Research question: How do population processes, productivity, and model assumptions shape inference about the state and dynamics of exploited pelagic populations? Why it matters: Reliable assessment requires integrating biomass with recruitment, mortality, selectivity, and productivity while accounting for structural uncertainty in the models used for fisheries advice.
+```
+
+### Projects and research directions
```{=html}
Research question: How do climate and oceanographic variability, natural forcing, fishing pressure, and their interactions alter productivity and the state of pelagic populations? Why it matters: Eastern Boundary Upwelling Systems are highly variable, so separating environmental forcing from fishing effects is essential for detecting pressure-state relationships, thresholds, and regime changes.
Research question: How do reproduction, growth, and individual condition vary through time, and how do these life-history processes contribute to changes in pelagic population state? Why it matters: Maturity, spawning, growth, and condition can respond before biomass does, providing complementary information on population performance and resilience.
```
-## Fisheries dynamics and management {#fisheries-dynamics}
+## Spatial ecology, species distribution and biodiversity {#spatial-biodiversity}
-Fishery season dynamics, fleet reorganization, fishing pressure, management benchmarks, and decision-relevant diagnostics under environmental variability.
+```{=html}
+
Research question: How do pelagic species, associated fauna, and non-target interactions vary across space and time, and which environmental processes shape habitat suitability and species distributions? Why it matters: Spatially explicit information from niche models, species distribution models, biodiversity observations, and bycatch patterns is needed to interpret ecosystem change and support spatial fisheries management.
Research question: How do pelagic fisheries reorganize through seasons, environmental variability, fleet behaviour, and management interventions, and how can those dynamics inform adaptive decisions? Why it matters: Fast changes in resource availability and fishing operations require diagnostics that separate ecological availability, biological risk, fishing pressure, and fleet response.
+```
+
+### Projects and research directions
```{=html}
Systematic evidence synthesis evaluating management responses to environmental variability and climate change and their transferability to Peruvian anchovy.
Framework separating resource availability, biological risk, operational risk, and regulation using environmental and fishery information with hindcast validation.
```
-## Stock condition and reproductive ecology {#stock-condition}
-
-Multidimensional stock condition, reproductive indicators, maturity, and biological responses used to describe population state beyond biomass alone.
-
-### Related outputs
+## Scientific computing and research software {#scientific-computing}
```{=html}
-
Research question: How can statistical methods, reproducible workflows, and research software make complex marine and fisheries analyses more transparent, reusable, and auditable? Why it matters: Heterogeneous marine data and complex models create hidden analytical variation; reusable software and reproducible workflows improve validation, transferability, and scientific efficiency.
```
-## Statistical ecology and scientific computing {#scientific-computing}
-
-Reusable statistical methods, research software, reproducible workflows, and marine-data infrastructure developed to support quantitative ecological analysis.
+### Projects and research directions
```{=html}
Potential software paper contingent on stable reuse, documentation, testing, and a defensible methodological contribution in the underlying fisheries-indicator framework.
Reproducible acquisition, quality control, harmonization, derivation, cataloguing, provenance, and reuse of environmental data for fisheries and marine-ecology analyses across the Humboldt Current System.
Open educational book on portable, auditable and reproducible digital research workflows spanning data, code, automation, collaboration, R, Python, SQL, Quarto, and responsible use of AI in fisheries science and quantitative ecology.
```
diff --git a/projects/index.qmd b/projects/index.qmd
index 96bc5506..5d41283f 100644
--- a/projects/index.qmd
+++ b/projects/index.qmd
@@ -4,12 +4,12 @@ description: "Research themes, projects at different stages of maturity, and rel
css: research.css
---
-::: {.qs-footnote-note}
-**Project-stage note.** This catalogue includes active analyses, manuscripts in development, reusable research infrastructure, and planned studies. The stage shown on each card describes its current maturity; inclusion here does not imply that all projects are being pursued simultaneously.
-:::
-
{{< include _generated.md >}}
::: {.qs-footnote-note}
**Research catalogue.** Each project card represents a canonical research repository or a stable public project record linked to its source repository. Formal publication, talk, software, teaching, and post metadata remain authoritative in their respective catalogues. [Explore the public Research Graph](/research-graph/) to see these records connected through common themes, projects, repositories, and provenance.
:::
+
+::: {.qs-footnote-note}
+**Project-stage note.** This catalogue includes active analyses, manuscripts in development, reusable research infrastructure, and planned studies. The stage shown on each card describes its current maturity; inclusion here does not imply that all projects are being pursued simultaneously.
