List of the directories and files  :
Gauthier Ligot - 17-01-2023
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1_prepare data.R - A R script that read the data (directory data), processed them, and store the processed data in tmp directory. This script takes time to execute (15 minutes)
2_generate results.qmd - A R quarto script that generate all the results used in the manuscript. 
2_generate results.pdf - the pdf produced by 2_generate results.qmd
2_generate results.tex - the tex file produced by 2_generate results.qmd
2_generate results_files - A directory produced by 2_generate results.qmd and containing all the figures of the manuscript

configs/myGGplotConfigs.R - Some personnal R functions used to improve the layout of the plots

tmp/prepared_data_v4.Rdata - the data produced by 1_prepare data.R

- analyses/data : The data generated by the simulation

	* 20221107-1015-TG3-ecoTable.csv - a table describing the costs and revenues of each simulation. There is one line per cost or revenenue. The table contains the following column : 
		- siteIndex : the site index (HDOM at 50 years of age)
		- bpr : bark-stripping rate
		- scenario_case : treatment ID (1 = Unprotected, 2 = bark-scraping 400, 3 = bark-scraping all, 4 = fence)
		- lofflerModel (deprecated) : is the Loffler model used to simulate spread decay
		- date : simulation year
		- label : label of the cost or the revenue
		- income : the amount of the revenue (euro/ha)
		- expense : the amount of the cost (euro/ha)
		- volume : the volume of the harvested timber (for thinnings)
		
	* 20221107-1015-TG3-standTable.csv -  a table describing stand through time and for each simulation. There is one line per year and simulation. The table contains the following column : 
		- siteIndex : the site index (HDOM at 50 years of age)
		- bpr : bark-stripping rate
		- scenario_case : treatment ID (1 = Unprotected, 2 = bark-scraping 400, 3 = bark-scraping all, 4 = fence)
		- lofflerModel (deprecated) : is the Loffler model used to simulate spread decay
		- date : simulation year
		- dmoy : the mean of tree diameter (cm)
		- dg : the quadratic mean of tree diameter (cm)
		- nha : tree density (tree/ha)
		- nha_d0 : the density of damaged unprotected trees (tree/ha)
		- nha_dp : the density of damaged protected trees (tree/ha)
		- nha_0p : the density of undamaged unprotected trees (tree/ha)
		- nha_00 : the density of undamaged protected trees (tree/ha)
		- gha : stand basal area (m²/ha)
		- vha : total stand volume (m³/ha)
		- vha_eco : free-of-decay stand volume (m³/ha)
		- rdi : relative density index
		- hdom : stand top height (m)
		- peeled_prop : the proportion of bark-stripped trees
		- decay_length : the mean length of decay columns (cm)
		- purge_height : the mean height of decay column top (cm)
		- purge_height_min : the minimum height of decay column top (cm)
		- purge_height_max : the maximum height of decay column top (cm)
		- stumpage : stand stumpage value (euro/ha)

- analyses/tmp : The data pre-processed and ready to be analyzed
