DOI: 10.5281/zenodo.17701912
title: Data and code for "Network analysis reveals the plant and bird species underpinning Nature's Contributions to People" submitted to Oikos

description: Data and code for "Network analysis reveals the plant and bird species underpinning Nature’s Contributions to People"

submitted to Oikos

--------------------------

In this folder you will find all the relevant data and scripts to replicate the results presented in the article.

Please do not share the "NCP_supply.csv" because it contains data from a tree inventory that will be made public once all papers in progress for the research unit "Kili-SES" will be published. 

All other data sources are of public domain. 

Because of the multi-step nature of this analysis, scripts have been numbered. It is recommended to run them in sequence, because the outputs of certain scripts are used in analysis steps later on. When running a script, the most important objects for analysis are saved as .RDS files. This allows to reuse these contents without sourcing the respective scripts multiple times.

Some analysis requires packages to be downloaded from GitHub, because they are not currently reposited on CRAN. 

 

Here's an outline of what each of the file in this folder does:

#### CSV FILES ####

fruits_dispersed.csv <- This dataset contains data on the fruit length for each of the plant species which are dispersed by birds in each ecosystem

kili_frugivores_abundance.csv<- This dataset contains information on the recorded abundance of each frugivorous bird species across all ecosystem types. Data obtained from 

NCP_supply.csv<- This dataset contains information on the abundance of every tree species and its estimated  supply of NCP across all habitat types.

plant_species_newtaxonomy.csv <- This dataset contains the alternative names of all tree species to be used in the creation of the phylogenetic trees.

#### NEXUS FILES ###

output.nex <- this is the phylogenetic tree in nexus format for the frugivorous bird species.

plant_phylo.nex <- this is the phylogenetic tree in nexus format for the tree species.

### FUNCTIONS, DATASETS AND PACKAGES #####

These scripts can be sourced or run to load the datasets, packages and functions necessary to the analysis.

0_Functions_TM.R<- This script contains the functions to calculate interaction probability between plants and frugivores. It has been adapted from the functions presented by Donoso et al. (2017).

0.3_datasets.R <- This script assembles the basic dataset needed for the analysis

0.4_packages.R <- This script loads all packages required for analysis and calls for the installation of packages from GitHub.

###### ANALYSIS #############

1_Interactions.R<- This script uses trait data and trait matching functions to build the interaction networks between trees and frugivores for all 10 ecosystems. 

2_ProviderScores.R<- This script calculates the Provider scores for every tree species in every ecosystem from the NCP supply raw data. 

3_RegulatorScores.R<- This script calculates the regulator scores using the provider scores and the interaction probabilities calculated in script 2 and 1 respectively.

4_Analysis.R<- This script runs models and produces figures presented in the results shown in Figure 2.

4.2_Specialisation.R <- This script calculates the specialisation parameter H2' of the networks realised with trait-matching and proves it is close to observed specialisation recorded on Kilimanjaro. 

5_SpeciesAccumulation.R <-This script calculates the species accumulation curves shown in Figure 3.

6.3_Phylogenies_ggtreeExtra <- This script generates the phylogenies for trees and birds in Figures 4 and 5.

6.5_Abouheif_C.R<- This script tests providers and regulators' scores for phylogenetic signal.

6.6_PlantPhylogeny_Phylomaker.R<- This scripts uses V.Phylomaker to generate a phylogeny of tree species with branch length.

6.8_Phylogenetic_Diversity.R <- This script calculates the phylogenetic diversity of providers and regulators.