Statistical distributions for fisheries and marine ecology. A practical guide to choosing probability distributions for common response variables in fisheries and marine ecology. TopicStatistical ecologyLevelIntermediateRead8 minUpdatedSep 9, 2026
Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis.
Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis.
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 96bc550..5d41283 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 f66e4ae..e8ed698 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 9b7a0be..e7e341c 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/reproducibility/_generated.md b/reproducibility/_generated.md
index 7e2d5a9..afa224a 100644
--- a/reproducibility/_generated.md
+++ b/reproducibility/_generated.md
@@ -2,16 +2,19 @@
This page reports an **internal technical self-certification** of approved public repositories. It is not external accreditation and it does not assess scientific validity, novelty, or inferential quality.
-Repositories assessed: **6** · certified at Level 2 or above: **1** · below certification threshold: **5**.
+Repositories assessed: **9** · certified at Level 2 or above: **1** · below certification threshold: **8**.
## Certification records
| Repository | Status | Level | Certification ID | Next priority |
|---|---|---:|---|---|
| [qselmer/oceancube](https://github.com/qselmer/oceancube) | Certified | 3 - Automated | `QS-RC1-qselmer-oceancube` | archive a stable release and register a DOI |
+| [qselmer/.template-mse](https://github.com/qselmer/.template-mse) | Not certified | 1 - Documented | `QS-RC1-qselmer-template-mse` | document a computational environment or add tests |
| [qselmer/.template-training](https://github.com/qselmer/.template-training) | Not certified | 1 - Documented | `QS-RC1-qselmer-template-training` | add an explicit license |
+| [qselmer/fisheries-research-workflows-book](https://github.com/qselmer/fisheries-research-workflows-book) | Not certified | 1 - Documented | `QS-RC1-qselmer-fisheries-research-workflows-book` | add an explicit license |
| [qselmer/git-github-training](https://github.com/qselmer/git-github-training) | Not certified | 1 - Documented | `QS-RC1-qselmer-git-github-training` | add an explicit license |
| [qselmer/humboldt-ocean-watch](https://github.com/qselmer/humboldt-ocean-watch) | Not certified | 1 - Documented | `QS-RC1-qselmer-humboldt-ocean-watch` | add CITATION.cff |
+| [qselmer/oceHCS-environmental-data-workflow](https://github.com/qselmer/oceHCS-environmental-data-workflow) | Not certified | 1 - Documented | `QS-RC1-qselmer-ocehcs-environmental-data-workflow` | document a computational environment or add tests |
| [qselmer/pel-climate-adaptive-management-paper](https://github.com/qselmer/pel-climate-adaptive-management-paper) | Not certified | 1 - Documented | `QS-RC1-qselmer-pel-climate-adaptive-management-paper` | add CITATION.cff |
| [qselmer/pelagicPER-availability-risk-paper](https://github.com/qselmer/pelagicPER-availability-risk-paper) | Not certified | 1 - Documented | `QS-RC1-qselmer-pelagicper-availability-risk-paper` | add an explicit license |
@@ -29,9 +32,12 @@ Repositories assessed: **6** · certified at Level 2 or above: **1** · below ce
The queue is generated from missing evidence. It deliberately does not create licenses, DOIs, releases, or archive records automatically where those require a scientific or legal decision.
- **qselmer/oceancube:** archive a stable release and register a DOI; add ORCID to CITATION.cff; add CodeMeta metadata when useful; link release preservation metadata when archived.
+- **qselmer/.template-mse:** document a computational environment or add tests; add CodeMeta metadata when useful.
- **qselmer/.template-training:** add an explicit license; add CodeMeta metadata when useful.
+- **qselmer/fisheries-research-workflows-book:** add an explicit license; add CITATION.cff; document a computational environment or add tests; add CodeMeta metadata when useful.
- **qselmer/git-github-training:** add an explicit license; add CITATION.cff; document a computational environment or add tests; add CodeMeta metadata when useful.
- **qselmer/humboldt-ocean-watch:** add CITATION.cff; add CodeMeta metadata when useful.
+- **qselmer/oceHCS-environmental-data-workflow:** document a computational environment or add tests; add CodeMeta metadata when useful.
- **qselmer/pel-climate-adaptive-management-paper:** add CITATION.cff; add CodeMeta metadata when useful.
- **qselmer/pelagicPER-availability-risk-paper:** add an explicit license; add CITATION.cff; document a computational environment or add tests; add CodeMeta metadata when useful.
diff --git a/research-graph/_generated.md b/research-graph/_generated.md
new file mode 100644
index 0000000..8ef4953
--- /dev/null
+++ b/research-graph/_generated.md
@@ -0,0 +1,167 @@
+
+
+```{=html}
+
+
6Themes
+
9Projects
+
10Publications
+
7Talks
+
1Poster
+
2Software
+
2Teaching
+
1Post
+
+
Public graph: canonical public mirrors and curated registries only. Private repository metadata is excluded before serialization.
+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 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.
+
+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.
+
+```
+
+## 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.
+
+```
+
+## Spatial ecology, species distribution and biodiversity {#spatial-biodiversity}
+
+```{=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.
+
+```
+
+## Stock assessment and population dynamics {#stock-assessment}
+
+```{=html}
+
+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.
+
+```
+
+## Provenance and graph contract {#provenance}
+
+The graph is generated from public scholarly mirrors and curated website registries. Repository metadata enters the public graph only after it has been selected for a public Project, Software, or Teaching catalogue. ORCID and OpenAlex contribute public scholarly records and metrics; the raw repository catalogue is not serialized into this website graph.
diff --git a/scripts/build_home.py b/scripts/build_home.py
index 9a2d1d8..a38bc99 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 92d3667..0e9755d 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 [
'',
'
Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis.
oceancube. Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis. Repository·Documentation·Project page.TypeR packageStageStableLanguageRReleasev0.2.0
-
+
+
+
```
## Research applications I develop {#applications}
```{=html}
-
-
Python and Streamlit system for reproducible thermal monitoring of Niño 1+2 using validated local analytics, quality control, event diagnostics, and optional grounded scientific briefs.
humboldt-ocean-watch. Python and Streamlit system for reproducible thermal monitoring of Niño 1+2 using validated local analytics, quality control, event diagnostics, and optional grounded scientific briefs. Repository·Project page.TypeApplicationStageExperimentalLanguagePythonReleaseUnreleased
+
-
+
+
```
## Incubating and concept-stage work {#incubating}
-These records are preserved for continuity but are not presented as released or validated scientific software.
-
- [`seasignals`](/software/seasignals/) - Public R-package repository exists, but its current README is still a package skeleton with placeholder installation and example sections.
- [Pelagytics](/software/pelagytics/) - Concept and prototype only; no canonical public repository has been verified.
