integration of Tristan comments

paper.md

@@ -27,18 +27,18 @@ affiliations:
 	  index: 3
 	- name: Department of Applied Economics, University of Valladolid, Spain
 	  index: 4
-date: 16 July 2024
+date: 25 September 2024
 bibliography: paper.bib
 ---
 
 # Summary
 The international scientific community assessing on climate change and mitigation scenarios requests standardization and harmonization of results in integrated assessment models to ensure full transparency about the origin and structure of data; facilitate the comparison across models in both the historical period and future scenarios; and discuss on conceptual ideas about the internal structure of models, so to what extent different models representing the same system present similar results and conclusions.
 
-Results from different measurement procedures for the same measure should be equivalent (harmonized) within stated specifications to measure uncertainty. A task that is already mandatory to contribute on high-level international reports such as those elaborated by the Intergovernmental Pannel of Climate Change (IPCC) while necessary in the daily work of collaborative projects where different tools are applied to solve the same research question. The present `wiliamcformat` library (what we developed is not a library as it is just a piece of code, Python libraries are collections of pre-written code and functions that extend the capabilities of the Python programming language. So, if we want to transform to library, we need to change the structure. We can present it as helpers to handle the translation to IAMC format.) aims to adapt and extend the potential of existing material for users of a novel integrated assessment model, WILIAM. A pending task that has not been documented before although the urgency for improving transparency and responsability of this model to meet open-science principles (FAIR [@Wilkinson2016] and TRUST [@Lin2020]), as well as usability. Furthermore, we hope that these materials will inspire students to engage move deeply with the science of climate change and social transitions (A extended documentation need to be written to help the student to use it. Like that, I think every one agree that it will not be useful for students) . 
+Results should be harmonized under the same framework to transparently and easily compare different models, scenarios, and uncertainties. A task that is already mandatory to contribute on high-level international reports such as those elaborated by the Intergovernmental Pannel of Climate Change (IPCC) while necessary in the daily work of collaborative projects where different tools are applied to solve the same research question. The present `wiliamcformat` code is a set of helpers to handle the translation of results to IAMC format. This code aims to adapt and extend the potential of existing material for users of a novel integrated assessment model, WILIAM. A pending task that has not been documented before although the urgency for improving transparency and responsability of this model to meet open-science principles (FAIR [@Wilkinson2016] and TRUST [@Lin2020]), as well as usability. Furthermore, we hope that these materials bring students closer to the science of climate change and social transitions. 
 
 
 # Statement of need
-Integrated assessment models (IAMs) have been used for a wide range of problems in the climate change field. From generating consensus to identify key parameters and complex feedbacks on future between the world economies and nature [@Sarofim2011]. However, [@Wilson2021] highlight that IAM evaluation should improve interpretability of results to communicate insights, credibility as producers of knowledge under a 'sceptical review', and relevance of modelling analysis for informing scientific understanding to policymakers and stakeholders. A challenge that may be achieved (at least partially) with model inter-comparisons, which are mostly used to compare outputs and insights to explore uncertainties, and diagnostics, which proposes descriptive indicators to explain characteristics of the performance in terms of model structure and assumptions.
+Integrated assessment models (IAMs) have been used for a wide range of problems in the climate change field. From generating consensus to identify key parameters and complex feedbacks on future between the world economies and nature [@Sarofim2011]. However, [@Wilson2021] highlight that IAM evaluation should improve interpretability of results to communicate insights, credibility as producers of knowledge under a 'sceptical review', and relevance of modelling analysis for informing scientific understanding to policymakers and stakeholders. A challenge that may be partially achieved with model inter-comparisons, which are mostly used to compare outputs and insights to explore uncertainties, and diagnostics, which proposes descriptive indicators to explain characteristics of the performance in terms of model structure and assumptions.
 
