Reproducible software, methods and workflows, technical protocols, reports, and scientific paper repositories developed by the Dirección de Investigaciones del Subsistema Pelágico (DIPEL) of the Instituto del Mar del Perú (IMARPE). The organization uses GitHub to document and maintain scientific methods, source code, report-generation systems, reusable software, reproducible research, and institutional standards for pelagic fisheries research and stock assessment.
Repositories associated with a particular species, stock, or assessment unit follow the structure:
speciesSTOCK-analysis-or-product-repository-type
The species and stock codes are written together, without a hyphen. The remaining components are separated with hyphens and describe the analytical purpose and repository class.
<species><STOCK>-<analysis-or-product>-<repository-type>
| Component | Format | Function | Examples |
|---|---|---|---|
species |
Lowercase abbreviation | Identifies the species or resource group | anc, jjm, spb, cdf, pcm, pel |
STOCK |
Uppercase abbreviation | Identifies the stock, assessment unit, or geographic domain | NC, SUR, TP, SP |
analysis-or-product |
Lowercase kebab-case | Describes the method, model, indicator, process, or product | cpue-standardization, survey-indicators, stock-assessment |
repository-type |
Controlled final term | Identifies the principal function expressed by the repository name | protocol, manual, workflow, report, dashboard, app, paper |
The repository name is descriptive; the canonical classification is the GitHub type-* topic defined in TOPICS.md.
| Code | Resource |
|---|---|
anc |
Peruvian anchovy |
jjm |
Jack mackerel / jurel |
spb |
Bonito |
cdf |
Common dolphinfish / perico |
pcm |
Pacific chub mackerel / caballa |
pel |
Pelagic resources |
| Code | Assessment unit |
|---|---|
NC |
North–central stock or assessment unit |
SUR |
Southern stock or assessment unit |
TP |
National Peruvian assessment domain |
SP |
Peruvian stock |
The precise biological and geographic definition of each assessment unit should also be documented in the corresponding repository README and metadata.
cdfTP-cpue-sdmtmb-workflow
│ │ │ │
│ │ │ └──────── repository type: reproducible method/workflow
│ │ │
│ │ └──────────────── analytical method: CPUE standardization using sdmTMB
│ │
│ └──────────────────────── stock or management unit: Peruvian national domain
│
└─────────────────────────── species: common dolphinfish / perico
Packages, organization-level repositories, templates, handbooks, and websites are exempt from the species–stock prefix when their scope covers multiple resources or the organization as a whole. Examples include pelagicSurvey, PBPtools, .handbook, and dipel-imarpe.github.io. New resource-scoped repositories should use lowercase kebab-case after the species+stock prefix. Legacy names remain valid links but should be migrated only after dependency review.
| Section | Content | Access |
|---|---|---|
| 📦 Packages | Reusable R, Python, Julia, C++, and other scientific software | View section |
| 📘 Protocols & manuals | Standardized methodological protocols, technical manuals, operational manuals, and procedures | View section |
| 🔁 Methods & workflows | Reproducible scientific methods and computational workflows | View section |
| 📄 Reports | Reproducible resource, stock-assessment, monitoring, operational, and technical reports | View section |
| 📊 Dashboards & apps | Interactive visual products and applications | View section |
| ✍️ Papers | Scientific-paper reproducibility repositories, including approved external member-owned repositories | View section |
| 🏛 Institutional repositories | Templates, handbook, profile, workflows, website, and organization infrastructure | View section |
Data policy: DIPEL's scientific data infrastructure is separate from GitHub and may contain very large datasets (for example, hundreds of gigabytes). Raw, confidential, sensitive, restricted, or operational institutional datasets are not represented as a GitHub repository type. GitHub is used for source code, documentation, metadata, schemas, configurations, reproducible examples, simulated or small approved example datasets, and instructions for accessing authorized institutional data sources.
Reusable software and analytical tools for marine and fisheries research.
| Repository | Main purpose | Primary language | Access |
|---|---|---|---|
PBPtools |
Herramientas para procesar, analizar y visualizar datos del Programa de Bitácoras de Pesca (PBP) en R. | R | Repository |
pelagicSurvey |
PelagicSurvey | R | Repository |
popeProjection |
PopeProjection | R | Repository |
retroSurvey |
RetroSurvey | R | Repository |
TAC |
TAC | R | Repository |
TBE |
Automatization tools for IMARPE's Pelagic Acoustic Surveys data analysis and biomass estimation | R | Repository |
Scientific protocols, methodological standards, technical and operational manuals, standardized procedures, and digitization guidance. Both protocols and manuals use the canonical topic type-protocol.
