runjags:an R package providing interface utilities, model templates, parallel computing methods and additional distributions for MCMC models in JAGS

The runjags package provides a set of interface functions to facilitate running Markov chain Monte Carlo models in JAGS from within R. Automated calculation of appropriate convergence and sample length diagnostics, user-friendly access to commonly used graphical outputs and summary statistics, and parallelized methods of running JAGS are provided. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. Automated simulation study functions are implemented to facilitate model performance assessment, as well as drop-k type cross-validation studies, using high performance computing clusters such as those provided by parallel. A module extension for JAGS is also included within runjags, providing the Pareto family of distributions and a series of minimally-informative priors including the DuMouchel and half-Cauchy priors. This paper outlines the primary functions of this package, and gives an illustration of a simulation study to assess the sensitivity of two equivalent model formulations to different prior distributions

Selection of Meat Inspection Data for an Animal Welfare Index in Cattle and Pigs in Denmark

National welfare indices of cattle and pigs are constructed in Denmark, and meat inspection data may be used to contribute to these. We select potentially welfare-relevant abattoir recordings and assess the sources of variation within these with a view towards inclusion in the indices. Meat inspection codes were pre-selected based on expert judgement of having potential animal welfare relevance. Random effects logistic regression was then used to determine the magnitude of variation derived at the level of the farm or abattoir, of which farm variation might be associated with welfare, whereas abattoir variation is most likely caused by differences in recording practices. Codes were excluded for use in the indices based on poor model fit or a large abattoir effect. There was a large abattoir effect for most of the codes modelled and these codes were deemed to be not appropriate to be carried forward to the welfare index. A few were found to be potentially useful for a welfare index: Eight for slaughter pigs, 15 for sows, five for cattle <18 months of age, and six for older cattle. The absolute accuracy of each code/combination could not be assessed, only the relative variation between farms and abattoirs

Farm-level risk factors for Fasciola hepatica infection in Danish dairy cattle

Recent studies suggest that liver fluke (Fasciola hepatica) infections in cattle have increased in Denmark in recent years. This study aimed to identify potential farm level risk factors for liver fluke infection in Danish dairy farms using two different diagnostic methods. Based on liver condemnation data of all individual cattle slaughtered in Denmark, 145 and 77 farms were selected as cases and matched controls. The selection criteria were; 1) minimum 50 animals were slaughtered in 2013, 2) minimum three cases of liver condemnation due to liver flukes in 2013 (case) / no history of liver condemnation due to liver flukes for the last three years (control), and 3) control farms were located within 10 km from the case farms. Bulk tank milk (BTM) samples from the farms were analysed using enzyme-linked immunosorbent assay (ELISA), and telephone interviews were used to obtain information on the type of production, the farmers’ knowledge about liver fluke infection, grazing pattern, anthelmintic treatments and management routines. Preliminary results based on 132 case and 64 control farms indicate that grazing was significantly associated with liver fluke infection (p=0.006). However, in 12 case herds, grazing was not applied (all-in systems), suggesting indoor rearing does not completely prevent liver fluke infections, although misdiagnosis or incorrect registration at slaughter is possible. The percentage of farms allowing heifers to graze on wet areas was significantly higher in case than control farms (p<0.001). Using grazing for heifers and drinking from natural waterways were associated with liver fluke infections (p=0.07 and p=0.01). Approximately 30% of case farms tried actively to avoid infection by anthelmintic treatment or preventive management measures. The prevalences of liver flukes estimated by BTM ELISA were 75% and 12.5% for case and control groups, respectively. The negative ELISA results in some of the case herds may be due to their low in-herd prevalence, but it is still under investigation. Based on the risk analysis, we expect grazing management can be improved on many infected farms as part of the control of liver fluke. The substantial discrepancy between different diagnostic methods should be taken into account for future studies

Comparison of recording of pericarditis and lung disorders at routine meat inspection with findings at systematic health monitoring in Danish finisher pigs

BACKGROUND: The use of secondary data is widespread in a range of surveillance and monitoring applications because of the low cost and high availability associated with this form of data. However, as they are often collected for quite unrelated purposes, they are not necessarily fit for the new purpose that is required of them. Routine meat inspection data were originally collected with the purpose of safeguarding food, but have been re-tasked to also include animal welfare assessment. The objective of the present study was to compare the recording of pericarditis, pleuritis and lungs with lesions at routine meat inspection (RMI) with those performed at systematic health monitoring (SHM) in Danish pigs at slaughter, in order to assess the usefulness of RMI for monitoring the prevalence of these diseases. Data originating from 165 Danish pig herds were collected in the period September 2011 to November 2013. From each herd, a batch consisting of all pigs slaughtered on a specific day from a specific farm were included as the RMI data, while lungs and hearts sampled from the batches were used for the SHM. The RMI data and SHM data included recordings related to a) chronic pericarditis, b) chronic pleuritis and c) lung lesions. The proportion of carcases with a specific disease recording was estimated for each batch of pigs, and linear regression was used to relate the RMI-proportion to the SHM-proportion for the conditions mentioned above. RESULTS: The coefficients of determination (R(2)) were estimated as R(2)(,pericarditis) = 0.16; R(2)(,pleuritis) = 0.67; R(2)(,lungs with lesions) = 0.40. R(2)(,pericarditis) changed to 0.42 when the regression analysis included inspection type at the abattoir (with purely visual inspection of the hearts versus traditional inspection including an incision into the heart). CONCLUSIONS: Overall, the results suggest that the correlation between findings at RMI and SHM was moderate for pleuritis and lungs with lesions, but poor for pericarditis. The latter could partly be explained by the type of meat inspection conducted at the abattoir. We conclude that caution should be used whenever RMI data are used for purposes other than those for which they were originally intended

Equine Cyathostominae can develop to infective third-stage larvae on straw bedding

Background Domesticated grazing animals including horses and donkeys are frequently housed using deep litter bedding systems, where it is commonly presumed that there is no risk of infection from the nematodes that are associated with grazing at pasture. We use two different approaches to test whether equids could become infected with cyathostomines from the ingestion of deep litter straw bedding. Methods Two herbage plot studies were performed in horticultural incubators set up to simulate three straw bedding scenarios and one grass turf positive control. Faeces were placed on 16 plots, and larval recoveries performed on samples of straw/grass substrate over 2- to 3-week periods. Within each incubator, a thermostat was set to maintain an environmental temperature of approximately 10 °C to 20 °C. To provide further validation, 24 samples of straw bedding were collected over an 8-week period from six barns in which a large number of donkeys were housed in a deep litter straw bedding system. These samples were collected from the superficial bedding at 16 sites along a “W” route through each barn. Results No infective larvae were recovered from any of the plots containing dry straw. However, infective cyathostomine larvae were first detected on day 8 from plots containing moist straw. In the straw bedding study, cyathostomine larvae were detected in 18 of the 24 samples. Additionally, in the two barns which were sampled serially, the level of larval infectivity generally increased from week to week, except when the straw bedding was removed and replaced. Conclusions We have demonstrated that equine cyathostomines can develop to infective larvae on moist straw bedding. It is therefore possible for a horse or donkey bedded in deep litter straw to become infected by ingesting the contaminated straw. This has implications for parasite control in stabled equids and potentially in housed ruminants, and further investigation is required in order to establish the relative infective pressure from pasture versus straw bedding

Associations between Antibacterial Treatment and the Prevalence of Tail- Biting-Related Sequelae in Danish Finishers at Slaughter

Secondary infections as a result of tail biting cause substantial economic losses in pig production and are a subject of concern for animal welfare. The use of first-choice antibacterial agents in the treatment of tail biting in finishing pigs is hypothesized to be negatively correlated with the development of systemic infection. This would be expected to reduce the prevalence of post-mortem pyemic sequelae (such as osteomyelitis and abscesses) in finishers with tail-bite lesions. We performed a register-based study that included three Danish databases, holding information on the purchase of antibacterials at herd level (VetStat), herd demographics (Central Husbandry Register), and relevant observations at slaughter (meat inspection data). We included all finishers from indoor production finisher herds that met the inclusion criterion of at least one slaughtered finisher with a recorded tail-bite observation during 2015 at the single largest Danish abattoir. The final dataset held 1,070 herds with one or more tail-bite observations, from which 14,411 of 2,906,626 finishers (0.50%) had an individual record of a tail bite. Within this group of finishers with tail-bite observations, the recorded tail-biting-related sequelae included osteomyelitis (8.1%), abscesses in the hindquarters (10.5%), abscesses in the forequarters (2.3%), abscesses in the mid-section of the carcass (2.9%), abscesses in the limbs (2.4%), and chronic arthritis (0.5%). Due to a high-herd prevalence (&gt;25%), osteomyelitis and abscesses in the hindquarters were selected for further analysis. The occurrence of osteomyelitis and hindquarter abscesses in individual finishers with tail-bite observations was described using a generalized linear mixed effects model with binomial response and logit link. Herd was included as a random effect, while herd size and various antibacterial treatments were tested for inclusion in the model as fixed effects. The final models indicated a significant association between herd size and both osteomyelitis (p = 0.014) and hindquarter abscesses (p &lt; 0.001), with larger herds (2,001–12,000 registered finisher pigs) showing a reduced risk. Further, a negative association was found between the occurrence of hindquarter abscesses and the use of oral pleuromutilin (p = 0.022). The significant association with herd size highlights the potential importance of management factors in reducing the occurrence of tail-bite lesions in finishing pigs