tidycreel

Tidy Interface for Creel Survey Design, Estimation, and Reporting

tidycreel provides a pipe-friendly interface for creel survey design, data management, estimation, visualisation, and reporting. Built on the survey package for design-based inference, it lets fisheries biologists work in creel vocabulary — dates, strata, counts, effort, catch, lengths, schedules — without managing survey-package internals directly.

Installation

install.packages("tidycreel")

Or the development version from GitHub:

# install.packages("pak")
pak::pak("chrischizinski/tidycreel")

# or with devtools
devtools::install_github("chrischizinski/tidycreel")

Survey Types

Key Capabilities

• Design-based inference — wraps the survey package; biologists write creel vocabulary, not survey-package internals.
• Single design entry point — creel_design() dispatches to the correct workflow for each survey type.
• Core estimation surface — effort, catch rate, harvest rate, release rate, and total-catch estimators share a common API.
• Extended estimation methods — camera effort indexing, NB GLMM count imputation, weighted length distributions, mark-recapture population and harvest estimators (Petersen, Schnabel), and exploitation rate from tag returns (Pollock et al.).
• Stratification auditing — audit_strata(), simulate_strata_collapse(), and reallocate_strata() diagnose stratum weights, inclusion probabilities, and coverage; test collapse scenarios before committing to a redesign.
• Validation and cleaning — field-level validation, species standardisation, data-validation summaries, and toy datasets for examples.
• Planning and QA — schedule generation, count-window planning, completeness checks, sample-size tools, and power calculators.
• Visualisation and reporting — autoplot() methods, theme_creel(), creel_palette(), a Quarto Creel Report template scaffold, and the legacy flexdashboard scaffold.
• Documentation and onboarding — glossary, workflow vignettes, statistical-method articles, and a pkgdown site.

Quick Start

Instantaneous Count Survey

library(tidycreel)

# 1. Define survey structure with tidy selectors
design <- creel_design(example_calendar, date = date, strata = day_type)

# 2. Attach count observations
design <- add_counts(design, example_counts)

# 3. Estimate effort with design-based variance
estimate_effort(design)

Bus-Route Survey

# Probability-proportional-to-size site selection
design <- creel_design(
  example_calendar,
  date = date,
  strata = day_type,
  survey_type = "bus_route",
  sampling_frame = my_site_frame,
  site = site_id
)

design <- add_interviews(design, interview_data,
  catch = catch_total,
  effort = hours_fished,
  harvest = catch_kept
)

estimate_catch_rate(design)

Where to Start

Functions at a Glance

Survey Design

• creel_design() — single entry point; dispatches on survey_type.
• add_counts(), add_interviews(), add_catch(), add_lengths(), add_ages(), add_sections() — attach observation data.

Estimation

• estimate_effort() — total effort with Taylor linearization, bootstrap, or jackknife variance.
• estimate_catch_rate(), estimate_harvest_rate(), estimate_release_rate() — ratio-based interview estimators.
• estimate_total_catch(), estimate_total_harvest(), estimate_total_release() — totals via delta-method propagation.
• est_effort_camera(), est_length_distribution(), est_mean_length(), est_age_distribution(), est_mean_age() — camera effort indexing and weighted size- and age-structure estimation.
• estimate_exploitation_rate() — exploitation rate from tag returns (Pollock et al.; simple and T-weighted stratified paths).
• estimate_angler_n() — Petersen and Schnabel mark-recapture population size estimators.
• estimate_mr_harvest() — population-scale total harvest from mark-recapture data.

Validation and Diagnostics

• validate_creel_data(), validation_report(), standardize_species() — clean and validate real-world creel inputs.
• validate_incomplete_trips(), validate_design(), check_completeness(), compare_variance(), adjust_nonresponse() — QA and estimator diagnostics.
• audit_strata(), simulate_strata_collapse(), reallocate_strata() — stratification diagnostics; verify weights, simulate collapse scenarios, and rebalance allocations.

Planning and Reporting

• generate_schedule(), generate_bus_schedule(), generate_count_times(), attach_count_times() — planning/scheduling helpers.
• creel_n_effort(), creel_n_cpue(), creel_n_camera(), creel_power(), cv_from_n() — sample-size and power tools.
• season_summary(), summary.creel_estimates(), write_estimates() — report-ready summary/export helpers.
• autoplot.creel_estimates(), autoplot.creel_schedule(), autoplot.creel_length_distribution(), theme_creel(), creel_palette() — visualisation helpers.

Vignettes

All vignettes ship with the package — open one with vignette("<name>", package = "tidycreel"). They are also published at https://chrischizinski.com/tidycreel/articles/.

Get Started

Survey Types

Estimation

Reporting & Planning

Statistical Methods

Ecosystem

Getting Help and Reporting Bugs

Questions about usage

If you have questions about which survey type to use, how to interpret results, or how to structure your data, the best place to start is GitHub Discussions:

https://github.com/chrischizinski/tidycreel/discussions

GitHub Discussions works like a threaded forum attached to the repository. If you do not already have a GitHub account, you can create one for free at https://github.com/signup — it only requires an email address. Once signed in, click New discussion, select the Q&A category, and describe what you are trying to do. Searching existing threads first is worth a moment; your question may already have an answer.

Reporting a bug or unexpected result

If a function returns an error, produces a result that does not look right, or behaves differently from what the documentation describes, please open a GitHub Issue:

https://github.com/chrischizinski/tidycreel/issues

Step-by-step for first-time GitHub users:

1. Go to the Issues link above. If you are not signed in, click Sign in in the top-right corner (or Sign up if you do not yet have an account).
2. Click the green New issue button.
3. Select the Bug report template — it will open a pre-filled form.
4. Fill in each section of the form:
   • Survey type — which design you are using (instantaneous, bus_route, ice, camera, or aerial)
   • tidycreel version — run packageVersion("tidycreel") in R and paste the result (e.g., 1.6.0)
   • What you expected — describe the output or behavior you expected
   • What actually happened — paste the full error message, or describe the result that does not look right
   • Reproducible example — a short R snippet that shows the problem (see below)
5. Click Submit new issue at the bottom of the form.

Writing a reproducible example

The single most useful thing you can include is a short, self-contained R snippet that demonstrates the problem without needing your real data. Use the package’s built-in example datasets (example_calendar, example_counts, example_interviews, etc.) wherever possible, or create a small data frame that triggers the issue.

A good example looks like this:

library(tidycreel)

design <- creel_design(example_calendar, date = date, strata = day_type)
design <- add_counts(design, example_counts)

# The call that produces the unexpected result
estimate_effort(design)
#> Error: ...  (paste the full error message here)

The snippet should run from scratch without any additional files or setup. If reducing your data to a minimal example is not straightforward, share what you have and describe the context — that is still very helpful. The reprex package can automatically format and share R output if you want a polished submission: install it with install.packages("reprex") and run reprex::reprex() around your code.

For guidance on contributing code, requesting new features, or the development workflow, see CONTRIBUTING.md.

License

MIT License — see LICENSE.md for details.

AI Use Acknowledgement

Artificial intelligence coding assistants were used during the development of tidycreel, including for code refinement, consistency across functions, GitHub Actions workflows, error checking, code review, and the development of testing infrastructure.

All functions and analytical outputs have been reviewed by the author team and validated against real-world creel survey data and expected analytical behavior. Despite these review and testing efforts, errors may still occur. If you identify a problem or unexpected result, please submit an issue so that it can be reviewed and addressed.

mirror server hosted at Truenetwork, Russian Federation.