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reservebenefit
worldmap_fish_genetic_diversity
Commits
3fd5ca81
Commit
3fd5ca81
authored
Sep 23, 2019
by
peguerin
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readme update
parent
0dbcdb02
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README.md
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3fd5ca81
...
...
@@ -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
)
```
...
...
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