Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS

Unifying Optimization Algorithms to Aid Software System Users:optimxforR

(2015) John C. Nash et al.   Journal of Statistical Software

Approximate Bayesian inference for large spatial datasets using predictive process models

(2011) Jo Eidsvik et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Direct fitting of dynamic models using integrated nested Laplace approximations — INLA

(2011) Ramiro Ruiz-Cárdenas et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Estimation methods for nonlinear state-space models in ecology

(2011) M.W. Pedersen et al.   ECOLOGICAL MODELLING

Estimability and Likelihood Inference for Generalized Linear Mixed Models Using Data Cloning

(2011) Subhash R. Lele et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

(2011) David A. Fournier et al.   OPTIMIZATION METHODS & SOFTWARE

The arcsine is asinine: the analysis of proportions in ecology

(2010) David I. Warton et al.   ECOLOGY

Determining the parametric structure of models

(2010) D.J. Cole et al.   MATHEMATICAL BIOSCIENCES

Do not log-transform count data

(2010) Robert B. O’Hara et al.   Methods in Ecology and Evolution

Simple means to improve the interpretability of regression coefficients

(2010) Holger Schielzeth   Methods in Ecology and Evolution

Reproducible research and Biostatistics

(2009) Roger D. Peng   BIOSTATISTICS

Preaching to the unconverted

(2009) María Uriarte et al.   ECOLOGICAL APPLICATIONS

Learning hierarchical models: advice for the rest of us

(2009) Ben Bolker   ECOLOGICAL APPLICATIONS

Parameter identifiability, constraint, and equifinality in data assimilation with ecosystem models

(2009) Yiqi Luo et al.   ECOLOGICAL APPLICATIONS

Drawbacks of complex models in frequentist and Bayesian approaches to natural-resource management

(2009) Milo D. Adkison   ECOLOGICAL APPLICATIONS

Hierarchical models in ecology: confidence intervals, hypothesis testing, and model selection using data cloning

(2009) José Miguel Ponciano et al.   ECOLOGY

The BUGS project: Evolution, critique and future directions

(2009) David Lunn et al.   STATISTICS IN MEDICINE

Using Redundant Parameterizations to Fit Hierarchical Models

(2008) Andrew Gelman et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS