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: relative tolerance in
function arguments, relative tolerance in function value, absolute tolerance
in function arguments, and maximum number of iterations</dd>
<dt>...</dt>
<dd>Any other arguments of the function to be optimimzed, 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: relative tolerance in
function arguments, relative tolerance in function value, absolute tolerance
in function arguments, and maximum number of iterations</dd>


<dt>...</dt>
<dd>Any other arguments of the function to be optimimzed, 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