fix : move reports diffrents than user_manual into pkg OptirigDocs & add icon for all pkg

README.md

 
-# <img src="man/figures/logo_OptirrigManual.png" alt="Optirrig" align="right" style="width:200px"/> OptirrigManual: User Manual & Documentation : R Package support
+# <img src="man/figures/logo_OptirrigManual_200px.png" alt="Optirrig" align="right" style="width:200px"/> OptirrigManual: User Manual & Documentation : R Package support
 
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README.rmd

@@ -2,7 +2,7 @@
 output: github_document
 ---
 
-# <img src="man/figures/logo_OptirrigManual.png" alt="Optirrig" align="right" style="width:200px"/> OptirrigManual: User Manual & Documentation : R Package support
+# <img src="man/figures/logo_OptirrigManual_200px.png" alt="Optirrig" align="right" style="width:200px"/> OptirrigManual: User Manual & Documentation : R Package support
 
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 [![CRAN](https://www.r-pkg.org/badges/version-ago/OptirrigManual)]( https://forgemia.inra.fr/optirrigdev/OptirrigManual.git)

reports/Advanced_Parametrization_of_the_Optirrig_for_Sugar_Beet_Cases/01-Introducing_the_optirrig_Model.Rmd

-# Introducing the optirrig Model
-
-In this section, we will detail the Optirrig model as well as the key concepts associated with it. We will also explore the specifications related to the data required for its operation, both for input data and for expected output results. Additionally, we will discuss the integration of this model within an R package specifically designed to automate its use and simplify access for users. This package aims to provide a user-friendly interface to fully exploit the capabilities of the Optirrig model, thereby facilitating irrigation decision-making processes.
-
-```{r 01-setup, include=FALSE, file = 'setup.R'}
-library(OptirrigCore)
-library(OptirrigBeet)
-
-cfg <- OptirrigBeet::loadConfig()
-```
-
-## The conceptual Model
-
-Optirrig is a one-dimensional (1D) conceptual model based on thermal time calculations. It is designed to elaborate irrigation strategies based on climatic and pedological data and dedicated cropping calendars. The model uses a simplified approach to describe the biophysical processes influencing plant growth, integrates a water balance based on available soil characteristics, and analyzes yield in terms of dry biomass. The aim of this tool is to simulate crop growth and soil water dynamics as a function of established crop parameters. The model models the crop's water requirements at different thermal stages of growth. This approach makes it possible to improve irrigation strategies by taking into account climatic forcings such as precipitation, temperature and evapotranspiration.
-
-Optirrig is versatile in its applications, and can be used initially to analyze irrigation strategies retrospectively, making it possible to examine decisions taken in the past to better guide future choices.In this way, the model is fed by in situ data collected over an entire season.Similarly, Optirrig can be used for exploratory purposes, based on future climate projections, such as those described by RCP/GRM (future climate scenarios), which can be integrated into the model.
-
-Optirrig can also be used as a decision-support tool.
-Unlike retrospective use, where irrigation decisions are already established, the decision support approach (DSA) enables irrigation decisions to be made at each stage of the season, adjusting decisions according to climate forecasts over a given confidence horizon (around 7 days).This offers the possibility of adjusting strategy, improving crop yields and increasing irrigation efficiency.
-
-```{r, out.width='100%'}
-# knitr::include_graphics(system.file("Optirrig_Conceptual_Model.png", package = "OptirrigBeet"))
-knitr::include_graphics("images/Optirrig_Conceptual_Model.png")
-```
-
-### Model inputs
-
-- **Climate forcing :**
-
-The Optirrig model, based on the concept of crop heat units, initially requires the collection of temperature data specific to the study area. This information is crucial for allowing the model to adjust biological process descriptions according to the developmental stage of the crops. Furthermore, Optirrig necessitates the incorporation of historical data on rainfall and evapotranspiration. The compilation of these data enables Optirrig to account for climatic variability, thus offering a more accurate estimate of natural water availability. This approach ensures an efficient and environmentally specific irrigation management.
-
-- **Soil description :**
-
-The model also incorporates an in-depth pedological analysis of soils, which can be based on a simple classification using the soil texture triangle of the studied soil, or rely on a more detailed understanding of soil characteristics, such as the permanent wilting point and field capacity. These data are conceptually integrated into reservoir models representing the soil profile. Thus, the model simulates water infiltration through these different reservoirs, taking into account evapotranspiration and drainage over time. Through this process, the model gathers crucial information such as the total amount of water present in the soil profile and the portion of this water that is actually accessible to plants. This approach allows for precise irrigation management, optimizing water use based on the specific needs of the crops and the pedological characteristics of the land.
-
-### The Optirrig package
-
-To facilitate the use and configuration of the Optirrig model, it has been integrated into an R package named OptirrigCore^[https://optirrigdev.pages.mia.inra.fr/OptirrigCore/]. This package makes it easier to incorporate climatic data and soil parameters by using a general configuration file. During the simulation process, OptirrigCore allows for the recording of key simulated variables over time, such as the Leaf Area Index (LAI), Total Dry Matter (TDM), soil profile infiltration, and the amount of water available for each reservoir. At the end of the simulation, the package provides a dynamic display of the key variables necessary for analyzing the irrigation strategy. This feature significantly improves the accessibility and efficiency of irrigation management, enabling users to make informed decisions based on accurate and relevant data.
-
-### Example of use
-
-Here is an example for Soybeans on a trial without irrigation dating from 2021: 
-```{r, out.width='100%'}
-# knitr::include_graphics(system.file("2021_soja_OptirrigCore_expl.png", package = "OptirrigBeet"))
-knitr::include_graphics("images/2021_soja_OptirrigCore_expl.png")
-```
-

reports/Advanced_Parametrization_of_the_Optirrig_for_Sugar_Beet_Cases/02-Optimization_of_LAI_Parameters.Rmd

-# Optimization of LAI Parameters
-
-Sensitivity testing of model parameters for beets
-
-```{r 02-setup, include = FALSE, file = 'setup.R'}
-```
-
-## Key Parameter Analysis for Leaf Area Index (LAI) Calculation
-
-Introducing the multiplicative formula for calculating LAI
-
-### Defining shape parameters
-
-Describe alpha & beta parameters and influence 
-
-### Defining stress parameters
-
-Describe DaysSwlai & estresslai paramters and influences (equifinality and decisions)
-
-## Analysis of different irrigation strategies
-
-## discussion & conclusion

reports/Advanced_Parametrization_of_the_Optirrig_for_Sugar_Beet_Cases/03-Optimization_of_TDM_Parameters.Rmd

-# Optimization of TDM Parameters
-
-Sensitivity testing of model parameters for beets
-
-```{r 03-setup, include = FALSE, file = 'setup.R'}
-```
-
-## Key Parameter Analysis for Total dry matter Calculation
-
-Introducing dry matter repartition
-
-### Defining stress parameters
-
-Describe DaysSwtdm & estresstdm paramters and influences (equifinality and decisions)
-
-## Analysis of different irrigation strategies
-
-## discussion & conclusion

reports/Advanced_Parametrization_of_the_Optirrig_for_Sugar_Beet_Cases/04-Conclusion.Rmd

-# Conclusion
-
-```{r 04-setup, include = FALSE, file = 'setup.R'}
-```