ch03R_maize_parallel                  ch03. R introduction. Improving performance with parallel code for maize.model
ch04Simulation.exponential            ch04. Simulation. Exponential model. Comparison of numerical integration with analytical solution. Influence of time step on error of integration. Improved Euler integration method.
ch04Simulation.prey.predator          ch04. Simulation. Predator-Prey Lotka-Volterra model with deSolve integration library.
ch04Simulation.population.age         ch04. Simulation. Population dynamics model with a representation of population with age classes.
ch04Simulation.watbal                 ch04. Simulation. WaterBalance model.
ch04Simulation.maize                  ch04. Simulation. Maize model.
ch04Simulation.epirice                ch04. Simulation. Epirice model (up to 10 min).
ch05USA_Magarey                       ch05. Uncertainty and Sensitivity analysis. Example on Magarey model
ch05USA_Weed                          ch05. Uncertainty and Sensitivity analysis. Example of Monte Carlo, Morris, Fast, Sobol and ANOVA for weed.model. Attention: run time can be long (up to 30 min).
ch05USA_Lactation                     ch05. Sensitivity analysis. Example on Lactation model.
ch05USA_Carcass                       ch05. Sensitivity analysis. Example on Carcass model. Morris.
ch07Bayes_Carbon                      ch07. Bayes. Example with carbonsoil.model
ch08DLM_WheatYieldGreece              ch08. Data Assimilation. Example of Dynamic Linear Model (DLM) for analyzing yield time series.
ch08DLM_CarbonSoil                    ch08. Data Assimilation. Example of Dynamic Linear Model (DLM) with carbonsoil.model.
ch08DLM_watbal                        ch08. Data Assimilation. Example of Dynamic Linear Model (DLM) with watbal.model.
ch10maize1data                        ch10. Case study. Exploration of data.
ch10maize2evaluation                  ch10. Case study, Maize model. Evaluation.
ch10maize3uncertainty                 ch10. Case study, Maize model. Uncertainty analysis (may take up to 20 min).
ch10maize4sensitivity                 ch10. Case study, Maize model. Sensitivity analysis (may take up to 40 min).
ch10maize5aparameterOLS_gradient      ch10. Case study, Maize model. Parameter estimation with OLS and gradient method (may take up to 10 min)
ch10maize5bparameterOLS_simplex       ch10. Case study, Maize model. Parameter estimation with OLS simplex method (may take up to 120 min)
ch10maize5cparameterConcL             ch10. Case study, Maize model. Parameter estimation with concentrated likelihood - simplex method (may take up to 120 min)
ch10maize5dparameterConcL_log         ch10. Case study, Maize model. Parameter estimation with concentrated likelihood and a log transformation of variable - simplex method (may take up to 120 min)
ch10maize6aMSEP_OLS                   ch10. Case study, Maize model. Estimation of MSEP by cross-validation after OLS parameter estimation (may take up to 120 min)
ch10maize6bMSEP_ConcL                 ch10. Case study, Maize model. Estimation of MSEP by cross-validation after concentrated likelihood parameter estimation (may take up to 120 min)
ch10maize7scenario                    ch10. Case study, Maize model. Use of final model for multi-site multi-year simulations (may take a few minutes)
ch10maizeB5aBayesEstimRUE             ch10. Case study, Maize model. Parameter estimation using a Bayesian approach, using MCMC - only RUE is estimated (may take up to a few hours)
ch10maizeB5bBayesEstimAllparam        ch10. Case study, Maize model. Parameter estimation using a Bayesian approach, using MCMC - all parameters (may take up to 4-5 days for 30000 iterations and 2 chains)
ch10maizeB7BayesUncertainty           ch10. Case study Maize model. Use the posterior distribution for multi-site multi-year simulations. You must run ch10maizeB5bBayesEstimAllparam before this demo in the same session or adapt both scripts may take up to a few hours).
ch10maizeB7Bayes_functionsMH          ch10. Case study Maize model. Load specific functions for Bayesian approach. No calculation.
ch10maizeS8DataAssimilation           ch10. Case study Maize model. Data assimilation using DLM (few minutes)
