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Code
The code used to produce the results presented in the paper. All the code files are located in this repository under a folder with the same name.
This script contains the main code producing the results in the paper. It contains:
- Island-scale prediction.
- Jaccard analysis
- Distance decay
- Correlations
emln dataset no. 60: dataset of plant-pollinator interactions collected in the canary islands that was archived in the emln R package. used to build the layers of the network.
data/distance_between_sites_canary.csv: used to calculate correlations in the analysis. Taken from the paper that collected the data.
results/predictions_island_scale.rds: The results of the link prediction. used for further analysis in the same scripts as well as in other scripts
Plots:
results/paper_figs/optimal_threshold.pdf: figure S8
results/paper_figs/predicted_original.pdf: figure S10
results/paper_figs/pr_roc.pdf: figure S9
results/paper_figs/hist_f1a_legend_bottom.pdf: figure 2b
results/paper_figs/netsize_f1_nnse.pdf: figure S13
netdensity_f1_nnse.pdf: figure S5
degree_unobserved_links.pdf: figure 3c
map_missing_links.pdf: figure 3a
map_missing_links_diags_offs.pdf: figure S11
pie_chart.pdf: figure 3b
island_heatmap_f1.pdf: figure 2c
degree_occurrence.pdf: figure S12
results/paper_figs/isl_jaccard_distance.pdf: figure 4 \
This script handles a sensitivity analysis to check the combined effect of different Ks and lambdas.
results/predictions_island_scale.rds: The predictions found by Abramov_et_al_spatial_prediction_analysis.R script
plot: boxplot to visualize f1s for each lambda and K tested. not saved in a new file.
This script contains the code for site scale analysis. It contains:
- Island-scale prediction.
- Jaccard analysis
- Distance decay
- ecological inference
emln dataset no. 60: dataset of plant-pollinator interactions collected in the canary islands that was archived in the emln R package. used to build the layers of the network.
data/distance_between_sites_canary.csv: used to calculate correlations in the analysis. Taken from the paper that collected the data.
results/predictions_site_scale.rds: The results of the link prediction, but this time, site scale.
Plots:
hist_f1_site.pdf: figure S3
site_netsize_f1_nnse.pdf: figure S6
site_netdensity_f1_nnse.pdf: figure S7
site_heatmap_f1.pdf: figure S2
jaccard_site_f1.pdf: figure S4
cor_plot_site_dif_f1.pdf: figure S5
nnse_f1_scales.pdf: figure S1 \
This script contains the code to compare prediction quality when using the entire species pools of A and P for prediction vs. prediction done based on subsetting only the species they share.
emln dataset no. 60: dataset of plant-pollinator interactions collected in the canary islands that was archived in the emln R package. used to build the layers of the network.
results/predictions_island_scale.rds: The results of the link prediction, on the island scale (only if it didn't exist already).
Plots:
subset_analysis.pdf: figure 2a,b