainland for data from lineages colonizing several islands/archipelagos. It also outputs the corresponding loglikelihood that can be used in model comparisons.
A note on the sigmoidal functions used in distance_dep: For anagenesis and cladogenesis, the functional relationship is k * (d/d0)^x/(1 + (d/d0)^x); for colonization the relationship is: k - k * (d/d0)^x/(1 + (d/d0)^x). The d0 parameter is the 11th parameter entered. In 'sigmoidal_col_ana', the 11th parameter is the d0 for colonization and the 12th is the d0 for anagenesis.
DAISIE_MW_ML(
datalist,
initparsopt,
idparsopt,
parsfix,
idparsfix,
res = 100,
ddmodel = 11,
cond = 0,
island_ontogeny = NA,
tol = c(1e-04, 1e-05, 1e-07),
maxiter = 1000 * round((1.25)^length(idparsopt)),
methode = "lsodes",
optimmethod = "subplex",
CS_version = 1,
verbose = 0,
tolint = c(1e-16, 1e-10),
distance_type = "continent",
distance_dep = "power",
parallel = "local",
cpus = 3,
num_cycles = 1
)The output is a dataframe containing estimated parameters and maximum loglikelihood.
gives the maximum likelihood estimate of lambda^c, the rate of cladogenesis for unit area
gives the maximum likelihood estimate of y, the exponent of area for the rate of cladogenesis
gives the maximum likelihood estimate of mu0, the extinction rate
gives the maximum likelihood estimate of x, the exponent of 1/area for the extinction rate
gives the maximum likelihood estimate of K0, the carrying-capacity for unit area
gives the maximum likelihood estimate of z, the exponent of area for the carrying capacity
gives the maximum likelihood estimate of gamma0, the immigration rate for unit distance
gives the maximum likelihood estimate of alpha, the exponent of 1/distance for the rate of colonization
gives the maximum likelihood estimate of lambda^a0, the rate of anagenesis for unit distance
gives the maximum likelihood estimate of beta, the exponent of 1/distance for the rate of anagenesis
gives the maximum loglikelihood
gives the number of estimated parameters, i.e. degrees of feedom
gives a message on convergence of optimization; conv = 0 means convergence
Data object containing information on colonisation and branching times of species for several islands or archipelagos, as well as the area, isolation and age of each of the islands/archipelagos. See data(archipelagos41) for an example.
The initial values of the parameters that must be optimized; they are all positive
The ids of the parameters that must be optimized. The ids
are defined as follows (see Valente et al 2020 Supplementary Tables 1 and 2
a better explanation of the models and parameters):
id = 1 corresponds to lambda^c0 (cladogenesis rate for unit area)
id = 2 corresponds to y (exponent of area for cladogenesis rate)
id = 3 corresponds to mu0 (extinction rate for unit area)
id = 4 corresponds to x (exponent of 1/area for extinction rate)
id = 5 corresponds to K0 (clade-level carrying capacity for unit area)
id = 6 corresponds to z (exponent of area for clade-level carrying capacity)
id = 7 corresponds to gamma0 (immigration rate for unit distance)
id = 8 corresponds to alpha (exponent of 1/distance for immigration rate)
id = 9 corresponds to lambda^a0 (anagenesis rate for
unit distance)
id = 10 corresponds to beta (exponent of 1/distance for anagenesis rate)
id = 11 corresponds to d0 in models M15 to M19, and models with
distance_dep = 'sigmoidal_col', 'sigmoidal_ana' or 'sigmoidal_clado';
or d0 for colonisation (when specifying distance_dep = 'sigmoidal_col_ana'
id = 12 corresponds to d0 for anagenesis when specifying
distance_dep = 'sigmoidal_col_ana'
The values of the parameters that should not be optimized
The ids of the parameters that should not be optimized, e.g. c(1,3) if lambda^c and K should not be optimized.