diff --git a/talks/_generated.md b/talks/_generated.md
index a95cae3..2429bdb 100644
--- a/talks/_generated.md
+++ b/talks/_generated.md
@@ -1,15 +1,26 @@
-## Oral presentations {#oral}
+
-- **Quispe-Salazar, E.** & Tam, J. (2026, May 6). Multivariate Health Index of the anchovy: Understanding the dynamics of small pelagic fish under environmental variability. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, Baja California Sur, Mexico. TypeOralVideopublicDetailspage
+## Conference talks {#conference-talks}
-## Poster presentations {#posters}
+- **Quispe-Salazar, E.** & Tam, J. (2026, May 6). Multivariate Health Index of the anchovy: Understanding the dynamics of small pelagic fish under environmental variability. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, MX. TypeOralLocationLa Paz, MXDetailspage
-- **Quispe-Salazar, E.**, Recoba, Á., & Tam, J. (2026, May 8). Critical points of natural and anthropogenic pressures and responses in the state of the north–central anchovy stock in the pelagic system of the Peruvian Sea. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, Baja California Sur, Mexico. TypePosterMaterialPDFDetailspage
+- **Quispe-Salazar, E.** (2026, March 12). Bayesian state-space assessment of Peruvian dolphinfish (Coryphaena hippurus). *4th IATTC Technical Meeting on Dolphinfish (DOR-04)*, San José, CR. TypeOralLocationSan José, CRDetailspage
-## Other conference presentations {#other}
+- **Quispe-Salazar, E.** (2024, December 12). PelagicSurveys: an R package for biometric and biological data from pelagic hydroacoustic surveys. *Conecta Pesquero 2024 - III Research, Development and Innovation Meeting, UNALM*, Lima, PE. TypeOralLocationLima, PE
-- **Quispe-Salazar, E.** & Sánchez, J. (2024, November 11). Suitability of the gonadosomatic index in Peruvian Anchoveta (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation. *VI Simpósio Ibero-Americano de Ecologia Reprodutiva, Recrutamento e Pesca (VI SIBECORP)*, Lisbon, Portugal. TypeConferenceDOI10.13140/rg.2.2.32795.73767MaterialpublicDetailspage
+- **Quispe-Salazar, E.** & Sánchez, J. (2024, November 11). Suitability of the gonadosomatic index in Peruvian anchovy (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation. *VI Ibero-American Symposium on Reproductive Ecology, Recruitment and Fisheries (VI SIBECORP)*, Lisbon, PT. TypeOralLocationLisbon, PTDetailspage
-- Díaz, E., Marín, P., & **Quispe-Salazar, E.** (2022, September 1). Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953–2022) within the Humboldt Current System. *Open Science Conference on Eastern Boundary Upwelling Systems: Past, Present and Future and Second International Conference on the Humboldt Current System*, Peru. TypeConferenceDetailspage
+- **Quispe-Salazar, E.** (2024, May 8-10). Pelagic community changes associated with the 2023-2024 El Niño in the Humboldt Current Ecosystem off Peru. *Scientific Workshop: El Niño 2023-2024 - Effects and outlook for the Peruvian sea and its living resources*, Callao, PE. TypeOralLocationCallao, PE
+
+- Díaz, E., Marin, P., **Quispe-Salazar, E.**, Torrejón, J., & Grados, D. (2024, May 8-10). Impacts of the 2023-2024 El Niño on Peruvian anchovy population dynamics. *Scientific Workshop: El Niño 2023-2024 - Effects and outlook for the Peruvian sea and its living resources*, Callao, PE. TypeOralLocationCallao, PE
+
+- Díaz, E., Marín, P., & **Quispe-Salazar, E.** (2022, September 1). Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953-2022) within the Humboldt Current System. *Open Science Conference on Eastern Boundary Upwelling Systems: Past, Present and Future and Second International Conference on the Humboldt Current System*, Lima, PE. LocationLima, PEDetailspage
+
+## Posters {#posters}
+
+- **Quispe-Salazar, E.**, Recoba, Á., & Tam, J. (2026, May 8). Critical points of natural and anthropogenic pressures and responses in the state of the north-central anchovy stock in the pelagic system of the Peruvian Sea. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, MX. TypePosterLocationLa Paz, MXDetailspage
diff --git a/teaching/_generated.md b/teaching/_generated.md
index 9f94bbb..c06e8a8 100644
--- a/teaching/_generated.md
+++ b/teaching/_generated.md
@@ -1,9 +1,17 @@
-## Courses and training {#courses}
+## Courses and workshops {#courses}
-- git-github-training. Structured teaching materials, practices, and reusable resources for learning Git and GitHub through a progressive version-control workflow. TypeCourse materialsStatusActiveLanguageRTeachingpageRepositoryGitHub
+```{=html}
+
+
GIT & GITHUB. Structured teaching materials, practices, and reusable resources for learning Git and GitHub through a progressive version-control workflow. Duration: Multi-session ·Materials: Lessons, practices & cheatsheets.Teaching page·Repository.RoleInstructorAudienceBeginnersLanguageSpanish
+
+```
## Teaching infrastructure {#infrastructure}
-- Scientific Training Template. Reusable Quarto structure for classes, workshops, short courses, technical training, and semester teaching, with modules, labs, exercises, metadata, and reproducible publishing. TypeTeaching templateStatusReusable templateLanguagePythonRepositoryGitHub
+```{=html}
+
+
SCIENTIFIC TRAINING TEMPLATE. Reusable Quarto structure for classes, workshops, short courses, technical training, and semester teaching, with modules, labs, exercises, metadata, and reproducible publishing. Duration: Reusable ·Materials: Quarto modules, labs & exercises.Repository.RoleTemplate developerAudienceInstructorsLanguageSpanish
+
+```
From de70e69269faa6600fd7b31a4f72a72a252c0cc8 Mon Sep 17 00:00:00 2001
From: Elmer Quispe-Salazar <44510819+qselmer@users.noreply.github.com>
Date: Mon, 14 Sep 2026 10:47:24 -0500
Subject: [PATCH 3/4] chore: prune unrelated generated changes
---
.../workflows/prune-refinement-diff-temp.yml | 55 +++++++++++++++++++
1 file changed, 55 insertions(+)
create mode 100644 .github/workflows/prune-refinement-diff-temp.yml
diff --git a/.github/workflows/prune-refinement-diff-temp.yml b/.github/workflows/prune-refinement-diff-temp.yml
new file mode 100644
index 0000000..fe5b57e
--- /dev/null
+++ b/.github/workflows/prune-refinement-diff-temp.yml
@@ -0,0 +1,55 @@
+name: Prune refinement diff
+
+on:
+ push:
+ branches:
+ - apply-web-refinements-20260914
+
+permissions:
+ contents: write
+
+jobs:
+ prune:
+ if: github.actor != 'github-actions[bot]'
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ ref: apply-web-refinements-20260914
+ fetch-depth: 0
+ - name: Restore unrelated generated artifacts
+ shell: bash
+ run: |
+ git fetch origin master
+ paths=(
+ assets/data/conferences.json
+ assets/data/reproducibility-certification.json
+ assets/data/research-graph.json
+ assets/data/scholarly-graph.json
+ assets/data/scholarly-infrastructure.json
+ blog/_generated.md
+ blog/index.xml
+ data/_generated.md
+ includes/about-selected.html
+ open-science/_generated.md
+ reproducibility/_generated.md
+ research-graph/_generated.md
+ software/_generated.md
+ talks/_generated.md
+ teaching/_generated.md
+ )
+ for path in "${paths[@]}"; do
+ if git cat-file -e "origin/master:${path}" 2>/dev/null; then
+ git checkout origin/master -- "$path"
+ else
+ rm -f "$path"
+ git add -A -- "$path" || true
+ fi
+ done
+ rm -f .github/workflows/prune-refinement-diff-temp.yml
+ git config user.name 'github-actions[bot]'
+ git config user.email '41898282+github-actions[bot]@users.noreply.github.com'
+ git add -A
+ git diff --cached --quiet && exit 0
+ git commit -m 'Keep web refinement diff focused'
+ git push origin HEAD:apply-web-refinements-20260914
From 944fb45adf0612448ea940a490eecab31539db1d Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
<41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 14 Sep 2026 15:47:33 +0000
Subject: [PATCH 4/4] Keep web refinement diff focused
---
.../workflows/prune-refinement-diff-temp.yml | 55 -
assets/data/conferences.json | 148 +-
.../data/reproducibility-certification.json | 284 +---
assets/data/research-graph.json | 186 +--
assets/data/scholarly-graph.json | 1269 -----------------
assets/data/scholarly-infrastructure.json | 304 ----
blog/_generated.md | 27 +-
blog/index.xml | 20 -
data/_generated.md | 123 +-
includes/about-selected.html | 10 +-
open-science/_generated.md | 55 -
reproducibility/_generated.md | 8 +-
research-graph/_generated.md | 167 ---
software/_generated.md | 36 +-
talks/_generated.md | 25 +-
teaching/_generated.md | 14 +-
16 files changed, 196 insertions(+), 2535 deletions(-)
delete mode 100644 .github/workflows/prune-refinement-diff-temp.yml
delete mode 100644 assets/data/scholarly-graph.json
delete mode 100644 assets/data/scholarly-infrastructure.json
delete mode 100644 blog/index.xml
delete mode 100644 open-science/_generated.md
delete mode 100644 research-graph/_generated.md
diff --git a/.github/workflows/prune-refinement-diff-temp.yml b/.github/workflows/prune-refinement-diff-temp.yml
deleted file mode 100644
index fe5b57e..0000000
--- a/.github/workflows/prune-refinement-diff-temp.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-name: Prune refinement diff
-
-on:
- push:
- branches:
- - apply-web-refinements-20260914