| Repository | Species | Stock / management unit | Main purpose | Primary language | Access |
|---|---|---|---|---|---|
ancNC-tac-decision-table-protocol |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
Tac decision table | TeX | Repository |
jjmSP-stock-assessment-protocol |
Jack mackerel (Trachurus murphyi) | Peruvian stock (SP) |
Stock assessment | TeX | Repository |
pelTP-ebfp-fishery-protocol |
Pelagic resources | Peruvian management unit (TP) |
Manuals for digitization of biological and fisheries information developed under the project "Estimation of Biological and Fishery Parameters (EBFP)" | TeX | Repository |
Reproducible scientific methods and computational workflows used for technical and research applications.
| Repository | Species | Stock / management unit | Main purpose | Primary language | Access |
|---|---|---|---|---|---|
anchNC-NicheModel-workflow |
— | — | NicheModel | R | Repository |
anchNC-standardization-CPUE-workflow |
— | — | Standardization CPUE | R | Repository |
ancNC-catch-at-length-workflow |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
Construye vectores de captura a la talla anchoveta NC ponderados al desembarque, cualquier unidad y periodo de tiempo | R | Repository |
ancNC-mse-workflow |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
Reproducible Management Strategy Evaluation workflow for the North-Central stock of Peruvian anchovy (Engraulis ringens). | Python | Repository |
ancNC-recruiment-workflow |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
Recruiment | R | Repository |
ancNC-SPiCT-stock-assessment-workflow |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
SPiCT stock assessment | R | Repository |
ancNC-ss3-stock-assessment-workflow |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
Ss3 stock assessment | Scheme | Repository |
ancNC-survey-indicators-workflow |
Peruvian anchovy (Engraulis ringens) | North–central stock (NC) |
Survey indicators | R | Repository |
ancSUR-cpue-standardization-workflow |
Peruvian anchovy (Engraulis ringens) | Southern stock (SUR) |
Cpue standardization | R | Repository |
cdfTP-cpue-sdmtmb-workflow |
Common dolphinfish (Coryphaena hippurus) | Peruvian management unit (TP) |
Reproducible workflow for standardizing common dolphinfish CPUE using sdmTMB. | R | Repository |
EnvirData |
— | — | EnvirData | R | Repository |
spbTP-selectivity-at-size-workflow |
Pacific bonito (Sarda chiliensis) | Peruvian management unit (TP) |
Selectivity at size | R | Repository |
Reproducible report-generation repositories for stock/resource assessments, monitoring, operational, institutional, and other technical reports. All use the canonical topic type-report.
| Repository | Main purpose | Primary language | Access |
|---|---|---|---|
ancNC-national-assessment-report |
Evaluación del stock norte-centro de la anchoveta basada en cruceros | R | Repository |
ancSUR-national-assessment-report |
National assessment | R | Repository |
cdfTP-national-assessment-report |
Evaluación de referencia con el modelo JABBA | R | Repository |
pcmTP-national-assessment-report |
National assessment | Visual Basic 6.0 | Repository |
spbTP-national-assessment-report |
National assessment | Scheme | Repository |
Interactive dashboards, applications, and visual tools.
No repositories currently registered.
Reproducibility repositories directly associated with scientific papers.
| Repository | Ownership / relationship | Main purpose | DOI | Primary language | Access |
|---|---|---|---|---|---|
ancNC-selectivity-length-paper |
DIPEL-IMARPE | Selectivity length | — | R | Repository |
Templates, handbook, profile, workflows, environments, website, and institutional infrastructure.
| Repository | Main purpose | Primary language | Access |
|---|---|---|---|
.github |
.github | Markdown | Repository |
.handbook |
.handbook | Markdown | Repository |
.template_analytical_processes |
Template for reproducible analytical workflows in DIPEL-IMARPE | R | Repository |
dipel-imarpe.github.io |
Imarpe.github.io | HTML | Repository |
Each scientific or analytical repository should include, as applicable:
- A concise statement of its scientific or operational purpose.
- The species, stock, assessment unit, and geographic scope when relevant.
- Input-data requirements, the authoritative data source, and access restrictions without copying restricted institutional datasets into GitHub.
- A description of the method or workflow and its principal outputs.
- Reproducibility instructions, including software and package versions.
- A minimal executable example using public, simulated, anonymized, aggregated, or otherwise approved small data.
- The responsible technical team, citation information, license, and contribution rules.
- Explicit links to upstream/downstream DIPEL repositories when the product depends on, generates, or documents another repository, for example
workflow → report → paper. - A root
CITATION.cfffor citable software and paper repositories when the repository itself is a scholarly output.
DIPEL-IMARPE
Dirección de Investigaciones del Subsistema Pelágico · Instituto del Mar del Perú