 The demand from model inter-comparison projects (MIPs) is a fruitful enterprise [@EdNature2015]. Recently, some authors [@Nikas2021] identified several MIPs and inter-comparison studies. An emerging practice in the field of IAMs that will surely place these tools at the same level of reliability than climate and energy models. To overcome the limitations, the IAM Consortium and the International Institute for Applied Systems Analysis (IIASA) started with a common standard, the IAMC format [@IAMCformatIIASA] and a plotting module to play with timeseries called *pyam* [@Huppmann2021]. Some prominent studies using the IAMC format have been recently identified by [@Claudia2024] including IPCC reports and multi-IAM studies.
 
@@ -51,7 +51,7 @@ This section describes the code with a short example to easily follow the whole
 
 ## A brief description
 
-The `wiliamcformat` package (it is not a package currently) is public, available at the domain https://github.com/Tristan22400/IAMC_format. Following the next steps (more detailed in the *README.md* file), the user can obtain the results of WILIAM under the IAMC format criteria and plot results in a general automatic report or customized graphs.
+The `wiliamcformat` code is public, available at the domain https://github.com/Tristan22400/IAMC_format. Following the next steps (more detailed in the *README.md* file), the user can obtain the results of WILIAM under the IAMC format criteria and plot results in a general automatic report or customized graphs.
 
 The user can follow the next steps to install a stable version of the code and play with examples:
 
@@ -67,7 +67,7 @@ The `wiliamcformat` package is built upon a suit of tools and functions provided
 
 The user can download WILIAM in two languages, Python (https://github.com/LOCOMOTION-h2020/pywiliam) and Vensim (https://github.com/LOCOMOTION-h2020/WILIAM_model_VENSIM), and generate the CSV file of a simulation. Both tools were developed during the European H2020 Locomotion project (Grant Agreement number 821105). 
 
-Regarding the translation, the notebook named *translation.ipynb* explains the automatic translation step by step to easily to learn the code. The translation is supported by dictionaries (folder *Create_Variable_Dict*) to solve the equivalence between the dimensions of WILIAM variables (subscripts in Vensim software) and the specific IAMC format. In the same folder, the file *Variable_name_IAMC.xlsx* facilitates the translation of WILIAM variable names. The code automatically builds the corresponding name list in the IAMC format then a manual correction needs to be performed to correct the last errors not handled by the automatic translation and create the final dictionary currently called *variable_name_dict.txt*. A important number of variables of Wiliam are already presented in the file *variable_name_dict.txt*, the dictionary of all the variables translated. If some variables are missing during the translation process, the automatic translation are applied to them. Then, the user can correct them manually in the file *list_missing_variable.txt* and add them to the dictionnary of translated variables. During the addition to the dictionnary, a check on the respect of the IAMC format is done in order to avoid the pollution of the dictionnary by incorrect variables. They will be included in the next process of translation. 
+Regarding the translation, the notebook named *translation.ipynb* explains the automatic translation step by step to easily to learn the code. The translation is supported by dictionaries (folder *Create_Variable_Dict*) to solve the equivalence between the dimensions of WILIAM variables (subscripts in the Vensim software) and the specific IAMC format. In the same folder, the file *Variable_name_IAMC.xlsx* facilitates the translation of WILIAM variable names. The code automatically builds the corresponding name list in the IAMC format then a manual correction needs to be performed to correct the last errors not handled by the automatic translation and create the final dictionary currently called *variable_name_dict.txt*. A important number of variables of Wiliam are already presented in the file *variable_name_dict.txt*, the dictionary of all the variables translated. If some variables are missing during the translation process, the automatic translation are applied to them. Then, the user can correct them manually in the file *list_missing_variable.txt* and add them to the dictionnary of translated variables. During the addition to the dictionnary, a check on the respect of the IAMC format is done in order to avoid the pollution of the dictionnary by incorrect variables. They will be included in the next process of translation. 
 
 Finally, several notebooks are available in the folder *Visualization* to facilitate the learning process, including a general report with principal variables of the model, as well as specific examples of customizable plots.