-
-permissions:
- contents: write
-
-jobs:
- prune:
- if: github.actor != 'github-actions[bot]'
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v4
- with:
- ref: apply-web-refinements-20260914
- fetch-depth: 0
- - name: Restore unrelated generated artifacts
- shell: bash
- run: |
- git fetch origin master
- paths=(
- assets/data/conferences.json
- assets/data/reproducibility-certification.json
- assets/data/research-graph.json
- assets/data/scholarly-graph.json
- assets/data/scholarly-infrastructure.json
- blog/_generated.md
- blog/index.xml
- data/_generated.md
- includes/about-selected.html
- open-science/_generated.md
- reproducibility/_generated.md
- research-graph/_generated.md
- software/_generated.md
- talks/_generated.md
- teaching/_generated.md
- )
- for path in "${paths[@]}"; do
- if git cat-file -e "origin/master:${path}" 2>/dev/null; then
- git checkout origin/master -- "$path"
- else
- rm -f "$path"
- git add -A -- "$path" || true
- fi
- done
- rm -f .github/workflows/prune-refinement-diff-temp.yml
- git config user.name 'github-actions[bot]'
- git config user.email '41898282+github-actions[bot]@users.noreply.github.com'
- git add -A
- git diff --cached --quiet && exit 0
- git commit -m 'Keep web refinement diff focused'
- git push origin HEAD:apply-web-refinements-20260914
diff --git a/assets/data/conferences.json b/assets/data/conferences.json
index 09c2d88..b5db131 100644
--- a/assets/data/conferences.json
+++ b/assets/data/conferences.json
@@ -1,16 +1,15 @@
{
"schema_version": 1,
- "source": "assets/data/publications.json + talks/registry.json",
+ "source": "assets/data/publications.json + talks/registry.json historical records",
"source_updated_at": "2026-09-09T21:07:59.043708+00:00",
- "count": 8,
- "canonical_count": 5,
- "standalone_count": 2,
+ "count": 4,
+ "canonical_count": 3,
"historical_count": 1,
"conferences": [
{
"record_origin": "canonical_profile",
"source_title": "Critical points of natural and anthropogenic pressures and responses in the state of the north--central anchovy stock in the pelagic system of the Peruvian sea",
- "title": "Critical points of natural and anthropogenic pressures and responses in the state of the north-central anchovy stock in the pelagic system of the Peruvian Sea",
+ "title": "Critical points of natural and anthropogenic pressures and responses in the state of the north–central anchovy stock in the pelagic system of the Peruvian Sea",
"year": "2026",
"source_type": "Conference Paper",
"source_url": "https://meetings.pices.int/Publications/Presentations/2026-SPF/POSTER-S05-P19-Recoba-for-Salazar.pdf",
@@ -18,17 +17,15 @@
"source": "ORCID",
"site_path": "/talks/2026-05-08-critical-points-anchovy-stock/",
"date": "2026-05-08",
- "end_date": "",
- "presentation_type": "Poster",
+ "presentation_type": "Poster presentation",
"event": "SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities",
- "location": "La Paz, MX",
+ "location": "La Paz, Baja California Sur, Mexico",
"authors": [
"Elmer Quispe-Salazar",
"Álvaro Recoba",
"Jorge Tam"
],
"presenter": "Álvaro Recoba",
- "presenter_note": "",
"summary": "A threshold-oriented diagnostic of natural and fishing-related pressures and their nonlinear relationships with the multidimensional state of the north-central Peruvian anchovy stock.",
"source_status": "",
"legacy_path": "",
@@ -54,16 +51,14 @@
"source": "ORCID",
"site_path": "/talks/2026-05-06-anchovy-health-index/",
"date": "2026-05-06",
- "end_date": "",
- "presentation_type": "Oral",
+ "presentation_type": "Oral presentation",
"event": "SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities",
- "location": "La Paz, MX",
+ "location": "La Paz, Baja California Sur, Mexico",
"authors": [
"Elmer Quispe-Salazar",
"Jorge Tam"
],
"presenter": "Elmer Quispe-Salazar",
- "presenter_note": "",
"summary": "A multivariate stock-health framework integrating complementary biological, demographic, spatial, and reproductive signals for highly variable small-pelagic populations.",
"source_status": "",
"legacy_path": "",
@@ -78,65 +73,10 @@
}
]
},
- {
- "record_origin": "canonical_profile",
- "source_title": "Bayesian state-space assessment of Peruvian dolphinfish (Coryphaena hippurus)",
- "title": "Bayesian state-space assessment of Peruvian dolphinfish (Coryphaena hippurus)",
- "year": "2026",
- "source_type": "International Technical Presentation",
- "source_url": "https://www.iattc.org/en-US/Event/DetailMeeting/Meeting-DOR-04",
- "doi": "",
- "source": "Career master + IATTC",
- "site_path": "https://www.iattc.org/en-US/Event/DetailMeeting/Meeting-DOR-04",
- "date": "2026-03-12",
- "end_date": "",
- "presentation_type": "Oral",
- "event": "4th IATTC Technical Meeting on Dolphinfish (DOR-04)",
- "location": "San José, CR",
- "authors": [
- "Elmer Quispe-Salazar"
- ],
- "presenter": "Elmer Quispe-Salazar",
- "presenter_note": "",
- "summary": "A Bayesian state-space production assessment of Peruvian dolphinfish integrating standardized CPUE, stock-status inference, biological reference levels, and a pathway toward management strategy evaluation.",
- "source_status": "",
- "legacy_path": "",
- "related_links": [
- {
- "label": "IATTC DOR-04 meeting",
- "url": "https://www.iattc.org/en-US/Event/DetailMeeting/Meeting-DOR-04"
- }
- ]
- },
- {
- "record_origin": "canonical_profile",
- "source_title": "PelagicSurveys: an R package for biometric and biological data from pelagic hydroacoustic surveys",
- "title": "PelagicSurveys: an R package for biometric and biological data from pelagic hydroacoustic surveys",
- "year": "2024",
- "source_type": "Invited Scientific Presentation",
- "source_url": "",
- "doi": "",
- "source": "Career master",
- "site_path": "/talks/",
- "date": "2024-12-12",
- "end_date": "",
- "presentation_type": "Oral",
- "event": "Conecta Pesquero 2024 - III Research, Development and Innovation Meeting, UNALM",
- "location": "Lima, PE",
- "authors": [
- "Elmer Quispe-Salazar"
- ],
- "presenter": "Elmer Quispe-Salazar",
- "presenter_note": "",
- "summary": "Invited presentation on reproducible R workflows for biometric and biological data collected during pelagic-resource hydroacoustic assessment surveys.",
- "source_status": "",
- "legacy_path": "",
- "related_links": []
- },
{
"record_origin": "canonical_profile",
"source_title": "Suitability of the gonadosomatic index in Peruvian Anchoveta (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation",
- "title": "Suitability of the gonadosomatic index in Peruvian anchovy (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation",
+ "title": "Suitability of the gonadosomatic index in Peruvian Anchoveta (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation",
"year": "2024",
"source_type": "Conference Output",
"source_url": "https://www.researchgate.net/doi/10.13140/RG.2.2.32795.73767",
@@ -144,17 +84,15 @@
"source": "ORCID",
"site_path": "/talks/2024-11-11-anchoveta-gsi-sibecorp/",
"date": "2024-11-11",
- "end_date": "",
- "presentation_type": "Oral",
- "event": "VI Ibero-American Symposium on Reproductive Ecology, Recruitment and Fisheries (VI SIBECORP)",
- "location": "Lisbon, PT",
+ "presentation_type": "Conference presentation",
+ "event": "VI Simpósio Ibero-Americano de Ecologia Reprodutiva, Recrutamento e Pesca (VI SIBECORP)",
+ "location": "Lisbon, Portugal",
"authors": [
"Elmer Quispe-Salazar",
"Javier Sánchez"
],
"presenter": "Elmer Quispe-Salazar",
- "presenter_note": "",
- "summary": "An evaluation of the gonadosomatic index as a reproducible indicator of gonadal maturity in Peruvian anchovy, including classification models, critical-threshold estimation, and seasonal variation.",
+ "summary": "An evaluation of the gonadosomatic index as a reproducible indicator of gonadal maturity in Peruvian anchoveta, including classification models, critical-threshold estimation, and seasonal variation.",
"source_status": "",
"legacy_path": "",
"related_links": [
@@ -168,64 +106,10 @@
}
]
},
- {
- "record_origin": "career_master",
- "source_title": "Pelagic community changes associated with the 2023-2024 El Niño in the Humboldt Current Ecosystem off Peru",
- "title": "Pelagic community changes associated with the 2023-2024 El Niño in the Humboldt Current Ecosystem off Peru",
- "year": "2024",
- "source_type": "Conference Abstract",
- "source_url": "",
- "doi": "",
- "source": "IMARPE Book of Abstracts + career master",
- "site_path": "/talks/",
- "date": "2024-05-08",
- "end_date": "2024-05-10",
- "presentation_type": "Oral",
- "event": "Scientific Workshop: El Niño 2023-2024 - Effects and outlook for the Peruvian sea and its living resources",
- "location": "Callao, PE",
- "authors": [
- "Elmer Quispe-Salazar"
- ],
- "presenter": "",
- "presenter_note": "Oral presentation delivered by a colleague; presenter name not yet documented in the public source.",
- "summary": "Changes in species occurrence, spatial distribution, and size composition of the Peruvian pelagic community before, during, and after the 2023-2024 El Niño.",
- "source_status": "Abstract-book contribution, p. 49; oral modality and colleague presentation confirmed by the author.",
- "legacy_path": "",
- "related_links": []
- },
- {
