--- title: "Bus-Route Surveys" output: rmarkdown::html_vignette: highlight: null vignette: > %\VignetteIndexEntry{Bus-Route Surveys} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r setup, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ``` ## What is a Bus-Route Survey? A bus-route survey visits multiple access points (sites) in a fixed route, called a circuit. Unlike an access-point creel survey that stations an interviewer at one location for the day, a bus-route crew travels the circuit repeatedly, counting and interviewing anglers at each site as they pass through. Sites are not sampled uniformly. Instead, each site is assigned a selection probability proportional to its expected fishing effort: high-use sites appear in the sampling frame with higher probability and are therefore visited more often, while low-use sites appear with lower probability. This deliberate, probability-proportional-to-size design is what makes valid inference possible. Two types of data are collected during each visit: - **Enumeration counts** — every angler party at the site is counted (`n_counted`). - **Interviews** — a subset of parties is interviewed to collect effort and catch data (`n_interviewed`). The ratio `n_counted / n_interviewed` (the enumeration expansion factor) scales the interviewed catch and effort up to represent all parties at the site, including those not interviewed. Without this expansion, busy sites are systematically underrepresented in the total estimate. The statistical framework follows Malvestuto et al. (1978) and Jones & Pollock (2012, Chapter 19). tidycreel implements the general Horvitz-Thompson estimators from that chapter directly. ## Key Concepts ### Inclusion Probability (πᵢ) The inclusion probability πᵢ is the probability that a given sampling unit (site × period combination) is included in the sample. For a two-stage bus-route design: $$\pi_i = p\_site_i \times p\_period$$ where `p_site` is the probability of selecting site _i_ in a given pass, and `p_period` is the probability that the period containing the visit is sampled. Sites with higher expected effort get higher `p_site` values, meaning they are selected more often — and correspondingly receive a lower inverse-probability weight in the estimator. The inclusion probability πᵢ belongs to the *sampling design*, not to a site or its anglers. Specify it when designing the survey; do not compute it from the interview data. ### Enumeration Counts During each circuit pass, the crew counts every visible angler party at the site (`n_counted`) and then interviews as many as possible (`n_interviewed`). When not all parties are interviewed, the expansion factor $$\text{expansion} = \frac{n\_counted}{n\_interviewed}$$ rescales the interviewed data so it represents all parties. If all parties are interviewed (n_counted = n_interviewed), the expansion is 1 and no adjustment is needed. This is the case in Malvestuto (1996) Box 20.6 Example 1, used in this vignette. ### Horvitz-Thompson Estimator The total effort estimator (Jones & Pollock 2012, Eq. 19.4) is: $$\hat{E} = \sum_i \frac{e_i}{\pi_i}$$ where $e_i = \text{hours\_fished}_i \times \text{expansion}_i$ is the enumeration-expanded effort for interview _i_. Each site's contribution is weighted by the reciprocal of its inclusion probability. A site sampled with probability 0.20 receives weight 5 — five times the weight of a site sampled with probability 1.0. This inverse-probability weighting is what makes the estimator statistically unbiased. The harvest estimator (Jones & Pollock 2012, Eq. 19.5) follows the same structure: $$\hat{H} = \sum_i \frac{h_i}{\pi_i}$$ ## A Note on Existing Implementations Some R packages that support bus-route surveys hardcode $\pi_i = 0.5$ or compute the inclusion probability as `wait_time / circuit_time`. Neither is the inclusion probability as defined by Horvitz-Thompson theory or by Jones & Pollock (2012). Using an incorrect $\pi_i$ produces biased estimates whose magnitude of bias grows with the heterogeneity of site probabilities. tidycreel computes $\pi_i = p\_site \times p\_period$ directly from the sampling frame you supply to `creel_design()`. This matches the primary source definition in Jones & Pollock (2012, p. 912) and the worked example in Malvestuto (1996, Box 20.6). The implementation is validated against that published example in the package test suite. ## Step-by-Step Example We demonstrate the full bus-route workflow using the data from Malvestuto (1996) Box 20.6, Example 1 — a four-site, single-circuit survey with 15 interviews over four days. ### Step 1: Define the Sampling Design The sampling frame specifies the four sites, their selection probabilities (`p_site`), and the period sampling probability (`p_period`). Site probabilities must sum to 1.0 within each circuit. ```{r design} library(tidycreel) # Sampling frame: 4 sites, 1 circuit # p_site values are proportional to expected fishing effort at each site sampling_frame <- data.frame( site = c("A", "B", "C", "D"), circuit = "circ1", p_site = c(0.30, 0.25, 0.40, 0.05), # must sum to 1.0 p_period = 0.50 # uniform period sampling ) # Inclusion probability: pi_i = p_site * p_period # Site A: 0.30 * 0.50 = 0.15 # Site B: 0.25 * 0.50 = 0.125 # Site C: 0.40 * 0.50 = 0.20 # Site D: 0.05 * 0.50 = 0.025 # Survey