LifeHist-package {LifeHist}R Documentation

Life History Models of Individuals

Description

Likelihood-based estimation of individual growth and sexual maturity models for organisms, usually fish and invertebrates. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions.

Details

The DESCRIPTION file:

Package: LifeHist
Type: Package
Title: Life History Models of Individuals
LazyLoad: yes
LazyData: yes
Version: 1.0-1
Date: 2015-08-31
Author: Ruben H. Roa-Ureta
Maintainer: Ruben H. Roa-Ureta <ruben.roa.ureta@mail.com>
Depends: R (>= 3.0.0), Hmisc
Imports: optimx (>= 2013.8.6), BB
Description: Likelihood-based estimation of individual growth and sexual maturity models for organisms, usually fish and invertebrates. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions.
License: GPL (>= 2)

Index of help topics:

BlackAngler.agematdat   Black Anglerfish Age, Sex, Month, Maturity
                        Stage Data
BlackAngler.lenmatdat   Black Anglerfish Length, Sex, Month, Maturity
                        Stage Data
BlackAngler.wgtmatdat   Black Anglerfish Body Weight, Sex, Month,
                        Maturity Stage Data
GroAgeData              Class Attribute of LifeHist Data Object
GroAgeExp               Class Attribute of LifeHist Exploratory Model
                        Object
GroAgeFit               Fit Growth Model with Age and Length Data by
                        Maximum Likelihood
GroAgeMod               Class Attribute of LifeHist Fitted Model Object
LifeHist-package        Life History Models of Individuals
MatCount                Build Databases for Sexual Maturity Modeling by
                        Logistic Regression
MatData                 Class Attribute of LifeHist Data Object
MatFit                  Wrapper Function to Estimate a 2- or
                        3-Parameters Logistic Regression of Sexual
                        Maturity
as.GroAgeData           Create a Data Object to Fit Individual Growth
                        Models with Age-Length Observations
deltamethod             First-order Taylor Series Expansion of
                        Functions of Random Variables
groageexp               Exploratory Growth Modeling with Age and Length
                        Data
groagemod               Predictions from an Object of Class GroAgeMod
ksbream                 King Soldier Bream Individual Biological Data
plot.GroAgeData         Exploratory Analysis of Agen and Length
                        Individual Data
plot.GroAgeExp          Exploratory Modeling of Individual Growth with
                        Age and Length Data
plot.GroAgeMod          Examination of Results from Fitting Growth
                        Models
plot.MatData            Exploratory Analisys of a Logistic Model on a
                        Graphical Display

Create data objects for maturity and growth modeling with MatCount() and as.GroAgeData(), respectively. Fit sexual maturity models with MatFit() for two types of models and any numerical method accepted by optimx() from package optimx. Explore raw growth data with generic function plot() applied on an object of class 'GroAgeData' created by as.GroAgeData(). Create predictions with initial parameter values for growth models using groageexp() and examine how good these initial values are with generic function plot() applied on an object of class 'GroAgeExp' created by groageexp(). Fit any of four type of models with any of five likelihood models and any numerical method accpted by optimx() from package optimx, using GroAgeFit(). Graphically examines results with generic function plot() applied on an object of class 'GroAgeMod' created by GroAgeFit().

Author(s)

Ruben H. Roa-Ureta

Maintainer: Ruben H. Roa-Ureta <ruben.roa.ureta@mail.com>

References

R. Roa, B. Ernst, F. Tapia. 1999. Estimation of size at sexual maturity: evaluation of analytical and resampling procedures. Fishery Bulletin (US) 97:570-580.

Arkhipkin, A., Roa-Ureta, R. 2005. Identification of growth models for squids. Marine and Freshwater Research 56:371-386.

Roa-Ureta, R. 2010. A Likelihood-based Model of Fish Growth with Multiple Length Frequency Data. Journal of Agricultural, Biological and Environmental Statistics 15:416-429.

Examples

#See examples for functions MatFit() and GroAgeFit()

[Package LifeHist version 1.0-1 Index]