- "record_origin": "career_master",
- "source_title": "Impacts of the 2023-2024 El Niño on Peruvian anchovy population dynamics",
- "title": "Impacts of the 2023-2024 El Niño on Peruvian anchovy population dynamics",
- "year": "2024",
- "source_type": "Conference Abstract",
- "source_url": "",
- "doi": "",
- "source": "IMARPE Book of Abstracts + career master",
- "site_path": "/talks/",
- "date": "2024-05-08",
- "end_date": "2024-05-10",
- "presentation_type": "Oral",
- "event": "Scientific Workshop: El Niño 2023-2024 - Effects and outlook for the Peruvian sea and its living resources",
- "location": "Callao, PE",
- "authors": [
- "Erich Díaz",
- "Pablo Marin",
- "Elmer Quispe-Salazar",
- "Josymar Torrejón",
- "Daniel Grados"
- ],
- "presenter": "Elmer Quispe-Salazar",
- "presenter_note": "",
- "summary": "Population-level effects of the 2023-2024 El Niño on Peruvian anchovy biomass, spatial distribution, demographic structure, recruitment, and resilience.",
- "source_status": "Abstract-book contribution, p. 45; oral modality and Elmer Quispe-Salazar as presenter confirmed by the author.",
- "legacy_path": "",
- "related_links": []
- },
{
"record_origin": "legacy_site",
"source_title": "",
- "title": "Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953-2022) within the Humboldt Current System",
+ "title": "Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953–2022) within the Humboldt Current System",
"year": "2022",
"source_type": "Historical conference contribution",
"source_url": "",
@@ -233,17 +117,15 @@
"source": "Legacy qselmer.github.io record",
"site_path": "/talks/2022-09-01-anchoveta-biomass-variability/",
"date": "2022-09-01",
- "end_date": "",
"presentation_type": "Conference presentation",
"event": "Open Science Conference on Eastern Boundary Upwelling Systems: Past, Present and Future and Second International Conference on the Humboldt Current System",
- "location": "Lima, PE",
+ "location": "Peru",
"authors": [
"E. Díaz",
"P. Marín",
"Elmer Quispe-Salazar"
],
"presenter": "",
- "presenter_note": "",
"summary": "Conference contribution examining anchoveta biomass variability from interannual to multi-decadal scales and its implications for monitoring and management in the Humboldt Current System.",
"source_status": "Historical website record retained from the legacy site. A stable public proceedings or abstract-book source has not yet been verified.",
"legacy_path": "/publication/ebus-hcs-abstract-anchoveta-biomass/",
diff --git a/assets/data/reproducibility-certification.json b/assets/data/reproducibility-certification.json
index ea346e7..e5a5741 100644
--- a/assets/data/reproducibility-certification.json
+++ b/assets/data/reproducibility-certification.json
@@ -12,71 +12,25 @@
"qselmer/oceancube",
"qselmer/humboldt-ocean-watch",
"qselmer/git-github-training",
- "qselmer/.template-training",
- "qselmer/.template-mse",
- "qselmer/oceHCS-environmental-data-workflow",
- "qselmer/fisheries-research-workflows-book"
+ "qselmer/.template-training"
],
"certified_from_level": 2,
"summary": {
- "repositories_assessed": 9,
+ "repositories_assessed": 6,
"certified": 1,
- "not_certified": 8,
+ "not_certified": 5,
"levels": {
- "1": 8,
+ "1": 5,
"3": 1
}
},
"levels": [
- {
- "level": 0,
- "label": "Repository",
- "requirements": [
- "public repository"
- ]
- },
- {
- "level": 1,
- "label": "Documented",
- "requirements": [
- "README/documentation"
- ]
- },
- {
- "level": 2,
- "label": "Reproducible",
- "requirements": [
- "README/documentation",
- "explicit license",
- "CITATION.cff",
- "tests or computational environment"
- ]
- },
- {
- "level": 3,
- "label": "Automated",
- "requirements": [
- "Level 2",
- "continuous integration"
- ]
- },
- {
- "level": 4,
- "label": "Archived",
- "requirements": [
- "Level 3",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "level": 5,
- "label": "Research object",
- "requirements": [
- "Level 4",
- "bounded machine-readable research object with provenance"
- ]
- }
+ {"level": 0, "label": "Repository", "requirements": ["public repository"]},
+ {"level": 1, "label": "Documented", "requirements": ["README/documentation"]},
+ {"level": 2, "label": "Reproducible", "requirements": ["README/documentation", "explicit license", "CITATION.cff", "tests or computational environment"]},
+ {"level": 3, "label": "Automated", "requirements": ["Level 2", "continuous integration"]},
+ {"level": 4, "label": "Archived", "requirements": ["Level 3", "versioned release", "archival DOI"]},
+ {"level": 5, "label": "Research object", "requirements": ["Level 4", "bounded machine-readable research object with provenance"]}
],
"records": [
{
@@ -86,56 +40,11 @@
"status": "certified",
"level": 3,
"level_label": "Automated",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": true,
- "citation_cff": true,
- "citation_orcid": false,
- "tests": true,
- "environment": true,
- "ci": true,
- "release": true,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
+ "assessed_at": "2026-09-11T08:55:00Z",
+ "evidence": {"readme": true, "license": true, "citation_cff": true, "citation_orcid": false, "tests": true, "environment": true, "ci": true, "release": true, "archival_doi": false, "codemeta": false, "zenodo_metadata": false},
"release_tag": "v0.2.0",
"archival_doi": "",
- "next_actions": [
- "archive a stable release and register a DOI",
- "add ORCID to CITATION.cff",
- "add CodeMeta metadata when useful",
- "link release preservation metadata when archived"
- ]
- },
- {
- "repository": "qselmer/.template-mse",
- "url": "https://github.com/qselmer/.template-mse",
- "certificate_id": "QS-RC1-qselmer-template-mse",
- "status": "not-certified",
- "level": 1,
- "level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": true,
- "citation_cff": true,
- "citation_orcid": true,
- "tests": false,
- "environment": false,
- "ci": true,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
- "release_tag": "",
- "archival_doi": "",
- "next_actions": [
- "document a computational environment or add tests",
- "add CodeMeta metadata when useful"
- ]
+ "next_actions": ["archive a stable release and register a DOI", "add ORCID to CITATION.cff", "add CodeMeta metadata when useful", "link release preservation metadata when archived"]
},
{
"repository": "qselmer/.template-training",
@@ -144,56 +53,11 @@
"status": "not-certified",
"level": 1,
"level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": false,
- "citation_cff": true,
- "citation_orcid": true,
- "tests": false,
- "environment": true,
- "ci": true,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
+ "assessed_at": "2026-09-11T08:55:00Z",
+ "evidence": {"readme": true, "license": false, "citation_cff": true, "citation_orcid": true, "tests": false, "environment": true, "ci": true, "release": false, "archival_doi": false, "codemeta": false, "zenodo_metadata": false},
"release_tag": "",
"archival_doi": "",
- "next_actions": [
- "add an explicit license",
- "add CodeMeta metadata when useful"
- ]
- },
- {
- "repository": "qselmer/fisheries-research-workflows-book",
- "url": "https://github.com/qselmer/fisheries-research-workflows-book",
- "certificate_id": "QS-RC1-qselmer-fisheries-research-workflows-book",
- "status": "not-certified",
- "level": 1,
- "level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": false,
- "citation_cff": false,
- "citation_orcid": false,
- "tests": false,
- "environment": false,
- "ci": true,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
- "release_tag": "",
- "archival_doi": "",
- "next_actions": [
- "add an explicit license",
- "add CITATION.cff",
- "document a computational environment or add tests",
- "add CodeMeta metadata when useful"
- ]
+ "next_actions": ["add an explicit license", "add CodeMeta metadata when useful"]
},
{
"repository": "qselmer/git-github-training",
@@ -202,28 +66,11 @@
"status": "not-certified",
"level": 1,
"level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": false,
- "citation_cff": false,
- "citation_orcid": false,
- "tests": false,
- "environment": false,
- "ci": true,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
+ "assessed_at": "2026-09-11T08:55:00Z",
+ "evidence": {"readme": true, "license": false, "citation_cff": false, "citation_orcid": false, "tests": false, "environment": false, "ci": true, "release": false, "archival_doi": false, "codemeta": false, "zenodo_metadata": false},
"release_tag": "",
"archival_doi": "",
- "next_actions": [
- "add an explicit license",
- "add CITATION.cff",
- "document a computational environment or add tests",
- "add CodeMeta metadata when useful"
- ]
+ "next_actions": ["add an explicit license", "add CITATION.cff", "document a computational environment or add tests", "add CodeMeta metadata when useful"]
},
{
"repository": "qselmer/humboldt-ocean-watch",
@@ -232,54 +79,11 @@
"status": "not-certified",
"level": 1,
"level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": true,
- "citation_cff": false,
- "citation_orcid": false,
- "tests": true,
- "environment": true,
- "ci": false,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
- "release_tag": "",
- "archival_doi": "",
- "next_actions": [
- "add CITATION.cff",
- "add CodeMeta metadata when useful"
