Introduction | Scientific and technical context | The AgMIP calibration protocol | The STICS model and CroptimizR wrappers | The dataset | Observations and data formatting | Observed variables | The cropr format | Describing the calibration protocol | Principle | Excel-based specification | Converting the Excel file to R objects | Structure of the protocol for this example | Example: the phenology group | Parameter information | Running the protocol | Exploring the results | Global structure of the returned object | Exploring parameter selection results (Step 6) | Built-in diagnostics plots | Evaluating the results on an independent dataset | Conclusion

Introduction | Concepts | Parameter estimation | Specific features and interest of CroptimizR | Principle of use | Model wrappers | Observations | Examples | Model evaluation | References

Introduction | How to write a basic version of a model wrapper for CroptimizR | Model wrapper interface | Minimum required functionalities | Implementation | Test your wrapper | Optional issues | Examples | Example of a basic wrapper for an LAI toy model | Another version taking into account the different shapes param_values can take | Other examples

Introduction | Study Case | Initialisation step | Read and select the corresponding observations | Set information on the parameters to estimate | Set options for the model | Set options for the parameter estimation method | Run the optimization | Compare simulations and observations before and after optimization

Introduction | Study Case | Initialisation step | Set the list of situations and variables to consider in this example | Run the model before optimization for a prior evaluation | Read and select the corresponding observations | Set information on the parameters to estimate | Set options for the parameter estimation method | Run the optimization | Run the model after optimization | Plot the results

Introduction | Study Case | Initialisation step | Generate Stics input files from JavaStics input files | Run the model before optimization for a prior evaluation | Read and select the observations for the parameter estimation | Set information on the parameters to estimate | Set options for the parameter estimation method | Run the optimization | Run the model after optimization | Plot the results

Introduction | Study Case | Initialisation step | Read and select the corresponding observations | Set information on the parameters to estimate | Set options for the model | Set options for the DREAM method | Run the parameter estimation | Launch a new estimation starting from previous results

Introduction | Study Case | Plotting the observations | Setting information on the parameters to estimate | Choosing the default parameters values | Setting optimization options | Running the optimization | Generating diagnostics using CroPlotR

Overview | Getting parameter value | Getting the meteorological data | Setting parameter value | Set the output variables

Introduction | Converting JavaSTICS workspace files | Converting files into separated folders (one per usm) | Converting files into one folder (overwriting case)

Introduction | Package functions to be used | Getting a table file example | Getting inputs Excel example file from the SticsRFiles package | Getting an USMs inputs CSV example file from the SticsRFiles package | Description of tables expected content and use | Important information | Specificities of Excel sheets | Common tables specifications | Data consistency checks in tables | USMs table example | Generating the usms XML file (usms.xml) | Getting data | Generating the file | usms.xml file content | Generating the sols XML file (sols.xml) | sols.xml file content | Generating multiple crop management XML files (*_tec.xml) | Generating files | Generating multiple initialization XML files (*_ini.xml) | XML file content | Generating multiple meteorological station XML files (*_sta.xml) | Generating general parameters XML files (param_gen.xml and param_newform.xml)

Introduction | Understanding what are parameters in STICS XML files | XML files structures describing parameters | Functions for XML files manipulations | Getting XML files examples from the SticsRFiles library | Getting the XML files source directory | Examples files | Copying files in a local directory | A specific file | All files | Getting information about parameters | Searching parameters names from files | Getting all STICS parameters information | Getting information about one or more parameters | Getting parameters information using partial names matching | Searching parameters using keywords | Getting parameters values from XML files | Scalar parameters extraction | Vector parameters extraction | Getting all parameters values from files | Replacing parameters values in XML files | Defining the output file using function arguments | Scalar parameters | Vector parameters

Introduction | Concepts | Input files | Text files | XML files | Short example | Example data | Example usage | Find a STICS variable | Get informations on parameters | Get parameter values | Set parameter values | Generate observations files | Read observations files | Read simulation files

Java installation | Creating an alias to java 17 | Switching between version | Using the system tools | Using a shell script | Switch back to the previous Java version on the system

Upgrading a whole workspace | Upgrading a specific file kind

Frequentist algorithms | Bayesian algorithms | Criteria and likelihoods | References