+:::
diff --git a/projects/research.css b/projects/research.css
index f66e4ae9..e8ed698c 100644
--- a/projects/research.css
+++ b/projects/research.css
@@ -83,3 +83,38 @@
white-space: normal;
}
}
+
+/* Repository visibility is explicit without exposing private GitHub links. */
+.qs-project-topline {
+ display: flex;
+ align-items: center;
+ justify-content: space-between;
+ gap: .55rem;
+}
+
+.qs-project-visibility {
+ display: inline-flex;
+ align-items: center;
+ justify-content: center;
+ width: 1.45rem;
+ height: 1.45rem;
+ border-radius: 50%;
+ font-size: .82rem;
+ line-height: 1;
+}
+
+.qs-project-visibility-private {
+ color: #9a6200;
+ background: rgba(196, 132, 0, .11);
+}
+
+.qs-project-visibility-public {
+ color: #39724d;
+ background: rgba(57, 114, 77, .10);
+}
+
+.qs-project-repository-state {
+ color: #6b7280;
+ font-size: .84rem;
+ white-space: nowrap;
+}
diff --git a/publications/_generated.md b/publications/_generated.md
index 9b7a0be7..e7e341cf 100644
--- a/publications/_generated.md
+++ b/publications/_generated.md
@@ -3,6 +3,7 @@
@@ -10,26 +11,30 @@
## Peer-reviewed articles {#papers}
-- **Quispe-Salazar, E.**, Sánchez, J., & Perea, Á. (2025). Classification models based on the gonadosomatic index to determine gonadal maturity stages: a case study in the Peruvian anchovy Engraulis ringens. *Scientia Marina, 89*(4), e117. DOI10.3989/scimar.05636.117OpenaccessResearchReproduction & growthBibTeXview
@article{quispesalazar2025classification,
- author = {Elmer Quispe-Salazar and Javier Sánchez and Ángel Perea},
- title = {Classification models based on the gonadosomatic index to determine gonadal maturity stages: a case study in the Peruvian anchovy Engraulis ringens},
- year = {2025},
- journal = {Scientia Marina},
- volume = {89},
- number = {4},
- pages = {e117},
- doi = {10.3989/scimar.05636.117},
- url = {https://doi.org/10.3989/scimar.05636.117}
-}
+- **Quispe-Salazar, E.**, Sánchez, J., & Perea, Á. (2025). Classification models based on the gonadosomatic index to determine gonadal maturity stages: a case study in the Peruvian anchovy Engraulis ringens. *Scientia Marina, 89*(4), e117. DOI10.3989/scimar.05636.117Openaccess
## Theses {#theses}
-- **Quispe-Salazar, E.** (2025). Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022. *Cybertesis Revistas UNMSM Fondo editorial*. DOI10.5281/zenodo.17452484OpenaccessResearchReproduction & growthBibTeXview
@misc{quispesalazar2025interannual,
- author = {Elmer Quispe-Salazar},
- title = {Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022},
- year = {2025},
- howpublished = {Cybertesis Revistas UNMSM Fondo editorial},
- doi = {10.5281/zenodo.17452484},
- url = {https://zenodo.org/doi/10.5281/zenodo.17452484},
- note = {Dissertation Thesis}
-}
+- **Quispe-Salazar, E.** (2025). Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022. *Cybertesis Revistas UNMSM Fondo editorial*. DOI10.5281/zenodo.17452484Openaccess
+
+## Reports and institutional technical outputs {#reports}
+
+### 2026
+
+- IMARPE Pelagic Resources Team (2026). Decision-table protocol for seasonal catch advice in the north-central Peruvian anchovy fishery. Risk-based methodology linking abundance-at-length, biological parameters, environmental and exploitation scenarios, and spawning-biomass projections to seasonal harvest advice. Openaccess
+- IMARPE Pelagic Resources Team (2026). North-central Peruvian anchovy stock status and 2026 first-season exploitation outlook. Integrated stock-status assessment combining environmental conditions, fishery indicators, acoustic biomass, size structure, biological condition, and exploitation scenarios for management advice. Openaccess
+
+### 2025
+
+- IMARPE Pelagic Resources Team (2025). Jack mackerel fishery status in 2025 and exploitation outlook for 2026. Assessment synthesis covering the 2025 jack-mackerel fishery, stock status, spawning biomass, fishing mortality, recruitment, exploitation scenarios, and catch-limit advice; individual contribution is not attributed in the report itself.