- ]
- },
- {
- "repository": "qselmer/oceHCS-environmental-data-workflow",
- "url": "https://github.com/qselmer/oceHCS-environmental-data-workflow",
- "certificate_id": "QS-RC1-qselmer-ocehcs-environmental-data-workflow",
- "status": "not-certified",
- "level": 1,
- "level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": true,
- "citation_cff": true,
- "citation_orcid": true,
- "tests": false,
- "environment": false,
- "ci": true,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
+ "assessed_at": "2026-09-11T08:55:00Z",
+ "evidence": {"readme": true, "license": true, "citation_cff": false, "citation_orcid": false, "tests": true, "environment": true, "ci": false, "release": false, "archival_doi": false, "codemeta": false, "zenodo_metadata": false},
"release_tag": "",
"archival_doi": "",
- "next_actions": [
- "document a computational environment or add tests",
- "add CodeMeta metadata when useful"
- ]
+ "next_actions": ["add CITATION.cff", "add CodeMeta metadata when useful"]
},
{
"repository": "qselmer/pel-climate-adaptive-management-paper",
@@ -288,26 +92,11 @@
"status": "not-certified",
"level": 1,
"level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": true,
- "citation_cff": false,
- "citation_orcid": false,
- "tests": false,
- "environment": true,
- "ci": true,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
+ "assessed_at": "2026-09-11T08:55:00Z",
+ "evidence": {"readme": true, "license": true, "citation_cff": false, "citation_orcid": false, "tests": false, "environment": true, "ci": true, "release": false, "archival_doi": false, "codemeta": false, "zenodo_metadata": false},
"release_tag": "",
"archival_doi": "",
- "next_actions": [
- "add CITATION.cff",
- "add CodeMeta metadata when useful"
- ]
+ "next_actions": ["add CITATION.cff", "add CodeMeta metadata when useful"]
},
{
"repository": "qselmer/pelagicPER-availability-risk-paper",
@@ -316,28 +105,11 @@
"status": "not-certified",
"level": 1,
"level_label": "Documented",
- "assessed_at": "2026-09-13T17:15:00Z",
- "evidence": {
- "readme": true,
- "license": false,
- "citation_cff": false,
- "citation_orcid": false,
- "tests": false,
- "environment": false,
- "ci": false,
- "release": false,
- "archival_doi": false,
- "codemeta": false,
- "zenodo_metadata": false
- },
+ "assessed_at": "2026-09-11T08:55:00Z",
+ "evidence": {"readme": true, "license": false, "citation_cff": false, "citation_orcid": false, "tests": false, "environment": false, "ci": false, "release": false, "archival_doi": false, "codemeta": false, "zenodo_metadata": false},
"release_tag": "",
"archival_doi": "",
- "next_actions": [
- "add an explicit license",
- "add CITATION.cff",
- "document a computational environment or add tests",
- "add CodeMeta metadata when useful"
- ]
+ "next_actions": ["add an explicit license", "add CITATION.cff", "document a computational environment or add tests", "add CodeMeta metadata when useful"]
}
],
"policy": {
diff --git a/assets/data/research-graph.json b/assets/data/research-graph.json
index 4af9fe1..dcc0292 100644
--- a/assets/data/research-graph.json
+++ b/assets/data/research-graph.json
@@ -10,77 +10,61 @@
{
"id": "stock-assessment",
"heading": "Stock assessment and population dynamics",
- "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.",
+ "description": "Population-state reconstruction, assessment diagnostics, biological parameters, and methods for understanding how structural assumptions affect fisheries inference.",
"projects": [
"stock-assessment-misspecification"
],
"outputs": [
{
- "id": "talk:2026-05-06:multivariate health index of the anchovy understanding the dynamics of small pelagic fish under environmental variability",
- "type": "Talk",
- "year": "2026",
- "title": "Multivariate Health Index of the anchovy: Understanding the dynamics of small pelagic fish under environmental variability",
- "url": "/talks/2026-05-06-anchovy-health-index/",
- "source": "talks"
- },
- {
- "id": "talk:2026-03-12:bayesian state-space assessment of peruvian dolphinfish coryphaena hippurus",
- "type": "Talk",
- "year": "2026",
- "title": "Bayesian state-space assessment of Peruvian dolphinfish (Coryphaena hippurus)",
- "url": "https://www.iattc.org/en-US/Event/DetailMeeting/Meeting-DOR-04",
- "source": "talks"
- },
- {
- "id": "talk:2024-05-08:impacts of the 2023-2024 el nino on peruvian anchovy population dynamics",
- "type": "Talk",
- "year": "2024",
- "title": "Impacts of the 2023-2024 El Niño on Peruvian anchovy population dynamics",
- "url": "/talks/",
- "source": "talks"
+ "id": "publication:interannual variability in the growth of the northern-central stock of peruvian anchovy engraulis ringens during the period 1960-2022:2025",
+ "type": "Thesis",
+ "year": "2025",
+ "title": "Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022",
+ "url": "/publications/#theses",
+ "source": "publications"
},
{
"id": "talk:2022-09-01:multi-scale variability in the biomass dynamics of the north-central stock of the peruvian anchoveta 1953-2022 within the humboldt current system",
"type": "Talk",
"year": "2022",
- "title": "Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953-2022) within the Humboldt Current System",
+ "title": "Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953–2022) within the Humboldt Current System",
"url": "/talks/2022-09-01-anchoveta-biomass-variability/",
"source": "talks"
}
]
},
{
- "id": "environmental-variability",
- "heading": "Environmental variability and pressure-state relationships",
- "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.",
- "projects": [],
+ "id": "fisheries-dynamics",
+ "heading": "Fisheries dynamics and management",
+ "description": "Fishery season dynamics, fleet reorganization, fishing pressure, management benchmarks, and decision-relevant diagnostics under environmental variability.",
+ "projects": [
+ "season-benchmarking",
+ "pelagic-fishery-reorganization"
+ ],
"outputs": [
{
"id": "talk:2026-05-08:critical points of natural and anthropogenic pressures and responses in the state of the north-central anchovy stock in the pelagic system of the peruvian sea",
"type": "Poster",
"year": "2026",
- "title": "Critical points of natural and anthropogenic pressures and responses in the state of the north-central anchovy stock in the pelagic system of the Peruvian Sea",
+ "title": "Critical points of natural and anthropogenic pressures and responses in the state of the north–central anchovy stock in the pelagic system of the Peruvian Sea",
"url": "/talks/2026-05-08-critical-points-anchovy-stock/",
"source": "talks"
}
]
},
{
- "id": "life-history",
- "heading": "Reproductive biology, growth and condition",
- "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.",
+ "id": "stock-condition",
+ "heading": "Stock condition and reproductive ecology",
+ "description": "Multidimensional stock condition, reproductive indicators, maturity, and biological responses used to describe population state beyond biomass alone.",
"projects": [],
"outputs": [
{
- "id": "publication:interannual variability in the growth of the northern-central stock of peruvian anchovy engraulis ringens during the period 1960-2022:2025",
- "type": "Thesis",
- "year": "2025",
- "title": "Interannual variability in the growth of the Northern-Central stock of Peruvian anchovy (Engraulis ringens) during the period 1960–2022",
- "url": "/publications/#theses",
- "source": "publications"
+ "id": "talk:2026-05-06:multivariate health index of the anchovy understanding the dynamics of small pelagic fish under environmental variability",
+ "type": "Talk",
+ "year": "2026",
+ "title": "Multivariate Health Index of the anchovy: Understanding the dynamics of small pelagic fish under environmental variability",
+ "url": "/talks/2026-05-06-anchovy-health-index/",
+ "source": "talks"
},
{
"id": "publication:classification models based on the gonadosomatic index to determine gonadal maturity stages a case study in the peruvian anchovy engraulis ringens:2025",
@@ -91,112 +75,21 @@
"source": "publications"
},
{
- "id": "talk:2024-11-11:suitability of the gonadosomatic index in peruvian anchovy engraulis ringens sexual maturity a 5 critical threshold and seasonal variation",
+ "id": "talk:2024-11-11:suitability of the gonadosomatic index in peruvian anchoveta engraulis ringens sexual maturity a 5 critical threshold and seasonal variation",
"type": "Talk",
"year": "2024",
- "title": "Suitability of the gonadosomatic index in Peruvian anchovy (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation",
+ "title": "Suitability of the gonadosomatic index in Peruvian Anchoveta (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation",
"url": "/talks/2024-11-11-anchoveta-gsi-sibecorp/",
"source": "talks"
}
]
},
- {
- "id": "spatial-biodiversity",
- "heading": "Spatial ecology, species distribution and biodiversity",
- "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.",
- "projects": [],
- "outputs": [
- {
- "id": "talk:2024-05-08:pelagic community changes associated with the 2023-2024 el nino in the humboldt current ecosystem off peru",
- "type": "Talk",
- "year": "2024",