calendar: 4 weekdays calendar <- data.frame( date = as.Date(c("2024-06-01", "2024-06-02", "2024-06-03", "2024-06-04")), day_type = "weekday" ) # Build the bus-route design design <- creel_design( calendar, date = date, strata = day_type, survey_type = "bus_route", sampling_frame = sampling_frame, site = site, circuit = circuit, p_site = p_site, p_period = p_period ) print(design) ``` The design object stores the sampling frame and precomputes πᵢ for each site×circuit combination. Site C has the highest selection probability (p_site = 0.40) and therefore the highest πᵢ (0.20), which means its interviews will carry lower inverse-probability weight than Site D's (πᵢ = 0.025). ### Step 2: Attach Interview Data Each row of interview data represents one interviewed party. The `n_counted` and `n_interviewed` columns record how many parties were at the site vs. how many were actually interviewed. In this example both are equal (no expansion needed), but the columns must still be supplied for bus-route designs. ```{r interviews} # 15 interviews across 4 sites and 4 days # Site A: 4 interviews (all 4 parties interviewed) # Site B: 3 interviews (all 3 parties) # Site C: 6 interviews (all 6 parties) — highest effort site # Site D: 2 interviews (all 2 parties) interviews_raw <- data.frame( date = as.Date(c( "2024-06-01", "2024-06-01", "2024-06-02", "2024-06-02", # Site A "2024-06-01", "2024-06-02", "2024-06-03", # Site B "2024-06-01", "2024-06-02", "2024-06-03", # Site C (rows 1-3) "2024-06-03", "2024-06-04", # Site C (rows 4-5) "2024-06-03", "2024-06-04", # Site D "2024-06-03" # Site C (row 6) )), day_type = "weekday", site = c( "A", "A", "A", "A", "B", "B", "B", "C", "C", "C", "C", "C", "D", "D", "C" ), circuit = "circ1", hours_fished = c( 7.5, 7.5, 7.5, 7.5, # Site A: 4 x 7.5 = 30 h total 20.0 / 3, 20.0 / 3, 20.0 / 3, # Site B: 3 x 6.67 = 20 h total 57.5 / 6, 57.5 / 6, 57.5 / 6, # Site C rows 1-3 57.5 / 6, 57.5 / 6, # Site C rows 4-5 2.5, 2.5, # Site D: 2 x 2.5 = 5 h total 57.5 / 6 # Site C row 6: total = 57.5 h ), fish_kept = c( 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L ), fish_caught = c( 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L ), n_counted = c( 4L, 4L, 4L, 4L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 2L, 2L, 6L ), n_interviewed = c( 4L, 4L, 4L, 4L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 2L, 2L, 6L ), trip_status = "complete" ) # Attach interviews — pi_i is joined automatically from the sampling frame design <- add_interviews( design, interviews_raw, effort = hours_fished, catch = fish_caught, harvest = fish_kept, n_counted = n_counted, n_interviewed = n_interviewed, trip_status = trip_status ) print(design) ``` `add_interviews()` joins πᵢ from the sampling frame to each interview row (stored as `.pi_i`) and computes the enumeration expansion factor (`.expansion = n_counted / n_interviewed`). These are used internally by the estimation functions. ### Step 3: Estimate Effort `estimate_effort()` dispatches to the bus-route estimator and computes $\hat{E} = \sum(e_i / \pi_i)$. ```{r effort} # Estimate total angler-hours effort_est <- estimate_effort(design) print(effort_est) # Inspect per-site contributions to the total site_contribs <- get_site_contributions(effort_est) print(site_contribs) ``` The site contributions table shows exactly how each site's effort feeds into the total. Site C (πᵢ = 0.20, total effort = 57.5 h) contributes 57.5 / 0.20 = 287.5 angler-hours to the total — the largest single-site contribution, reflecting its high effort despite the relatively frequent sampling. Site D (πᵢ = 0.025, total effort = 5 h) contributes 5 / 0.025 = 200 angler-hours. Though Site D has little observed effort, its low sampling probability means it represents a much larger population of fishing activity. The total E_hat = 847.5 angler-hours matches Malvestuto (1996) Box 20.6 Example 1 exactly. ### Step 4: Estimate Harvest `estimate_harvest_rate()` applies the same Horvitz-Thompson logic to fish kept. ```{r harvest} # Estimate total fish kept (harvest) harvest_est <- estimate_harvest_rate(design) print(harvest_est) # Estimate total catch (kept + released) catch_est <- estimate_total_catch(design) print(catch_est) ``` ## Validation The effort estimate above (E_hat = 847.5 angler-hours) reproduces the published result from Malvestuto (1996) Box 20.6 Example 1 exactly. This agreement is verified by the package test suite in `tests/testthat/test-primary-source-validation.R`. Each of the four site contributions matches: | Site | e_i (h) | πᵢ | e_i / πᵢ | |------|---------|-------|----------| | A | 30.0 | 0.150 | 200.0 | | B | 20.0 | 0.125 | 160.0 | | C | 57.5 | 0.200 | 287.5 | | D | 5.0 | 0.025 | 200.0 | | **Total** | | | **847.5** | ## References - Jones, C. M., & Pollock, K. H. (2012). Recreational survey methods: estimation of effort, harvest, and abundance. Chapter 19 in *Fisheries Techniques* (3rd ed.), pp. 883–919. American Fisheries Society. - Malvestuto, S. P. (1996). Sampling the recreational angler. Chapter 20 in *Fisheries Techniques* (2nd ed.), pp. 591–623. American Fisheries Society. - Malvestuto, S. P., Davies, W. D., & Shelton, W. L. (1978). An evaluation of the roving creel survey with nonuniform probability sampling. *Transactions of the American Fisheries Society*, 107(2), 255–262.