| 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()