Commit ebabf1dc authored by peguerin's avatar peguerin
Browse files

readme update S5 permutation S6

parent 83744d45
......@@ -241,25 +241,29 @@ Rscript 00-scripts/step5/analysis/sensitive_analysis_model.R
Rscript 00-scripts/step5/analysis/sensitive_analysis_covtax.R
```
### 4.5.3 Supplementary figures (September 2019: the number of figure is not numbered as in the revised version of the mansucript. Number are going to be updated after acceptation of the paper)
### 4.5.3 Supplementary figures
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
* 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
* 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
* 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)
......@@ -267,16 +271,16 @@ Rscript 00-scripts/step5/supplementary_figures/figureS3.R
Rscript 00-scripts/step5/supplementary_figures/figureS4.R
```
5. Sampling effect (! Figure S6 in the current version of the paper)
* 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/figureS5.tiff)
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. Taxonomic coverage of the sequences used by the model (!Figure S5 in the current version of the manuscript)
* input : [watertype_all_modeles_effectives_family.csv](11-sequences_taxonomy_habitat/watertype_all_modeles_effectives_family.csv)
* output : [figureS6.pdf](10-figures/figureS6.pdf)
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
```
......
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