- "title": "Pelagic community changes associated with the 2023-2024 El Niño in the Humboldt Current Ecosystem off Peru",
- "url": "/talks/",
- "source": "talks"
- },
- {
- "id": "publication:critical appraisal of research approaches to inform evidence of connectivity of trachurus murphyi - a systematic review of 11 topics:2024",
- "type": "Report",
- "year": "2024",
- "title": "Critical appraisal of research approaches to inform evidence of connectivity of Trachurus murphyi – a systematic review of 11 topics",
- "url": "/publications/#reports",
- "source": "publications"
- },
- {
- "id": "publication:habitat conditions of jack mackerel trachurus murphyi and chub mackerel scomber japonicus in the peruvian sea between 2021 and 2023:2023",
- "type": "Report",
- "year": "2023",
- "title": "Habitat conditions of jack mackerel (Trachurus murphyi) and chub mackerel (Scomber japonicus) in the Peruvian sea between 2021 and 2023",
- "url": "/publications/#reports",
- "source": "publications"
- }
- ]
- },
- {
- "id": "fisheries-dynamics",
- "heading": "Fisheries dynamics and adaptive 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": [
- "season-benchmarking",
- "pelagic-fishery-reorganization",
- "climate-adaptive-management",
- "availability-risk"
- ],
- "outputs": [
- {
- "id": "publication:north-central peruvian anchovy stock status and 2026 first-season exploitation outlook:2026",
- "type": "Report",
- "year": "2026",
- "title": "North-central Peruvian anchovy stock status and 2026 first-season exploitation outlook",
- "url": "/publications/#reports",
- "source": "publications"
- },
- {
- "id": "publication:decision-table protocol for seasonal catch advice in the north-central peruvian anchovy fishery:2026",
- "type": "Report",
- "year": "2026",
- "title": "Decision-table protocol for seasonal catch advice in the north-central Peruvian anchovy fishery",
- "url": "/publications/#reports",
- "source": "publications"
- },
- {
- "id": "publication:southern peruvian anchovy status and 2026 first-season exploitation outlook:2025",
- "type": "Report",
- "year": "2025",
- "title": "Southern Peruvian anchovy status and 2026 first-season exploitation outlook",
- "url": "/publications/#reports",
- "source": "publications"
- },
- {
- "id": "publication:north-central peruvian anchovy status and 2025 second-season exploitation outlook:2025",
- "type": "Report",
- "year": "2025",
- "title": "North-central Peruvian anchovy status and 2025 second-season exploitation outlook",
- "url": "/publications/#reports",
- "source": "publications"
- },
- {
- "id": "publication:jack mackerel fishery status in 2025 and exploitation outlook for 2026:2025",
- "type": "Report",
- "year": "2025",
- "title": "Jack mackerel fishery status in 2025 and exploitation outlook for 2026",
- "url": "/publications/#reports",
- "source": "publications"
- }
- ]
- },
{
"id": "scientific-computing",
- "heading": "Scientific computing and research software",
- "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.",
+ "heading": "Statistical ecology and scientific computing",
+ "description": "Reusable statistical methods, research software, reproducible workflows, and marine-data infrastructure developed to support quantitative ecological analysis.",
"projects": [
- "fishcore-software-paper",
- "fisheries-mse-template",
- "hcs-environmental-data-workflow",
- "fisheries-research-workflows-book"
+ "fishcore-software-paper"
],
"outputs": [
{
@@ -214,26 +107,9 @@
"title": "humboldt-ocean-watch",
"url": "/software/humboldt-ocean-watch/",
"source": "software"
- },
- {
- "id": "talk:2024-12-12:pelagicsurveys an r package for biometric and biological data from pelagic hydroacoustic surveys",
- "type": "Talk",
- "year": "2024",
- "title": "PelagicSurveys: an R package for biometric and biological data from pelagic hydroacoustic surveys",
- "url": "/talks/",
- "source": "talks"
}
]
}
],
- "unclassified_outputs": [
- {
- "id": "publication:the joint jack mackerel jjm model a user guide to imarpe s proposal:2024",
- "type": "Report",
- "year": "2024",
- "title": "The Joint Jack Mackerel (JJM) model: a user guide to IMARPE's proposal",
- "url": "/publications/#reports",
- "source": "publications"
- }
- ]
+ "unclassified_outputs": []
}
diff --git a/assets/data/scholarly-graph.json b/assets/data/scholarly-graph.json
deleted file mode 100644
index 50ab63d..0000000
--- a/assets/data/scholarly-graph.json
+++ /dev/null
@@ -1,1269 +0,0 @@
-{
- "schema_version": 1,
- "graph_id": "qselmer-unified-scholarly-graph",
- "public_only": true,
- "person": "person:elmer-quispe-salazar",
- "source_contract": {
- "canonical_publications": "ORCID/Crossref public mirror",
- "metrics": "ORCID/OpenAlex public metrics mirror",
- "repositories": "GitHub metadata filtered through curated public registries",
- "curated_relations": "graph/registry.json + projects/registry.json",
- "forbidden": "Raw repository catalogue and private-repository metadata are never serialized into this graph"
- },
- "sources": [
- "config/site.json",
- "graph/registry.json",
- "projects/registry.json",
- "assets/data/publications.json",
- "assets/data/conferences.json",
- "assets/data/software.json",
- "assets/data/teaching.json",
- "blog/registry.json",
- "assets/data/research-metrics.json"
- ],
- "public_repository_allowlist": [
- "qselmer/.template-mse",
- "qselmer/.template-training",
- "qselmer/fisheries-research-workflows-book",
- "qselmer/git-github-training",
- "qselmer/humboldt-ocean-watch",
- "qselmer/oceHCS-environmental-data-workflow",
- "qselmer/oceancube",
- "qselmer/pel-climate-adaptive-management-paper",
- "qselmer/pelagicPER-availability-risk-paper"
- ],
- "stats": {
- "nodes": 48,
- "edges": 81,
- "by_kind": {
- "Person": 1,
- "Post": 1,
- "Poster": 1,
- "Project": 9,
- "Publication": 10,
- "Repository": 9,
- "Software": 2,
- "Talk": 7,
- "Teaching": 2,
- "Theme": 6
- },
- "unlinked_outputs_to_project": 23
- },
- "featured": {
- "project": "project:stock-assessment-misspecification",
- "paper": "publication:doi:10.3989/scimar.05636.117",
- "software": "software:github:qselmer/oceancube",
- "talk": "talk:2026-05-06:multivariate-health-index-of-the-anchovy-understanding-the-dynamics-of-small-pelagic-fish-under-environmental-variability"
- },
- "nodes": [
- {
- "id": "person:elmer-quispe-salazar",
- "kind": "Person",
- "title": "Elmer Quispe-Salazar",
- "canonical_url": "https://qselmer.github.io/",
- "visibility": "public",
- "identifiers": {
- "orcid": "0000-0001-9229-6379",
- "github": "https://github.com/qselmer",
- "google_scholar": "https://scholar.google.com/citations?user=wz83egoAAAAJ"
- },
- "metrics": {
- "citations": 0,
- "h_index": 0,
- "i10_index": 0,
- "orcid_works": 5,
- "openalex_works": 3
- },
- "provenance": [
- {
- "source": "config/site.json",
- "authority": "curated"
- },
- {
- "source": "assets/data/research-metrics.json",
- "authority": "ORCID + OpenAlex"
- }
- ]
- },
- {
- "id": "post:statistical-distributions-fisheries-marine-ecology",
- "kind": "Post",
- "title": "Statistical distributions for fisheries and marine ecology",
- "year": "2026",
- "canonical_url": "https://qselmer.github.io/blog/statistical-distributions-fisheries-marine-ecology/",
- "visibility": "public",
- "topic": "Statistical ecology",
- "summary": "A practical guide to choosing probability distributions for common response variables in fisheries and marine ecology.",
- "provenance": [
- {
- "source": "blog/registry.json",
- "authority": "curated"
- }
- ]
- },
- {
- "id": "talk:2026-05-08:critical-points-of-natural-and-anthropogenic-pressures-and-responses-in-the-state-of-the-north-central-anchovy-stock-in-the-pelagic-system-of-the-peruvian-sea",
- "kind": "Poster",
- "title": "Critical points of natural and anthropogenic pressures and responses in the state of the north-central anchovy stock in the pelagic system of the Peruvian Sea",
- "year": "2026",
- "canonical_url": "https://qselmer.github.io/talks/2026-05-08-critical-points-anchovy-stock/",
- "visibility": "public",
- "event": "SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities",
- "presentation_type": "Poster",
- "summary": "A threshold-oriented diagnostic of natural and fishing-related pressures and their nonlinear relationships with the multidimensional state of the north-central Peruvian anchovy stock.",
- "provenance": [
- {
- "source": "assets/data/conferences.json",
- "authority": "ORCID"
- }
- ]
- },
- {
- "id": "project:climate-adaptive-management",
- "kind": "Project",
- "title": "Climate-adaptive management of small pelagic fisheries in upwelling systems",
- "canonical_url": "https://github.com/qselmer/pel-climate-adaptive-management-paper",
- "visibility": "public",
- "status": "Systematic evidence synthesis",
- "summary": "Systematic evidence synthesis evaluating management responses to environmental variability and climate change and their transferability to Peruvian anchovy.",
- "provenance": [
- {
- "source": "projects/registry.json",
- "authority": "curated"
- }
- ],
- "repository": "qselmer/pel-climate-adaptive-management-paper"
- },
- {
- "id": "project:stock-assessment-misspecification",
- "kind": "Project",
- "title": "Diagnosing stock-assessment model misspecification with machine learning",