+- IMARPE Pelagic Resources Team (2025). North-central Peruvian anchovy status and 2025 second-season exploitation outlook. Seasonal assessment integrating fishery performance, environmental conditions, acoustic biomass, demographic structure, reproductive condition, and exploitation perspectives.
+- IMARPE Pelagic Resources Team (2025). Southern Peruvian anchovy status and 2026 first-season exploitation outlook. Regional assessment of southern anchoveta availability, fishery indicators, biomass projections, exploitation scenarios, and management advice.
+
+### 2024
+
+- SPRFMO Connectivity Task Team (2024). Critical appraisal of research approaches to inform evidence of connectivity of Trachurus murphyi – a systematic review of 11 topics. *SPRFMO 12th Meeting of the Scientific Committee*. Systematic evidence synthesis across 11 research domains relevant to population connectivity and management of Chilean jack mackerel. Openaccess
+- Geronimo, M., Lujan, C., Torrejón, J., & **Quispe-Salazar, E.** (2024). The Joint Jack Mackerel (JJM) model: a user guide to IMARPE's proposal. *SPRFMO 12th Meeting of the Scientific Committee*. Documents the population-dynamics equations, AD Model Builder implementation, inputs, outputs, model execution, and practical use of the JJM stock-assessment model. Openaccess
+
+### 2023
+
+- Gutiérrez, M., Tarazona, A., Grados, D., Valdez, C., **Quispe-Salazar, E.**, Pereyra, N., Peraltilla, S., Meneses, G., & Vásquez, L. (2023). Habitat conditions of jack mackerel (Trachurus murphyi) and chub mackerel (Scomber japonicus) in the Peruvian sea between 2021 and 2023. *SPRFMO 11th Meeting of the Scientific Committee*. Links oceanographic and habitat conditions with the distribution of jack mackerel and chub mackerel in Peruvian waters. Openaccess
diff --git a/scripts/build_home.py b/scripts/build_home.py
index 9a2d1d8c..a38bc992 100644
--- a/scripts/build_home.py
+++ b/scripts/build_home.py
@@ -109,7 +109,7 @@ def render_sidebar(data: dict, identity: dict) -> str:
{name}
-
Marine Quantitative Ecologist Fisheries Scientist
+
{html.escape(str(identity["headline"]))}
Instituto del Mar del Perú (IMARPE)
Peru · Humboldt Current
Pelagic fisheries · Statistical ecology
diff --git a/scripts/build_projects.py b/scripts/build_projects.py
index 92d3667e..0e9755d5 100644
--- a/scripts/build_projects.py
+++ b/scripts/build_projects.py
@@ -82,24 +82,39 @@ def render_badges(items: list[dict], owner: str, expected_labels: tuple[str, ...
def render_card(project: dict) -> list[str]:
- """Render a GitHub-backed project while making its maturity explicit."""
+ """Render a GitHub-backed project while making maturity and repository visibility explicit."""
slug = clean_class(project.get("slug"), "project slug")
title = str(project.get("title") or "").strip()
summary = str(project.get("summary") or "").strip()
context = str(project.get("context") or "").strip()
stage = str(project.get("stage") or "").strip()
repository = str(project.get("source_repository") or "").strip()
+ site_path = str(project.get("site_path") or "").strip()
if not all((title, summary, context, stage, repository)):
raise RuntimeError(f"Project {slug} is missing card content, stage, or source_repository")
- target = f"https://github.com/{repository}"
+
+ repository_url = f"https://github.com/{repository}"
+ is_private = bool(site_path) and not re.match(r"^https?://", site_path, flags=re.I)
+ target = site_path if is_private else repository_url
+ visibility = "Private repository" if is_private else "Public repository"
+ visibility_class = "private" if is_private else "public"
+ visibility_icon = "bi-lock-fill" if is_private else "bi-unlock-fill"
+ repository_action = (
+ 'Private repository'
+ if is_private
+ else f'Repository'
+ )
return [
'',
'
-
+
@@ -16,11 +16,5 @@
GitHub
LinkedIn
-
-
-
diff --git a/projects/_generated.md b/projects/_generated.md
index d98b8025..4300beae 100644
--- a/projects/_generated.md
+++ b/projects/_generated.md
@@ -2,112 +2,240 @@
```{=html}
```
## Stock assessment and population dynamics {#stock-assessment}
-Population-state reconstruction, assessment diagnostics, biological parameters, and methods for understanding how structural assumptions affect fisheries inference.
+```{=html}
+
-