Supplement 1. R source code for parameter estimation, model simulations, and calculation of Sobol' indices.

File List
FitUnstructuredModel.R

IterateUnstructuredModel.R

BootstrapDistributionsStageModel.R

IterateStageModel.R

SobolandCI.R

All files (WinZip archive)

Description
These are text files (readable by, e.g., Notepad or Wordpad on PCs or by any ASCII
text-file editor). They contain R-language source code for the data analyses and
model simulations in the paper. Because we are not at liberty to redistribute
all of the original data used in the analyses, only some portions of these programs
can be run by users. The purpose of presenting the complete source code is to
document in full detail calculations that are described conceptually in the paper.
A WinZip archive containing all the files is also provided.

FitUnstructuredModel.R contains
the statistical analyses behind the models for the distributions of Et and p4t
for the unstructured models. As noted in the paper, we considered a number of
models for p4t and only the final one is presented in the code here (a truncated
logistic distribution). Users cannot run any portions of this code.

IterateUnstructuredModel.R
contains code for iterating the structured model, including iterations using
bootstrap parameter distributions to account for parameter uncertainty. Users
can run portions of this code. The top part of the code (which reads in data
and fits models for Et and p4t) cannot be run by users. However at the comment
line 'USERS START HERE' we insert 'by hand' the necessary numerical results
from the analysis so that the rest of the code can be run, to replicate the
process leading to Fig. 2 in the paper.

BootstrapDistributionsStageModel.R
contains code for generating the bootstrap distribution of model parameters
for the stage-structured model, that is used for Sobol sensitivity indices and
confidence interval calculations. Users cannot run any portions of this code.

IterateStageModel.R contains
code for an R function that simulates the stage-structured model using user-supplied
parameters, and estimates the population growth rate as a function of parameter
values by doing multiple simulations of the model. Users can run this file (which
will load the model function into the current R workspace), but must supply
parameter values when calling the function.

SobolandCI.R contains code
to calculate confidence intervals on population growth rate, and Sobol' sensitivity
indices, for the structured population model. Users cannot run this code.