- "canonical_url": "https://qselmer.github.io/projects/stock-assessment-misspecification/",
- "visibility": "public",
- "status": "Methods development",
- "summary": "Simulation-estimation experiments testing whether multivariate diagnostics can identify structural sources of stock-assessment misspecification.",
- "provenance": [
- {
- "source": "projects/registry.json",
- "authority": "curated"
- }
- ]
- },
- {
- "id": "project:fisheries-research-workflows-book",
- "kind": "Project",
- "title": "Digital workflows for fisheries science and quantitative ecology",
- "canonical_url": "https://qselmer.github.io/fisheries-research-workflows-book/",
- "visibility": "public",
- "status": "Open book in development",
- "summary": "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.",
- "provenance": [
- {
- "source": "projects/registry.json",
- "authority": "curated"
- }
- ],
- "repository": "qselmer/fisheries-research-workflows-book"
- },
- {
- "id": "project:availability-risk",
- "kind": "Project",
- "title": "Dynamic environmental availability and biological risk in pelagic fisheries",
- "canonical_url": "https://github.com/qselmer/pelagicPER-availability-risk-paper",
- "visibility": "public",
- "status": "Planned study",
- "summary": "Framework separating resource availability, biological risk, operational risk, and regulation using environmental and fishery information with hindcast validation.",
- "provenance": [
- {
- "source": "projects/registry.json",
- "authority": "curated"
- }
- ],
- "repository": "qselmer/pelagicPER-availability-risk-paper"
- },
- {
- "id": "project:fisheries-mse-template",
- "kind": "Project",
- "title": "Fisheries Management Strategy Evaluation template",
- "canonical_url": "https://github.com/qselmer/.template-mse",
- "visibility": "public",
- "status": "Stable reusable template",
- "summary": "Reusable architecture for operating, observation and estimation models, management procedures, closed-loop simulation, uncertainty scenarios, performance metrics, provenance, and reproducible MSE projects.",
- "provenance": [
- {
- "source": "projects/registry.json",
- "authority": "curated"
- }
- ],
- "repository": "qselmer/.template-mse"
- },
- {
- "id": "project:hcs-environmental-data-workflow",
- "kind": "Project",
- "title": "Humboldt Current environmental data workflow",
- "canonical_url": "https://github.com/qselmer/oceHCS-environmental-data-workflow",
- "visibility": "public",
- "status": "Development workflow",
- "summary": "Reproducible acquisition, quality control, harmonization, derivation, cataloguing, provenance, and reuse of environmental data for fisheries and marine-ecology analyses across the Humboldt Current System.",
- "provenance": [
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diff --git a/assets/data/scholarly-infrastructure.json b/assets/data/scholarly-infrastructure.json
deleted file mode 100644
index f49b0ae..0000000
--- a/assets/data/scholarly-infrastructure.json
+++ /dev/null
@@ -1,304 +0,0 @@
-{
- "schema_version": 1,
- "phase": 9,
- "title": "Scholarly Visibility, Interoperability & Preservation",
- "public_only": true,
- "identity": {
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- "web_of_science": "https://www.webofscience.com/wos/author/record/AEA-6138-2022",
- "github": "https://github.com/qselmer"
- },
- "affiliation": {
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- "acronym": "IMARPE",
- "url": "https://www.imarpe.gob.pe/",
- "ror": "https://ror.org/01gbk3827",
- "verification_source": "https://revistas.imarpe.gob.pe/index.php/boletin/contacto"
- },
- "identifier_coverage": {
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- "profile_outputs_with_doi": 3,
- "formal_outputs": 10,
- "formal_outputs_with_doi": 2
- },
- "repositories": [
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- "url": "https://github.com/qselmer/.template-mse",
- "role": "Project",
- "readiness_level": 1,
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- "citation_cff": true,
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- "ci": true,
- "environment": false,
- "release": "",
- "archival_doi": "",
- "gaps": [
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- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/fisheries-research-workflows-book",
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- "citation_orcid": false,
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- "gaps": [
- "license",
- "CITATION.cff",
- "CodeMeta",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/oceHCS-environmental-data-workflow",
- "url": "https://github.com/qselmer/oceHCS-environmental-data-workflow",
- "role": "Project",
- "readiness_level": 1,
- "readiness_label": "Documented",
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- "citation_orcid": true,
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- "license": "MIT",
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- "environment": false,
- "release": "",
- "archival_doi": "",
- "gaps": [
- "CodeMeta",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/pel-climate-adaptive-management-paper",
- "url": "https://github.com/qselmer/pel-climate-adaptive-management-paper",
- "role": "Project",
- "readiness_level": 1,
- "readiness_label": "Documented",
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- "license": "MIT",
- "tests": false,
- "ci": true,
- "environment": true,
- "release": "",
- "archival_doi": "",
- "gaps": [
- "CITATION.cff",
- "CodeMeta",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/pelagicPER-availability-risk-paper",
- "url": "https://github.com/qselmer/pelagicPER-availability-risk-paper",
- "role": "Project",
- "readiness_level": 1,
- "readiness_label": "Documented",
- "citation_cff": false,
- "citation_orcid": false,
- "codemeta": false,
- "license": "",
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- "ci": false,
- "environment": false,
- "release": "",
- "archival_doi": "",
- "gaps": [
- "license",
- "CITATION.cff",
- "CodeMeta",
- "CI",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/humboldt-ocean-watch",
- "url": "https://github.com/qselmer/humboldt-ocean-watch",
- "role": "Software",
- "readiness_level": 1,
- "readiness_label": "Documented",
- "citation_cff": false,
- "citation_orcid": false,
- "codemeta": false,
- "license": "MIT",
- "tests": true,
- "ci": false,
- "environment": true,
- "release": "",
- "archival_doi": "",
- "gaps": [
- "CITATION.cff",
- "CodeMeta",
- "CI",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/oceancube",
- "url": "https://github.com/qselmer/oceancube",
- "role": "Software",
- "readiness_level": 3,
- "readiness_label": "Automated",
- "citation_cff": true,
- "citation_orcid": false,
- "codemeta": false,
- "license": "MIT",
- "tests": true,
- "ci": true,
- "environment": true,
- "release": "v0.2.0",
- "archival_doi": "",
- "gaps": [
- "ORCID in citation metadata",
- "CodeMeta",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/.template-training",
- "url": "https://github.com/qselmer/.template-training",
- "role": "Teaching",
- "readiness_level": 1,
- "readiness_label": "Documented",
- "citation_cff": true,
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- "release": "",
- "archival_doi": "",
- "gaps": [
- "license",
- "CodeMeta",
- "versioned release",
- "archival DOI"
- ]
- },
- {
- "repository": "qselmer/git-github-training",
- "url": "https://github.com/qselmer/git-github-training",
- "role": "Teaching",
- "readiness_level": 1,
- "readiness_label": "Documented",
- "citation_cff": false,
- "citation_orcid": false,
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- "license": "",
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- "gaps": [
- "license",
- "CITATION.cff",
- "CodeMeta",
- "versioned release",
- "archival DOI"
- ]
- }
- ],
- "readiness_distribution": {
- "1": 8,
- "3": 1
- },
- "standards": {
- "person": [
- "ORCID",
- "Schema.org Person"
- ],
- "organization": [
- "ROR",
- "Schema.org Organization"
- ],
- "publications": [
- "DOI",
- "Schema.org ScholarlyArticle"
- ],
- "software": [
- "CITATION.cff",
- "CodeMeta",
- "GitHub release",
- "archival DOI when available"
- ],
- "preservation": [
- "versioned release",
- "persistent identifier",
- "archival repository"
- ],
- "research_objects": [
- "RO-Crate when a project has a bounded reusable research object"
- ]
- },
- "reproducibility_levels": [
- {
- "level": 0,
- "label": "Repository",
- "criterion": "Public repository exists."
- },
- {
- "level": 1,
- "label": "Documented",
- "criterion": "Repository has usable documentation."
- },
- {
- "level": 2,
- "label": "Reproducible inputs",
- "criterion": "Documentation plus explicit license, citation metadata, and computational environment or tests."
- },
- {
- "level": 3,
- "label": "Automated",
- "criterion": "Level 2 plus continuous integration or an equivalent automated validation workflow."
- },
- {
- "level": 4,
- "label": "Archived release",
- "criterion": "Level 3 plus a versioned release and archival persistent identifier."
- },
- {
- "level": 5,
- "label": "Research object",
- "criterion": "Level 4 plus a bounded, machine-readable research object with provenance."
