Each colored line represents the period over which a single chicken flock was present on the farm, with the color code indicating the production type, which may vary during the course of the flock …
Three different outbreak timings are considered: same month (left), one month prior (middle), and two months prior (right). Two different classes of flock size are considered: small,<17 chickens …
Three different outbreak timings are considered: same month (left), one month prior (middle), and two months prior (right). Two different classes of flock size are considered: small (top) and large …
For the AI vaccination model (green) these covariates are flock size (n) (A), age (t) (B) and calendar time (T) (C). For the disinfection model (orange), the covariate is calendar time (T) (D). …
Continuous variable | Min | 1st quartile | Median | 3rd quartile | Max |
---|---|---|---|---|---|
Broiler chicken flocks (n = 391) | |||||
Number of flocks of broiler chickens per farm | 2 | 22 | 36 | 44 | 75 |
Number of observation months per broiler flock | 1 | 3 | 4 | 5 | 12 |
Broiler chicken flock-months (n = 1656) | |||||
Flock size (n) (number of birds) | 2 | 10 | 16 | 35 | 580 |
Anticipated age at maturity (t*) (weeks) | 9.5 | 13.1 | 17.4 | 19.6 | 43.6 |
Age at the time of observation (t) (weeks) | 1.6 | 6.3 | 12.3 | 19 | 53.6 |
Difference t- t* (δt) (week) | −37.2 | −11.1 | −5.2 | 1 | 36.1 |
Calendar time (T) | 3 | 7 | 11 | 16 | 20 |
Proportion harvested (%) | 0 | 0 | 0 | 33.3 | 100 |
Number of chicken flocks introduced in the same month onto the same farm | 0 | 0 | 0 | 1 | 4 |
Number of chicken flocks introduced in the month prior onto the same farm | 0 | 0 | 0 | 1 | 2 |
Number of broiler chickens present on the same farm in other flocks (bird) | 0 | 10 | 25 | 61 | 900 |
Number of broiler ducks present on the same farm (bird) | 0 | 0 | 0 | 25 | 3630 |
Number of broiler Muscovy ducks present on the same farm (bird) | 0 | 0 | 0 | 6 | 80 |
Number of layer chickens present on the same farm (bird) | 0 | 2 | 6 | 13 | 350 |
Number of layer ducks present on the same farm (bird) | 0 | 0 | 0 | 0 | 11 |
Number of layer Muscovy ducks present on the same farm (bird) | 0 | 0 | 0 | 2 | 30 |
Farm-months (n = 876) | |||||
Number of broiler chickens (bird) | 0 | 8 | 28 | 64 | 912 |
Number of broiler ducks (bird) | 0 | 0 | 4 | 31 | 3630 |
Number of broiler Muscovy ducks (bird) | 0 | 0 | 0 | 6 | 80 |
Number of layer chickens farm (bird) | 0 | 0 | 4 | 10 | 358 |
Number of layer ducks (bird) | 0 | 0 | 0 | 0 | 500 |
Number of layer Muscovy ducks (bird) | 0 | 0 | 0 | 2 | 30 |
Proportion flocks farmed with disinfection (%) | 0 | 0 | 100 | 100 | 100 |
Qualitative variable | Proportion of observations | ||||
Broiler chicken flock-months (n = 1656) | |||||
Occurrence of outbreak with no sudden death in chickens on the same farm in the current month | 18.8% | ||||
Occurrence of outbreak with sudden death in chickens on the same farm in the current month | 1.6% | ||||
Occurrence of outbreak in other species on the same farm in the current month | 7.2% | ||||
Confinement indoors or in enclosure | 32.8% | ||||
Previously vaccinated for AI | 20.2% | ||||
Previously vaccinated for Newcastle Disease | 7.1% | ||||
Farm-months (n = 876) | |||||
Occurrence of outbreak in any species | 23.4% |
Model | Variable | Odds-ratio (with 95% CI) | p-value | ||
---|---|---|---|---|---|
Harvest | Flock size ≤ 16 chickens | ONS chickens* | Same month | 2.06 (1.23; 3.45) | <10-2 |
−1 month | 2.06 (1.17; 3.62) | 0.02 | |||
−2 months | 0.41 (0.19; 0.92) | 0.03 | |||
OS chickens** | Same month | 9.34 (2.13; 40.94) | <10-2 | ||
−1 month | 0.18 (0.01; 4.95) | 0.32 | |||
−2 months | 0.88 (0.15; 5.04) | 0.89 | |||
Number of broiler chickens in the farm (square root) | 1.05 (1; 1.11) | 0.06 | |||
combined effect of the difference between current age and age at maturity () and the age at maturity () (spline transformation) | Figure 2 | <10-3 | |||
Flock size > 16 chickens | OS chickens** | Same month | 1.02 (0.23; 4.46) | 0.98 | |
−1 month | 3.89 (0.82; 18.46) | 0.09 | |||
−2 months | 3.1 (0.51; 18.77) | 0.22 | |||
Number of broiler chickens in the farm (square root) | 1.05 (1; 1.11) | 0.05 | |||
combined effect of the difference between current age and age at maturity () and the age at maturity () (spline transformation) | Figure 2 | <10-3 | |||
AI vaccination | Outbreak chickens | Same month | 0.75 (0.29–1.92) | 0.55 | |
−1 month | 0.78 (0.29–2.11) | 0.63 | |||
−2 months | 0.27 (0.08–0.89) | 0.04 | |||
Outbreak others | Same month | 4.62 (1.08–19.72) | 0.04 | ||
−1 month | 0.51 (0.09–2.89) | 0.45 | |||
−2 months | 0.42 (0.06–2.91) | 0.39 | |||
Number of broiler chickens in the farm (square root) | 0.92 (0.82–1.03) | 0.2 | |||
Number of broiler Muscovy ducks in the farm (square root) | 0.74 (0.57–0.96) | 0.03 | |||
Number of layer ducks in the farm (square root) | 2.95 (1.15–7.57) | 0.03 | |||
Number of layer Muscovy ducks in the farm (square root) | 1.9 (1.07–3.36) | 0.03 | |||
Confinement | 24.6 (6.32–95.6) | <10-3 | |||
Proportion harvested | 0.01 (0–0.37) | 0.02 | |||
Spline transform of the logarithm of the flock size () | Figure 3A | <10-3 | |||
Spline transform of the logarithm of the flock age () | Figure 3B | <10-3 | |||
Spline transform of the calendar time () | Figure 3C | <10-3 | |||
Disinfection | Number of broiler Muscovy ducks in the farm (square root) | 1.07 (1.01–1.13) | 0.02 | ||
Number of layer ducks in the farm (square root) | 1.25 (1.02–1.53) | 0.04 | |||
Number of layer chickens in the farm (square root) | 1.3 (1.12–1.51) | <10-3 | |||
Spline transform of the calendar time () | Figure 3D | <10-3 |
* ONS: Outbreak with no sudden deaths.
** OS: Outbreak with sudden deaths.
Destination | No outbreak | Outbreak with no sudden death (ONS) | Outbreak with sudden death (OS) |
---|---|---|---|
Sale to traders | 28% | 45% | 45% |
Sale at market | 5% | 16% | 0% |
Sale to other farmers | 2% | 3% | 0% |
Sale unspecified | 12% | 4% | 11% |
Slaughter at home | 36% | 20% | 11% |
Gift | 5% | 8% | 11% |
Feed farmed pythons | 5% | 1% | 22% |
Other | 7% | 3% | 0% |
Fitted parameters of the original broiler chicken harvest model.
Fitted parameters of the broiler chicken harvest model with aggregated effects of outbreaks with and without sudden deaths.