Sets the maximum number of species for which a probability must be computed, must be larger than the size of the largest clade
Sets the model of diversity-dependence:
ddmodel = 0 :
no diversity dependence
ddmodel = 1 : linear dependence in speciation rate
ddmodel = 11: linear dependence in speciation rate and in immigration rate
ddmodel = 2 : exponential dependence in speciation rate
ddmodel = 21: exponential dependence in speciation rate and in immigration rate
cond = 0 : conditioning on island age
cond = 1 : conditioning on island age and non-extinction of the island
biota
type of island ontonogeny. If NA, then constant ontogeny is assumed
Sets the tolerances in the optimization. Consists of:
reltolx = relative tolerance of parameter values in optimization
reltolf = relative tolerance of function value in optimization
abstolx = absolute tolerance of parameter values in optimization
Sets the maximum number of iterations in the optimization
Method of the ODE-solver. See package deSolve for details. Default is "lsodes"
Method used in likelihood optimization. Default is "subplex" (see subplex package). Alternative is 'simplex' which was the method in previous versions.
a numeric or list. Default is 1 for the standard DAISIE model, for a relaxed-rate model a list with the following elements:
model: the CS model to run, options are 1 for single rate
DAISIE model, 2 for multi-rate DAISIE, or 0 for IW test
model.
relaxed_par: the parameter to relax (integrate over). Options are
"cladogenesis", "extinction", "carrying_capacity",
"immigration", or "anagenesis".
sets whether parameters and likelihood should be printed (1) or not (0)
Vector of two elements containing the absolute and relative tolerance of the integration
Use 'continent' if the distance to the continent should be used, use 'nearest_big' if the distance to the nearest big landmass should be used, and use 'biologically_realistic' if the distance should take into account some biologically realism, e.g. an average of the previous two if both are thought to contribute.
Sets what type of distance dependence should be used.
Default is a power law, denoted as 'power' (models M1-14 in Valente et al 2020).
Alternatives are additive or interactive contributions of distance and area
to the rate of cladogenesis ("area_additive_clado"; "area_interactive_clado",
"area_interactive_clado1" and "area_interactive_clado2"). Other alternatives are
exponential relationship denoted by 'exp'; or sigmoids, either
'sigmoidal_col' for a sigmoid in the colonization, 'sigmoidal_ana' for sigmoidal anagenesis,
'sigmoidal_clado' for sigmoidal cladogenesis, and 'sigmoidal_col_ana' for
sigmoids in both colonization and anagenesis.
A key for the different options of distance_dep that should be specified to run the
models from Valente et al 2020 (Supplementary Data Table 1 and 2) is given below:
* M1 to M14 - 'power'
* M15 -'area_additive_clado'
* M16 and M19 -'area_interactive_clado'
* M17 -'area_interactive_clado1'
* M18 - 'area_interactive_clado2'
* M20 and M24 - sigmoidal_col'
* M21, M25 and M28 - sigmoidal_ana'
* M22 and M26 - 'sigmoidal_clado'
* M23 and M27 - 'sigmoidal_col_ana'
Sets whether parallel computation should be used. Use 'no' if no parallel computing should be used, 'cluster' for parallel computing on a unix/linux cluster, and 'local' for parallel computation on a local machine.
Number of cpus used in parallel computing. Default is 3. Will not have an effect if parallel = 'no'.
The number of cycles the optimizer will go through. Default is 1.
Rampal S. Etienne & Luis Valente
Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K, Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model explains island bird diversity worldwide (2020) Nature, 579, 92-96
DAISIE_ML_CS,
cat("
### Fit the M19 model as in Valente et al 2020, using the ML
parameters as starting values (see Supplementary Tables 1 and 2).
utils::data(archipelagos41)
DAISIE_MW_ML(
datalist= archipelagos41,
initparsopt =
c(0.040073803, 1.945656546, 0.150429656,
67.25643672, 0.293635061, 0.059096872, 0.382688527,
0.026510781),
idparsopt = c(1,3,4,7,8,9,10,11),
parsfix = c(0,Inf,0) ,
idparsfix = c(2,5,6),
res = 100,
ddmodel = 0,
methode = 'lsodes',
cpus = 4,
parallel = 'local',
optimmethod = 'subplex',
tol = c(1E-4, 1E-5, 1E-7),
distance_type = 'continent',
distance_dep = 'area_interactive_clado'
)
")
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