Please contact the lead author (n.graham@berkeley.edu) if you have any questions or confusion. The necessary data to run each script are discussed at the top under "load data" and are provided as CSV or fasta files in this dryad depository. Network analysis: beatingRedone.csv - The main analysis file with collection information and OTU abundances The following R markdowns were used for cleaning and analyzing the OTU table for species interaction analyses: 1. HDIM arth-plant networks Script 1.Rmd 2. HDIM arth-plant networks Script 2 null models.Rmd 3. HDIM arth-plant networks Script 1 correlations.Rmd The following R markdowns were used for cleaning and analyzing the DNA metabarcoding data: 1. OTU_cleanup.Rmd 2. filterFastabyRemainingOTUs.Rmd Several R scripts were used for cleaning the lidar data and for plot selection: 1. make_plots.R 2. find_pixels.R 3. find_rng.R 4. generate_plots.R 5. HDIM_plotselection_descriptive_lidar.R Fasta files: DNA barcode reference library: 1. knownASVs.fasta -- Curated database sequences fasta file. 2. HawiianBarcodeRef_Nov2020.csv - this file relates the fasta seq name with the taxonomic name and includes what the percent similarity is to metabarcode data matches DNA metabarcoding: First input file: 1. ARF_arthropodASVs_aligned.fasta - all 5046 zOTUs from USEARCH output before data cleaning. Non-arthropod sequences removed. *caution contains pseudogenes and low coverage possibly erroneous zOTUS* Last output file: 2. taxonomynamed.fasta - final 3785 OTUs used for community assembly analysis Intermediate files: 3. HDIM-beating_ARF_with_sizes.fasta = File generated after OTU formation. Sizes are the number of the OTUs across all pools. 4. HDIM-beating_ARF_with_names.fasta = Same as fasta "HDIM-beating_ARF_with_sizes". Use this to do ptp analysis and get species. 5. set461_validated.fasta = file from numtdumper run that you have done the validation of each top ten hit on so that you can call those OTUs the order that you have called them 6. set461_validated_wonames.fasta = you need to remove the names before you make the OTU table so this is the same sequences wo the names Phylogenetic tree: 7. set461_validated_UPGMA.nwk = tree file with order names to use to do the phylogenetic validation of the top ten hits for order Unix commands were applied in the order described in Graham et al. Ecological network structure in response to community assembly processes over evolutionary time. 1. making an otu table.txt - some notes and useful commands about the bioinformatics in USEARH here