DOI: 10.5061/dryad.69p8cz987
title: Data and code from: Moving towards better risk assessment for invertebrate conservation

description: Among the most widely used information underpinning international
 conservation efforts is the IUCN Red List of endangered species. The Red
 List designates species extinction risk based on geographic range,
 population size, or declines in either. However, the Red-List has poor
 representation of invertebrates, which comprise the majority of animal
 diversity, and it has frequently been questioned whether Red List criteria
 are appropriate for these organisms. Due to their small size, difficulty
 in identification, and general rarity, many invertebrates are hard to
 study, making the Red List criteria difficult to apply. Here we discuss
 these criticisms in the context of empirical evidence from one of the
 largest terrestrial arthropod surveys to date, documenting the abundance
 and distribution of over 13,000 species in Sweden. Using simple empirical
 examples from these data, we argue that even the most ambitious monitoring
 efforts are unlikely to produce enough observations to reliably estimate
 population sizes and ranges for more than a fraction of species. Thus,
 there is likely to be substantial uncertainty in classifying most species
 according to current criteria. In response, we discuss the introduction of
 potential new IUCN criteria to more accurately capture the conservation
 needs of invertebrates, and to increase the representation of
 invertebrates on the IUCN Red List.
description: # Data and code from: Moving towards better risk assessment for
 invertebrate conservation
 [https://doi.org/10.5061/dryad.69p8cz987](https://doi.org/10.5061/dryad.69p8cz987) The repository contains data and code needed to replicate figures and analysis for the article, DOI: [https://doi.org/10.1002/ecog.07819](https://doi.org/10.1002/ecog.07819). Note that the full invertebrate data can be downloaded from the IBA figshare:  [https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/5](https://figshare.scilifelab.se/articles/dataset/Amplicon_sequence_variants_from_the_Insect_Biome_Atlas_project/25480681/5) **Data:** Contains data required to run analyses. **malaise_samples_metadata_SE_2019.tsv** - Contains malaise trap metadata. * sampleID_FIELD/LAB: the field/lab-specific ID number for a sample.  * trapID: ID of the trap a sample was collected from.  * lab_sample_type: the type of sample (e.g., field sample or extraction blank) * biomass_grams: the biomass of the sample in grams. * latitude/longitude_WGS84: the WGS84 coordinates of a trap. * placing_time/date: the time/date a trap was placed. * collecting_time/date: the time/date a trap was collected. NA's in these metadata represent samples that were not collected from the field (e.g. extraction blanks) **filtered_arthropod_clusters.rds** - Contains raw OTU cluster observations derived from sequence data. Columns are labelled as follows * Cluster: the cluster ID of a detected organism. * Order::Species: Taxonomic designations of OTU clusters. * Lysate ID: The sample ID in which the organism was detected. * reads: The raw reads of an organism in a sample * contam_reads: The total number of reads for a given cluster found in all extraction blanks * reads_adj: The raw reads minus the contamination reads * pres: An indicator of whether an organism was present in a given sample. **species_incidence_abundance** - contains a summary of the incidence and read numbers for each cluster. * cluster: the cluster ID of an organism. * mean_reads: average reads per cluster. * total_reads: total reads per cluster. * total_occ: total number of observations per cluster. **family_tree** - contains a family-level taxonomic tree from which to plot the figure in box 1. **abundace/occupancy_sim_res.rds** - contains results from the simulation exercises. * iter: Simulation iteration * preds: Predicted abundance/occupancy * Ab/Occ: Simulated (real) abundance/occupancy * pTrend : predicted trend * rTrend : simulated trend * pBeta : predicted trend effect size. * rBeta: simulated trend effect size. * pBeta_0: predicted intercept. * rBeta_0: simulated intercept. * N: Simulated sample size. * conv_warn: Indicator of any convergence warnings (1 if convergence failed). * fit_0 : Indicator of whether model failed to fit (1 if fitting failed). * IUCN: IUCN trend category. NA values in simulation results are a consequence of fitting or convergence failures, of which there were very few.  The two files needed to replicate the figures are not contained in this folder due to licensing rights:   **red_list_assessments.csv** - contains data on species occurring on the IUCN red list. Data were downloaded from [https://www.iucnredlist.org/resources/spatial-data-download](https://www.iucnredlist.org/resources/spatial-data-download), where the relevant metadata can be found. **number_of_described_species.csv** A .csv summarising the number of described species, from: [https://www.iucnredlist.org/resources/summary-statistics#Summary%20Tables](https://www.iucnredlist.org/resources/summary-statistics#Summary%20Tables) Both of which can be downloaded from the supplied links. **R:** Contains scripts needed to run analyses, scripts contain a numerical prefix in the order they should be run (e.g. \_1). Scripts without a suffix do not require running in any particular order. *1_filter_clusters.R*: Filters clustered OTU data to only arthropods that match species level references, removes spike ins and potential contaminants. **Note** the original cluster data is not included in this repository and will be published in a separate data paper. This script is only provided for transparency. *2_get_incidence_abundace.R*: Derive incidence and abundance distributions for species included in analysis. *3_simulate_occupancy_trends.R*: Simulate occupancy trends. *4_simulate_abundance_trends.R*: Simulate abundance trends. *functions.R*: contains all functions for plotting and analysis *taxonomy.R*: contains code to replicate figure in box 1. *distribution_simulation_figures.R*: contains code to replicate figure in box 2.  *plot_assessments.R*: contains code to plot the number and type of Red List assessments. *RL_stats.R*: contains code to calculate summary measures from IUCN Red List data. The .Rproj file sets up the RStudio R project.