conbio-data-analysis

Data Analysis (conbio-data-analysis)

Conservation Biology reviewers are methodologically sophisticated, and the journal expects a

data-availability statement with data and code deposited at acceptance (see

conbio-reporting-and-data-policy). Analyze as if your code will be re-run — because it may be. This

skill covers execution and reporting norms; design decisions live in conbio-study-design.

When to trigger

• Running main and supporting analyses; building the results section
• A reviewer asked for robustness, alternative models, or uncertainty
• Reconciling exploratory vs. confirmatory analyses
• Making the analysis reproducible before deposit

Analysis norms Conservation Biology expects

1. Report uncertainty honestly. Confidence/credible intervals, not just stars or p-values; report

the magnitude and conservation meaning of the estimate, not only significance.

1. Use the right model for the data. Hierarchical/mixed models for nested data; occupancy and

N-mixture for detection; capture-recapture for survival/abundance; GLMs/GAMs for nonlinearity;

account for spatial autocorrelation and zero-inflation where present.

1. Robustness that probes, not decorates. Show specifications that could break the result

(alternative predictors, samples, priors, estimators), and say what you learn.

1. Right inference. Cluster/group at the correct level; avoid pseudoreplication in the analysis;

correct for multiple comparisons when testing many implications.

1. Confirmatory vs. exploratory. Separate preregistered/confirmatory tests from exploratory ones;

do not mine for a significant interaction and theorize it post hoc.

1. Model checking. Report convergence, residual diagnostics, validation/out-of-sample performance

for predictive models; show the result is not an artifact of one modeling choice.

Conservation-specific reporting

• Translate estimates into decision-relevant quantities (extinction risk, population trend,

effect of a management action, area needed) with uncertainty.

• For projections (PVA, SDM, climate), state the assumptions and the range of plausible outcomes —

not a single point forecast.

Reproducibility while you work (not at the end)

• One master script regenerates every table and figure from the (raw or constructed) data.
• Set and report seeds for bootstrap, MCMC, simulation, and any stochastic step.
• Pin software/package versions (renv.lock, requirements.txt, recorded installs).
• Keep table/figure numbers matched to script outputs.

Anti-patterns

• Stars/p-values with no effect sizes or intervals
• Raw counts analyzed as abundance with detection ignored
• "Robustness" that only reruns near-identical specs to manufacture stability
• p-hacking / HARKing exploratory results into confirmatory claims
• A single point projection presented as certain
• A results section whose numbers the code cannot reproduce

Evidence pass for Conservation Biology

Use this as a second-pass capability check. First lock the species/system threat, conservation decision, and uncertainty relevant to action; then test whether the manuscript addresses conservation-science reviewers who ask whether evidence changes biodiversity, management, or policy action.

• Primary move: Audit unit, comparison, uncertainty, missingness, sensitivity, and reproducibility before making any prose or submission recommendation.
• Decision ledger: return claim / evidence / blocker / next edit rows so the next pass can patch the manuscript directly.
• Neighbor test: compare against Biological Conservation for applied conservation breadth, Global Change Biology for climate/ecosystem process, Ecology Letters for theory-forward ecology; if the neighboring outlet has the stronger audience claim, recommend re-routing before polishing.
• Submission-ready gate: before final advice, re-open resources/official-source-map.md for upload-week rules and name the one live-check item that could change the recommendation.

Output format

【Main estimate】magnitude + interval + conservation meaning
【Model】why this model fits the data (detection / hierarchy / spatial)
【Robustness】specs that could break it → what held
【Confirmatory vs exploratory】clearly separated?
【Uncertainty in projections】range stated, not a point?
【Reproducible】master script + seeds + pinned versions? [Y/N]
【Next】conbio-figures-and-tables

Supplementary resources

• [../../resources/external_tools.md](../../resources/external_tools.md) — modeling, inference, and synthesis packages
• [../../resources/official-source-map.md](../../resources/official-source-map.md) — data-availability and reproducibility expectations