Commit 3fd5ca81 authored by peguerin's avatar peguerin
Browse files

readme update

parent 0dbcdb02
......@@ -198,21 +198,21 @@ Rscript 00-scripts/step5/descripteurs.R
```
### 4.5.2 Figures
1. Map of the global distribution of genetic diversity for marine species
#### 4.5.2.1 Map of the global distribution of genetic diversity for marine species
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [grid_equalarea200km](01-infos/grid_equalarea200km), [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank), [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp)
* output : [figure1.eps](10-figures/figure1.eps)
```
Rscript 00-scripts/step5/figures/figure1.R
```
2. Congruence between fish genetic and species diversity
#### 4.5.2.2 Congruence between fish genetic and species diversity
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [equalarea_id_coordsCA_FWRS_MR_RS.csv](01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv), [grid_equalarea200km](01-infos/grid_equalarea200km), [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank), [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp)
* output : [figure2.tiff](10-figures/figure2.tiff)
```
Rscript 00-scripts/step5/figures/figure2.R
```
3. Determinant of the patterns of fish genetic diversity
#### 4.5.2.3 Determinant of the patterns of fish genetic diversity
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv),[EnvFreshwater.csv](01-infos/EnvFreshwater.csv),[distanceCote](01-infos/distanceCote.csv),[equalarea_id_coordsCA_FWRS_MR_RS.csv](01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv)
* output : [figure3.pdf](10-figures/figure3.pdf)
```
......@@ -221,19 +221,19 @@ Rscript 00-scripts/step5/figures/figure3.R
### 4.5.3 Analysis
1. Wilcoxon test to assess whether genetic diversity means differ between marine and freshwater species.
#### 4.5.3.1 Wilcoxon test to assess whether genetic diversity means differ between marine and freshwater species.
```
Rscript 00-scripts/step5/analysis/wilcoxon_tests.R
```
2. Sensitivity analysis
#### 4.5.3.2 Sensitivity analysis
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [equalarea_id_coordsCA_FWRS_MR_RS.csv](01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv), [grid_equalarea200km](01-infos/grid_equalarea200km)
* outputs : [marine_sensitivity.csv](13-analysis/marine_sensitivity_model.csv), [freshwater_sensitivity_model.csv](13-analysis/freshwater_sensitivity_model.csv)
```
Rscript 00-scripts/step5/analysis/sensitive_analysis_model.R
```
3. Sensitivity analysis based on taxonomic coverage
#### 4.5.3.3 Sensitivity analysis based on taxonomic coverage
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [equalarea_id_coordsCA_FWRS_MR_RS.csv](01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv), [grid_equalarea200km](01-infos/grid_equalarea200km)
* outputs : [marine_sensitivity_covtax.csv](13-analysis/marine_sensitivity_covtax.csv), [freshwater_sensitivity_covtax.csv](13-analysis/freshwater_sensitivity_covtax.csv)
......@@ -243,56 +243,56 @@ Rscript 00-scripts/step5/analysis/sensitive_analysis_covtax.R
### 4.5.4 Supplementary figures
1. Spatial autocorrelogramme based on the I-Moran coefficient
#### 4.5.4.1 Spatial autocorrelogramme based on the I-Moran coefficient
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [grid_equalarea200km](01-infos/grid_equalarea200km)
* output : [figureS1.pdf](10-figures/figureS1.pdf)
```
Rscript 00-scripts/step5/supplementary_figures/figureS1.R
```
2. Global distribution of higher and lower percentiles of genetic diversity
#### 4.5.4.2 Global distribution of higher and lower percentiles of genetic diversity
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [grid_equalarea200km](01-infos/grid_equalarea200km), [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank), [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp)
* output : [figureS2.tiff](10-figures/figureS2.tiff)
```
Rscript 00-scripts/step5/supplementary_figures/figureS2.R
```
3. Latitudinal distribution of species diversity
#### 4.5.4.3 Latitudinal distribution of species diversity
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [equalarea_id_coordsCA_FWRS_MR_RS.csv](01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv), [grid_equalarea200km](01-infos/grid_equalarea200km)
* output : [figureS3.pdf](10-figures/figureS3.pdf)
```
Rscript 00-scripts/step5/supplementary_figures/figureS3.R
```
4. Regional effect on the global genetic diversity pattern
#### 4.5.4.4 Regional effect on the global genetic diversity pattern
* input : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv)
* output : [figureS4.pdf](10-figures/figureS4.pdf)
```
Rscript 00-scripts/step5/supplementary_figures/figureS4.R
```
5. Taxonomic coverage of the sequences used by the model
#### 4.5.4.5 Taxonomic coverage of the sequences used by the model
* input : [watertype_all_modeles_effectives_family.csv](11-sequences_taxonomy_habitat/watertype_all_modeles_effectives_family.csv)
* output : [figureS6.pdf](10-figures/figureS5.pdf)
```
Rscript 00-scripts/step5/supplementary_figures/figureS5.R
```
6. Sampling effect
#### 4.5.4.6 Sampling effect
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [grid_equalarea200km](01-infos/grid_equalarea200km), [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank), [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp)
* output : [figureS5.tiff](10-figures/figureS6.tiff)
```
Rscript 00-scripts/step5/supplementary_figures/figureS6.R
```
7. Spatial distribution of taxonomic coverage
#### 4.5.4.7 Spatial distribution of taxonomic coverage
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [grid_equalarea200km](01-infos/grid_equalarea200km), [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank), [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp), [equalarea_id_coordsCA_FWRS_MR_RS.csv](01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv)
* ouputs : [species_taxon_coverage_number_cells.csv](12-taxonomic_coverage/species_taxon_coverage_number_cells.csv), [figureS7.tiff](10-figures/figureS7.tiff)
```
Rscript 00-scripts/step5/supplementary_figures/figureS7.R
```
8. Intraspecific genetic diversity mean in each 10° latitudinal bands (not in the paper)
#### 4.5.4.8 Intraspecific genetic diversity mean in each 10° latitudinal bands (not in the paper)
* inputs : [freshwater_latbands_bootstraps.csv](08-genetic_diversity/freshwater_latbands_bootstraps.csv), [marine_latbands_bootstraps.csv](08-genetic_diversity/marine_latbands_bootstraps.csv)
* output : [figureS8.pdf](10-figures/figureS8.pdf)
```
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment