R: Wrapper Function to Estimate a 2- or 3-Parameters Logistic...
MatFit
R Documentation
Wrapper Function to Estimate a 2- or 3-Parameters Logistic Regression of Sexual
Maturity
Description
Define the logistic model, pass the initial parameter values, the data, and
the numerical optimization method(s) to estimate the model and to organize results
in a list.
Usage
MatFit(p, par, matdat, method, control = ls(), itnmax)
Arguments
p
Integer, either 2 or 3, determining if the asymptotic proportion is assumed
known at 1 or estimated.
par
Numeric vector of 2 or 3 components with initial paramater values.
matdat
A data.frame where each row is an individual fish, and the columnds are a
continuous predictor, and ordinal keys for sex, month, and maturity stage.
method
Character or character vector, defining the list of numerical methods to use.
See help pages for function optimx().
control
List, optimization control parameters to be passed to optimx. See help for
function optimx().
itnmax
Integer, maximum number of iterations, to be passed to optimx().
Details
The function controls the estimation process. From a valid value of p, it will
define the proper process model, either 2-parameters or 3-parameters logistic
regression. The 3-parameter model might be useful outside the reproductive season
when not all adult individuals are ready to reproduce, whereas the 2-parameter
model assumes that above certain value of the continuous predictor all individuals
are reproducing.
The function will re-organize optimx()'s output by adding some items (AIC,
standard errors, correlation matrix) and ignoring other items. The output is a
list of results in a list of optimization methods.
Value
model
Type of model, matlik.2p or matlik.3p
method
Name of numerical optimization method
converg
Convergence message
kkt
The Karush-Kuhn-Tucker optimality conditions
AIC
The Akaike Information Criterion
pars
Maximum likelihood estimates of model parameters
num.grads
Numerical gradients at the maximum likelihood estimates
stdev
Estimated standard deviations of maximum likelihood estimates of model parameters
Cor
The estimated correlation matrix of maximum likelihood estimates of model parameters
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(LifeHist)
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, round.POSIXt, trunc.POSIXt, units
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LifeHist/MatFit.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MatFit
> ### Title: Wrapper Function to Estimate a 2- or 3-Parameters Logistic
> ### Regression of Sexual Maturity
> ### Aliases: MatFit
> ### Keywords: optimize models
>
> ### ** Examples
>
> data(BlackAngler.lenmatdat)
> BA.matlen <- MatCount(matdat=BlackAngler.lenmatdat,
+ fem.key=2,
+ mal.key=1,
+ stage.key=2,
+ season.key=c(5,7))
> plot(BA.matlen[[2]],
+ pred.50=35,
+ pred.95=55,
+ pred.unit="Length (cm)",
+ top.text="Males Rep Season",
+ lwd=2, xlab="", ylab="")
> par(mfrow=c(2,2), mar=c(4,4,1,1), oma=c(4,4,1,1))
> plot(BA.matlen[[1]],pred.50=35,pred.95=55,pred.unit="Length (cm)",
+ top.text="Males NoRep Season", lwd=2, xlab="", ylab="")
> plot(BA.matlen[[2]],pred.50=35,pred.95=55,pred.unit="Length (cm)",
+ top.text="Males Rep Season", lwd=2, xlab="", ylab="")
> plot(BA.matlen[[3]],pred.50=85,pred.95=110,pred.unit="Length (cm)",
+ top.text="Females NoRep Season", lwd=2, xlab="", ylab="")
> plot(BA.matlen[[4]],pred.50=55,pred.95=75,pred.unit="Length (cm)",
+ top.text="Females Rep Season", lwd=2, xlab="", ylab="")
> require(optimx)
Loading required package: optimx
> BA.matlen.mal <- MatFit(p=2,
+ par=c(35,55),
+ matdat=BA.matlen[[2]],
+ method=c("spg", "CG", "Nelder-Mead"),
+ itnmax=100)
> #
> plot(BA.matlen[[2]],
+ pred.50=BA.matlen.mal[[1]]$par.mle[1],
+ pred.95=BA.matlen.mal[[1]]$par.mle[2],
+ pred.unit="Length (cm)",
+ top.text="Males Reproductive Season",
+ lwd=2,
+ xlab="Length (cm)",
+ ylab="Proportion Mature")
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
