Commit 5d347cab authored by peguerin's avatar peguerin
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Update README.md

parent 2dd7d739
......@@ -94,28 +94,28 @@ You're ready to run the analysis. Now follow the instructions at [Running the pi
- R scripts
* [equalareacoords.R](00-scripts/step2/equalareacoords.R) : attributes at each sequence an ID of cell of the shapefile of worldmap equal area projection from its coordinates.
## 3.3 [00-scripts/step3](00-scripts/step3) : filter raw data
## 3.3 [00-scripts/step3](00-scripts/step3) : species sequence pairwise comparison
- JULIA scripts
* [Lib_Compare_Pairwise.jl](00-scripts/step3/Lib_Compare_Pairwise.jl) : functions to compute the Genetic Diversity value from a set of sequences.
* [Lib_Create_Master_Matrices.jl](00-scripts/step3/Lib_Create_Master_Matrices.jl) : functions to create master data matrices that are used to compute genetic diversity.
* [master_matrices.jl](00-scripts/step3/master_matrices.jl) : generates master data matrices from species sequences alignments.
## 3.4 `00-scripts/step4` : Genetic Diversity calculation
## 3.4 [00-scripts/step4](00-scripts/step4) : genetic Diversity calculation
- R scripts
* `gdval_by_site.R` : removes the cells that are not in the area of at least one marine/freshwater species according to IUCN shapefiles, creates the data files used to generate Figure 1
* [gdval_by_site.R](00-scripts/step4/gdval_by_site.R) : removes the cells that are not in the area of at least one marine/freshwater species according to IUCN shapefiles, creates the data files used to generate Figure 1
- JULIA scripts
* `equalarea_numbers.jl` : attributes mean genetic diversity at each equal area grid cell. Genetic diversity is calculated from master data matrices
* `metrics_by_area_and_species.jl`: generates files for statistical analysis at next step : mean genetic diversity per cell, genetic diversity per species per cell, number of individuals per species, number of species per cell, cell coordinates, cell ID...
* `Lib_GD_summary_functions.jl` : functions to calculate genetic diversity at species level and cell level
* [equalarea_numbers.jl](00-scripts/step4/equalarea_numbers.jl) : attributes mean genetic diversity at each equal area grid cell. Genetic diversity is calculated from master data matrices
* [metrics_by_area_and_species.jl](00-scripts/step4/metrics_by_area_and_species.jl): generates files for statistical analysis at next step : mean genetic diversity per cell, genetic diversity per species per cell, number of individuals per species, number of species per cell, cell coordinates, cell ID...
* [Lib_GD_summary_functions.jl](00-scripts/step4/Lib_GD_summary_functions.jl) : functions to calculate genetic diversity at species level and cell level
## 3.5 `00-scripts/step5` : Statistical analysis
## 3.5 [00-scripts/step5](00-scripts/step5) : statistical analysis
- R scripts
* `descripteurs.R`
* `figures.R`
* `figures.R` WORK IN PROGRESS !!!
# 4. Reporting bugs
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