Update README.md

README.md

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 # sensitivity_paper
 Code associated with the paper "Mismatch between bird species sensitivity and the protection of intact habitats across the Americas"
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+This file describes the main goal of each script.
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+GBrow is the name of the general folder in which all data are stored
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+HFI.01.Data.export.R: Extract eBird data from raw data in the folder "0.Raw.data", makes a first triage and store them (with different files for data used in analyses and data used to calculate observer calibration index).
+HFI.02A and B: Calculate the observer calibration index (A prepare the dataset and B runs models and calculates the index)
+HFI.03 Data.format: Subset the data, add the observer calibration information and removes duplicates
+HFI.04: Extract GIS values for every checklists (coded by site rather than checklist to avoid running X times a calculation for X checklists made at the same site
+HFI.05: Merge checklists in a single table
+HFI.06: Apply taxonomy transformation using a table provided by CLO (HBW 3.0-eBird v2018 match). It involves some manual steps: the code stops and says "there is a issue with this species" and I go check manually what I should do, write in the speadsheets that will be used in this code (and is attached in this ZIP) and the code continues
+HFI.07A and B: Script reload the raw data, extract breeding code and adds it in the used data (because I removed breeding code at the beginning and it was faster to do that than starting from the scratch). B Calculates breeding season per latitude and apply the subsequent subset to all data
+HFI.08: Extracts or calculate the species-level data and stores in a common table with 1 species per line
+HFI.10: Run the sensitivity model for each species and stores the value of sensitivity
+HFI.10c: Extract the range of HF for each species (ie 1 and 99 quantiles)
+HFI.11: Removes species estimates when insufficient contrast in HF. Runs the impute model, plots link between traits and sensitivity and estimates imputed sensitivity
+HFI.20: Extract from distribution the species present in each ecoregion.
+HFI.21: Extract the number of sensitive species per ecoregion (and proportion, and number of threatened...). Some calculations are eventually not used in the paper
+HFI.30: Extract GIS values per ecoregion (coverage by intact protected habitats, trends...)
+HFI.31: Contrasts sensitivity and habitat of ecoregions and plot (Fig.2D, 2F)
+HFI.32: Calculates the proportion of intact protected habitats per species, contrast with species thresholds (Rodrigues et al. 2004) and maps species of major concern