simplex

Function to optimize target function using a
simplex method adopted from Matlab

models

Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574>,
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565> and
Laudanno et al. 2021. Syst. Biol. 70: 389–407,
<DOI:10.1093/sysbio/syaa048>.
Also contains functions to simulate the diversity-dependent
process.

Rampal Etienne

Diversity-Dependent Diversification

Rampal S. Etienne

Bart Haegeman

Hanno Hildenbrandt

Giovanni Laudanno

simplex function

<dl><dt>fun</dt>
<dd>Function to be optimized</dd>
<dt>trparsopt</dt>
<dd>Initial guess of the parameters to be optimized</dd>
<dt>optimpars</dt>
<dd>Parameters of the optimization: 1) relative tolerance in
function arguments, 2) relative tolerance in function value, 3) absolute 
tolerance in function arguments as well as the function value, 4) 
maximum number of iterations and 5) TRUE/FALSE flag to allow verbose output, 
default is TRUE</dd>
<dt>...</dt>
<dd>Any other arguments of the function to be optimimized, or settings
of the optimization routine</dd></dl>

Arguments

Author

Carries out optimization using a simplex algorithm (finding a minimum) — simplex

<dl>

<dt>fun</dt>
<dd>Function to be optimized</dd>


<dt>trparsopt</dt>
<dd>Initial guess of the parameters to be optimized</dd>


<dt>optimpars</dt>
<dd>Parameters of the optimization: 1) relative tolerance in
function arguments, 2) relative tolerance in function value, 3) absolute 
tolerance in function arguments as well as the function value, 4) 
maximum number of iterations and 5) TRUE/FALSE flag to allow verbose output, 
default is TRUE</dd>


<dt>...</dt>
<dd>Any other arguments of the function to be optimimized, or settings
of the optimization routine</dd>

</dl>

simplex: Carries out optimization using a simplex algorithm (finding a minimum)

Description

Usage

Value

Arguments

Author

Examples