- }
- ],
- "machine_interfaces": [
- "https://qselmer.github.io/assets/data/scholarly-graph.json",
- "https://qselmer.github.io/assets/data/scholarly-infrastructure.json"
- ],
- "source_contract": {
- "identity": "config/site.json + assets/data/research-metrics.json",
- "outputs": "assets/data/publications.json",
- "repository_evidence": "assets/data/repository-scholarly-metadata.json",
- "policy": "scholarly/registry.json",
- "no_identifier_invention": true
- }
-}
diff --git a/blog/_generated.md b/blog/_generated.md
index 6e974fc..d2f93ac 100644
--- a/blog/_generated.md
+++ b/blog/_generated.md
@@ -1,22 +1,17 @@
```{=html}
-
-```
-
-## Statistical ecology {#statistical-ecology}
-
-```{=html}
-
-
-
-
-
-
Statistical distributions for fisheries and marine ecology. A practical guide to choosing probability distributions for common response variables in fisheries and marine ecology. TopicStatistical ecologyLevelIntermediateRead8 minUpdatedSep 9, 2026
Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis.
Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis.
-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 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.
-
-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.
-
-```
-
-## 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.
-
-```
-
-## Spatial ecology, species distribution and biodiversity {#spatial-biodiversity}
-
-```{=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.
-
-```
-
-## Stock assessment and population dynamics {#stock-assessment}
-
-```{=html}
-
-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.
-
-```
-
-## Provenance and graph contract {#provenance}
-
-The graph is generated from public scholarly mirrors and curated website registries. Repository metadata enters the public graph only after it has been selected for a public Project, Software, or Teaching catalogue. ORCID and OpenAlex contribute public scholarly records and metrics; the raw repository catalogue is not serialized into this website graph.
diff --git a/software/_generated.md b/software/_generated.md
index a91462b..5fa5ace 100644
--- a/software/_generated.md
+++ b/software/_generated.md
@@ -3,34 +3,34 @@
## Software packages I am a lead developer for {#packages}
```{=html}
-
-
-
-
oceancube
-
-
oceancube. Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis. Repository·Documentation·Project page.TypeR packageStageStableLanguageRReleasev0.2.0
Validated R infrastructure for representing, inspecting, subsetting, extracting, visualizing, and transforming multidimensional ocean data cubes for reproducible marine analysis.
-
-
+
```
## Research applications I develop {#applications}
```{=html}
-
-
-
-
HOW
-
-
humboldt-ocean-watch. Python and Streamlit system for reproducible thermal monitoring of Niño 1+2 using validated local analytics, quality control, event diagnostics, and optional grounded scientific briefs. Repository·Project page.TypeApplicationStageExperimentalLanguagePythonReleaseUnreleased
Python and Streamlit system for reproducible thermal monitoring of Niño 1+2 using validated local analytics, quality control, event diagnostics, and optional grounded scientific briefs.
-
-
+
```
## Incubating and concept-stage work {#incubating}
+These records are preserved for continuity but are not presented as released or validated scientific software.
+
- [`seasignals`](/software/seasignals/) - Public R-package repository exists, but its current README is still a package skeleton with placeholder installation and example sections.
- [Pelagytics](/software/pelagytics/) - Concept and prototype only; no canonical public repository has been verified.
diff --git a/talks/_generated.md b/talks/_generated.md
index 2429bdb..a95cae3 100644
--- a/talks/_generated.md
+++ b/talks/_generated.md
@@ -1,26 +1,15 @@
-
+## Oral presentations {#oral}
-## Conference talks {#conference-talks}
+- **Quispe-Salazar, E.** & Tam, J. (2026, May 6). Multivariate Health Index of the anchovy: Understanding the dynamics of small pelagic fish under environmental variability. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, Baja California Sur, Mexico. TypeOralVideopublicDetailspage
-- **Quispe-Salazar, E.** & Tam, J. (2026, May 6). Multivariate Health Index of the anchovy: Understanding the dynamics of small pelagic fish under environmental variability. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, MX. TypeOralLocationLa Paz, MXDetailspage
+## Poster presentations {#posters}
-- **Quispe-Salazar, E.** (2026, March 12). Bayesian state-space assessment of Peruvian dolphinfish (Coryphaena hippurus). *4th IATTC Technical Meeting on Dolphinfish (DOR-04)*, San José, CR. TypeOralLocationSan José, CRDetailspage
+- **Quispe-Salazar, E.**, Recoba, Á., & Tam, J. (2026, May 8). Critical points of natural and anthropogenic pressures and responses in the state of the north–central anchovy stock in the pelagic system of the Peruvian Sea. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, Baja California Sur, Mexico. TypePosterMaterialPDFDetailspage
-- **Quispe-Salazar, E.** (2024, December 12). PelagicSurveys: an R package for biometric and biological data from pelagic hydroacoustic surveys. *Conecta Pesquero 2024 - III Research, Development and Innovation Meeting, UNALM*, Lima, PE. TypeOralLocationLima, PE
+## Other conference presentations {#other}
-- **Quispe-Salazar, E.** & Sánchez, J. (2024, November 11). Suitability of the gonadosomatic index in Peruvian anchovy (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation. *VI Ibero-American Symposium on Reproductive Ecology, Recruitment and Fisheries (VI SIBECORP)*, Lisbon, PT. TypeOralLocationLisbon, PTDetailspage
+- **Quispe-Salazar, E.** & Sánchez, J. (2024, November 11). Suitability of the gonadosomatic index in Peruvian Anchoveta (Engraulis ringens): Sexual maturity, a 5% critical threshold, and seasonal variation. *VI Simpósio Ibero-Americano de Ecologia Reprodutiva, Recrutamento e Pesca (VI SIBECORP)*, Lisbon, Portugal. TypeConferenceDOI10.13140/rg.2.2.32795.73767MaterialpublicDetailspage
-- **Quispe-Salazar, E.** (2024, May 8-10). Pelagic community changes associated with the 2023-2024 El Niño in the Humboldt Current Ecosystem off Peru. *Scientific Workshop: El Niño 2023-2024 - Effects and outlook for the Peruvian sea and its living resources*, Callao, PE. TypeOralLocationCallao, PE
-
-- Díaz, E., Marin, P., **Quispe-Salazar, E.**, Torrejón, J., & Grados, D. (2024, May 8-10). Impacts of the 2023-2024 El Niño on Peruvian anchovy population dynamics. *Scientific Workshop: El Niño 2023-2024 - Effects and outlook for the Peruvian sea and its living resources*, Callao, PE. TypeOralLocationCallao, PE
-
-- Díaz, E., Marín, P., & **Quispe-Salazar, E.** (2022, September 1). Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953-2022) within the Humboldt Current System. *Open Science Conference on Eastern Boundary Upwelling Systems: Past, Present and Future and Second International Conference on the Humboldt Current System*, Lima, PE. LocationLima, PEDetailspage
-
-## Posters {#posters}
-
-- **Quispe-Salazar, E.**, Recoba, Á., & Tam, J. (2026, May 8). Critical points of natural and anthropogenic pressures and responses in the state of the north-central anchovy stock in the pelagic system of the Peruvian Sea. *SPF-2026 International Symposium: Navigating Changes in Small Pelagic Fish and Forage Communities*, La Paz, MX. TypePosterLocationLa Paz, MXDetailspage
+- Díaz, E., Marín, P., & **Quispe-Salazar, E.** (2022, September 1). Multi-scale variability in the biomass dynamics of the north-central stock of the Peruvian anchoveta (1953–2022) within the Humboldt Current System. *Open Science Conference on Eastern Boundary Upwelling Systems: Past, Present and Future and Second International Conference on the Humboldt Current System*, Peru. TypeConferenceDetailspage
diff --git a/teaching/_generated.md b/teaching/_generated.md
index c06e8a8..9f94bbb 100644
--- a/teaching/_generated.md
+++ b/teaching/_generated.md
@@ -1,17 +1,9 @@
-## Courses and workshops {#courses}
+## Courses and training {#courses}
-```{=html}
-
-
GIT & GITHUB. Structured teaching materials, practices, and reusable resources for learning Git and GitHub through a progressive version-control workflow. Duration: Multi-session ·Materials: Lessons, practices & cheatsheets.Teaching page·Repository.RoleInstructorAudienceBeginnersLanguageSpanish
-
-```
+- git-github-training. Structured teaching materials, practices, and reusable resources for learning Git and GitHub through a progressive version-control workflow. TypeCourse materialsStatusActiveLanguageRTeachingpageRepositoryGitHub
## Teaching infrastructure {#infrastructure}
-```{=html}
-
-
SCIENTIFIC TRAINING TEMPLATE. Reusable Quarto structure for classes, workshops, short courses, technical training, and semester teaching, with modules, labs, exercises, metadata, and reproducible publishing. Duration: Reusable ·Materials: Quarto modules, labs & exercises.Repository.RoleTemplate developerAudienceInstructorsLanguageSpanish
-
-```
+- Scientific Training Template. Reusable Quarto structure for classes, workshops, short courses, technical training, and semester teaching, with modules, labs, exercises, metadata, and reproducible publishing. TypeTeaching templateStatusReusable templateLanguagePythonRepositoryGitHub
++- -
-