Quantitative eDNA abundances for multispecies monitoring along the US West Coast
Year: 2025
Type: article
Abstract: Read me code/ Core analysis code. R code 1_Run_QM_qPCR.qmd Runs the joint model that connects qPCR (absolute for the reference species) with metabarcoding (compositional) and produces model-ready objects + posterior outputs. 2_sdmTMB_smooths_13sp.qmd Fits spatial (sdmTMB) smooths to the joint-model concentration estimates and produces map-ready outputs. 3_All_Figures.qmd Produces final figures from model outputs (joint model + smooths). Stan model code (used by 1_Run_QM_qPCR.qmd): Joint_model.stan — Stan program implementing the joint statistical model linking qPCR (absolute, reference species) with metabarcoding (compositional, multi-species). Mock_model.stan — Stan program for the mock-community calibration component (e.g., amplification efficiency / bias parameters). Mock_model.rds — saved fitted object / calibration output associated with the mock model (generated by the workflow; kept here for reuse). R helper scripts load_QM-qPCR_data.R — loads raw inputs from data/ and standardizes formats. qm_data_prep_functions.R — shared utility functions for cleaning, joins, reshaping, QC, etc. smoothers.R — helper functions for the smoothing / mapping stage. plots/ Final manuscript figures generated by 3_All_Figures.qmd from the model outputs (joint model + spatial smooths). The leading number is a sort key, not the figure number. 2_Figure_2.jpg – 5_Figure_5.jpg — main-text Figures 2–5. 6_Supplemental_Figure_1.jpg – 16_Supplementary_Figure_11.jpg — Supplementary Figures 1–11. 10_Supplementary_Figure_5_A.jpg – ..._D.jpg — the four panels (A–D) of Supplementary Figure 5. Note: Figure 1 is not produced by the analysis code; it (and Supplementary Figure 1) are created in other software and live in raw_plots/. raw_plots/ Figures and source files created outside the analysis pipeline (not generated by the .qmd notebooks), kept for provenance and for assembling the final manuscript figures. 1_Figure_1.jpg / 1_Figure_1.pdf — main-text Figure 1 (study design / overview). 6_Supplementary_Figure_1.jpg / .pdf — Supplementary Figure 1. DAG.tex — TikZ/LaTeX source for the model directed acyclic graph. Literature_species_dist_1.jpg, Literature_species_dist_2.jpg — literature-derived species-distribution reference figures. data/ Raw and lightly processed inputs used by the workflow. hake_qpcr/ — qPCR inputs for the reference species. metabarcoding/ — metabarcoding reads for environmental samples. metabarcoding_db/ — taxonomy / reference database products used in assignment. metabarcoding_mocks/ — mock community inputs/outputs used for amplification-bias calibration. metadata/ — station/sample metadata (locations, depths, cruise/station IDs, etc.). Intermediate_data/ Cached outputs produced by the pipeline (to avoid re-running expensive steps). Important: everything in Intermediate_data/ is generated from: 1_Run_QM_qPCR.qmd and 2_sdmTMB_smooths_13sp.qmd Files: Joint_mod_data_input.rds — compiled data object passed into the joint model. Joint_mod_output.rds — joint model results / posterior summaries. Mock_mod_output.rds — mock-community calibration outputs (amplification efficiencies / bias correction objects). Log_D_est.rds — species-by-sample estimated log DNA concentrations from the joint model. Log_D_est_smoothed.rds — smoothed (sdmTMB) versions of Log_D_est. all_maps_se.rds — standard errors / uncertainty layers for mapped smooth predictions. Recommended run order Run the joint model + calibration Render / run: code/Stan_models/1_Run_QM_qPCR.qmd Writes model inputs/outputs to Intermediate_data/ Fit spatial smooths Render / run: code/Stan_models/2_sdmTMB_smooths_13sp.qmd Writes smoothed outputs and map uncertainty objects to Intermediate_data/ Build final figures Render / run: code/Stan_models/3_All_Figures.qmd Uses Intermediate_data/ as inputs Notes This is an RStudio project: open QM-qPCR-joint.Rproj to get the correct working directory.
Author: Guri, Gledis
Institution: University of Washington
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W6949376709
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