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Last data update: 2014.03.03

R: Maximization of the loglikelihood given the standard Neutral...

maxLikelihood.ESF

R Documentation

Maximization of the loglikelihood given the standard Neutral Model, using the Etienne Sampling Formula

Description

This function computes the maximum likelihood estimates of the parameters of the Neutral model, using the Etienne Sampling Formula

Usage

maxLikelihood.ESF(initVals, Abund, verbose = TRUE)

Arguments

`initVals`	A vector of initial starting values, of the format c(theta,m)
`Abund`	Vector containing a record of the number of individuals per species
`verbose`	TRUE/FALSE flag, indicates whether intermediate output is shown on screen

Value

the output is a list containing the following:

`par`	a vector containing the parameter values at the maximum likelihood
`fvalues`	the likelihood at the corresponding parameter values
`conv`	gives a message on convergence of optimization; conv = 0 means convergence

Author(s)

Thijs Janzen

References

Etienne, R.S. (2005). A new sampling formula for neutral biodiversity. Ecology Letters, 8(3), 253-260.

Examples

	A <- c(1,1,1,3,5,8)
	maxLikelihood.ESF(c(7,0.1),Abund = A)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GUILDS)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GUILDS/maxLikelihood.ESF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: maxLikelihood.ESF
> ### Title: Maximization of the loglikelihood given the standard Neutral
> ###   Model, using the Etienne Sampling Formula
> ### Aliases: maxLikelihood.ESF
> 
> ### ** Examples
> 
> 	A <- c(1,1,1,3,5,8)
> 	maxLikelihood.ESF(c(7,0.1),Abund = A)
1 7 0.1 -6.1820132693624 initial 
2 10.1111111111111 0.106716417910448 -5.79277681543811 expand 
3 11.6666666666667 0.116791044776119 -5.5883017918692 expand 
4 18.6666666666667 0.126305970149254 -5.37197336380037 expand 
5 25.2777777777778 0.151212686567164 -5.27490809861415 expand 
6 25.2777777777778 0.151212686567164 -5.27490809861415 reflect 
7 25.2777777777778 0.151212686567164 -5.27490809861415 contract inside 
8 25.2777777777778 0.151212686567164 -5.27490809861415 contract inside 
9 25.2777777777778 0.151212686567164 -5.27490809861415 contract inside 
10 25.2777777777778 0.151212686567164 -5.27490809861415 contract inside 
11 25.2777777777778 0.151212686567164 -5.27490809861415 contract inside 
12 25.2777777777778 0.151212686567164 -5.27490809861415 reflect 
13 22.75 0.152332089552239 -5.2737433799588 expand 
14 22.75 0.152332089552239 -5.2737433799588 reflect 
15 19.4444444444445 0.157929104477612 -5.27170825441626 expand 
16 19.4444444444445 0.157929104477612 -5.27170825441626 contract outside 
17 19.4444444444445 0.157929104477612 -5.27170825441626 reflect 
18 16.1388888888889 0.163526119402985 -5.2712004432258 reflect 
19 16.1388888888889 0.163526119402985 -5.2712004432258 reflect 
20 15.8958333333334 0.166044776119403 -5.27052800000531 reflect 
21 15.8958333333334 0.166044776119403 -5.27052800000531 contract inside 
22 15.8958333333334 0.166044776119403 -5.27052800000531 reflect 
23 15.6527777777778 0.168563432835821 -5.27029647806367 reflect 
24 15.6527777777778 0.168563432835821 -5.27029647806367 contract inside 
25 15.6527777777778 0.168563432835821 -5.27029647806367 contract inside 
26 15.6527777777778 0.168563432835821 -5.27029647806367 contract inside 
27 15.6527777777778 0.168563432835821 -5.27029647806367 reflect 
28 15.6527777777778 0.168563432835821 -5.27029647806367 contract outside 
29 15.6527777777778 0.168563432835821 -5.27029647806367 reflect 
30 15.6527777777778 0.168563432835821 -5.27029647806367 contract inside 
31 15.6527777777778 0.168563432835821 -5.27029647806367 contract outside 
32 15.5183109707303 0.169008847136996 -5.27029633737472 contract outside 
33 15.5472531848484 0.169014146434727 -5.27029577841133 contract inside 
34 15.5927799277836 0.168787464810841 -5.27029564681961 contract inside 
35 15.5927799277836 0.168787464810841 -5.27029564681961 reflect 
36 15.5772521098455 0.168902130447217 -5.2702955039305 contract inside 
37 15.6033690803581 0.168818780868801 -5.27029548540157 contract inside 
38 15.6033690803581 0.168818780868801 -5.27029548540157 contract inside 
39 15.587354640373 0.168861750499415 -5.27029547032767 contract inside 
40 15.587354640373 0.168861750499415 -5.27029547032767 contract inside 
41 15.5968865904983 0.168832856299071 -5.27029546970096 contract inside 
42 15.5927870881699 0.168839708179255 -5.2702954671626 contract inside 
43 15.5910957398535 0.168849016369289 -5.27029546711582 contract inside 
44 15.5910957398535 0.168849016369289 -5.27029546711582 contract inside 
45 15.5931777081334 0.168841485780471 -5.27029546684076 contract inside 
46 15.5924619060817 0.168842479627067 -5.27029546679036 contract inside 
47 15.5924619060817 0.168842479627067 -5.27029546679036 contract inside 
48 15.5926937739572 0.168842737681135 -5.27029546676938 contract inside 
49 15.59226780675 0.168844054095315 -5.27029546676026 contract inside 
50 15.59226780675 0.168844054095315 -5.27029546676026 contract inside 
51 15.5925316757205 0.168843116803808 -5.27029546675856 contract inside 
52 15.5924355447265 0.168843261603604 -5.27029546675592 contract inside 
53 15.5924355447265 0.168843261603604 -5.27029546675592 contract inside 
Optimization has terminated successfully. 
$par
[1] 15.5924355  0.1688433

$fvalues
[1] -5.270295

$conv
[1] 0

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>