Growth model of the reared sea urchin Paracentrotus ... - SciViews

Annex I: R code for fitting growth models
Annexes
Code (as well as dataset presented in annex II) is available at:
http://www.sciviews.org/_phgrosjean/growth/index.htm. This code
runs under the free (GNU Public License) statistical software R, which
is downloadable at: http://cran.r-project.org. It is available for almost
all plateforms (Unixes, Linux, Windows, MacOS). The 'nlrq' package
for nonlinear quantile regression is also downloadable from there.
Rem: LaboKit and ShellAxis used to assist in measurements of sea
urchins are available for free (GPL) at: http://www.sciviews.org.
a. Code for analyzing data and fitting envelope models
Main script file
This script runs a complete analysis of the dataset presented in annex
II, and discussed in Part IV. The dataset is first explored (distribution of
sizes, growth pattern…). Then, quantile regressions are fitted with
traditional models and with the original growth model. Finally, the
envelope model is designed, tested, and fitted on the same dataset.
## Demonstration of using R for analyzing growth data as in the paper:
# A functional growth model with intraspecific competition applied to
# sea urchins. Grosjean, Ph., Ch. Spirlet & M. Jangoux (in preparation)
#
# version 1.0 (30/08/2001)
#
# by Ph. Grosjean (phgrosjean@sciviews.org)
# GNU Public License v. 2 or above at your convenience
# Use at your own risks!
# You need:
# R v. 1.3.0 or above (tested only under Windows, please, report other)
# libraries nls, nlrq, akima (see http://cran.r-project.org)
# files Plividus.txt, GrowthFun.R, nlModels.R
# (see http://www.sciviews.org/_phgrosjean/growth/index.htm)
# Put all files in a common directory
# In R, change current directory to that one
# Enter: source("Growth.R", print.eval=TRUE)
cat("\n\n ===== DEMONSTRATION OF ANALYSIS OF GROWTH DATA =====\n")
# To do: put here a more detailed introduction!!!
library(nls)
library(nlrq)
source("GrowthFun.R")
source("nlModels.R")
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