Catriona J. MacLeod

SIMR: an R package for power analysis of generalized linear mixed models by simulation

Summary The r package simr allows users to calculate power for generalized linear mixed models from the lme4 package. The power calculations are based on Monte Carlo simulations. It includes tools for (i) running a power analysis for a given model and design; and (ii) calculating power curves to assess trade-offs between power and sample size. This paper presents a tutorial using a simple example of count data with mixed effects (with structure representative of environmental monitoring data) to guide the user along a gentle learning curve, adding only a few commands or options at a time.

Parasites lost - do invaders miss the boat or drown on arrival?

Host species that colonize new regions often lose parasite species. Using population arrival and establishment data for New Zealands introduced bird species and their ectoparasitic chewing lice species, we test the relative importance of different processes and mechanisms in causing parasite species loss. Few lice failed to arrive in New Zealand with their hosts due to being missed by chance in the sample of hosts from the original population (missing the boat). Rather, most lice were absent because their hosts or the parasite themselves failed to establish populations in their new environment. Given they arrived and their host established, parasite persistence was more strongly related to factors associated with transmission efficiency (number of host individuals introduced, host body size, host sociality and parasite suborder) than parasite propagule pressure and aggregation. Such insights into parasite success are invaluable to both understanding and managing their impact.

Intensification of New Zealand agriculture: Implications for biodiversity

Abstract Intensification of New Zealand agricultural practices is an ongoing and accelerating process which potentially threatens the environment, biodiversity and even the sustainability of agricultural production. However, neither the exact nature of this threat nor the extent of its impact has received adequate analysis. There is clear evidence that agricultural intensification has degraded aquatic biodiversity, but there is a critical lack of research and monitoring of robust indicators of terrestrial biodiversity in New Zealand production landscapes. Therefore, we can only infer a generalised likelihood that intensification has also reduced terrestrial biodiversity and agro‐ecosystem resilience. It is unknown whether biodiversity and ecological services provided by the actual land growing crops, pasture or wood fibre are degrading because of intensification. Increased use of ecological subsidies (nutrient and energy inputs) may have compensated, at least in part, for the increased rate of food production (nutrient and energy outputs). Lasting practical solutions to enhance sustainability can only be identified by long‐term transdisciplinary research of ecological disturbance in agro‐ecosystems. Working with intensification to identify environmental and social gains at the same time as capturing economic efficiencies is more likely to support biodiversity than simply attempting to stem or reverse intensification. A change in world view of both rural and urban dwellers, from the predominant philosophy that allocates land to either preservation or production to one that promotes sustainable land‐use practices that integrate extractive resource use with conservation, is the key to mitigating impacts of agricultural intensification in modified landscapes.

When experts disagree: the need to rethink indicator selection for assessing sustainability of agriculture

Sustainability indicators are well recognized for their potential to assess and monitor sustainable development of agricultural systems. A large number of indicators are proposed in various sustainability assessment frameworks, which raises concerns regarding the validity of approaches, usefulness and trust in such frameworks. Selecting indicators requires transparent and well-defined procedures to ensure the relevance and validity of sustainability assessments. The objective of this study, therefore, was to determine whether experts agree on which criteria are most important in the selection of indicators and indicator sets for robust sustainability assessments. Two groups of experts (Temperate Agriculture Research Network and New Zealand Sustainability Dashboard) were asked to rank the relative importance of eleven criteria for selecting individual indicators and of nine criteria for balancing a collective set of indicators. Both ranking surveys reveal a startling lack of consensus amongst experts about how best to measure agricultural sustainability and call for a radical rethink about how complementary approaches to sustainability assessments are used alongside each other to ensure a plurality of views and maximum collaboration and trust amongst stakeholders. To improve the transparency, relevance and robustness of sustainable assessments, the context of the sustainability assessment, including prioritizations of selection criteria for indicator selection, must be accounted for. A collaborative design process will enhance the acceptance of diverse values and prioritizations embedded in sustainability assessments. The process by which indicators and sustainability frameworks are established may be a much more important determinant of their success than the final shape of the assessment tools. Such an emphasis on process would make assessments more transparent, transformative and enduring.

Pathways for integration of biodiversity conservation into New Zealand's agricultural production

Our claim that integration approaches will be more effective than land allocation approaches for conserving biodiversity in New Zealands agricultural production landscapes (Moller et al. 2008b) has been challenged by Lee et al. (2008, this issue). Our critics also disagree with our conclusion that ongoing intensification is inevitable and assert that it must be counteracted if New Zealands globally

Social‐ecological scales and sites of action: Keys to conserving biodiversity while intensifying New Zealand's agriculture?

1 The Forum section contains short opinion articles on topics within the scope of the New Zealand Journal of Agricultural Research. Forum articles are not refereed, and editing is limited to style matters. They should be no more than the equivalent of 2500 words including references. Articles commenting on a specific paper will be referred to the author(s) of that paper for right of reply before publication. Forum articles should not be cited as scientific papers.

Does farm-scale habitat composition predict pest-bird numbers and distribution?

Context Bird damage to horticultural crops causes significant economic losses for growers around the globe. However, bird damage is unpredictable and pest-bird movements and abundance patterns are poorly understood. Aims To assess whether habitat management is likely to be an effective approach for controlling two pest-bird species (house sparrow, Passer domesticus, and greenfinch, Carduelis chloris) in New Zealand’s arable landscape. Methods Breeding- and winter-bird and habitat surveys were carried out over a 3-year period (2003–05) on 19 1-km × 1-km squares with arable crops on the Canterbury Plains, New Zealand. Bird abundance and/or distribution were analysed with respect to both temporal and spatial (crop- and boundary-habitat composition) variables. Results Estimated breeding-season densities for house sparrow were higher but more stable than those for greenfinch (which increased by 70% over a 3-year period), and for individual farms were more predictable across years than were winter densities. Boundary habitat was the best predictor of bird densities and distribution in the breeding season; features associated with enhanced seed abundance or access were important in the winter. However, habitat composition alone could not account for temporal and spatial variation in bird densities on farms. Conclusions Either habitat management or the reduction of key seed resources could potentially control pest-bird numbers. However, habitat management is likely to have adverse consequences for other important functions (such as the shelter and biodiversity benefits of shelterbelts), and any form of bird control applied at the farm scale is unlikely to be effective. Implications To make control actions both effective and economically viable, a coordinated program involving multiple farms is likely to be needed. We recommend investigating the effectiveness of an experimental manipulation of key food resources at the landscape scale.

Crop use by introduced bird species in winter in relation to crop structure and seed resources

Capsule Most species preferred to forage in grassland where seed resources were more abundant and the vegetation was uniform in height but heterogeneous in density. Aim To determine the influence of crop composition and structure, and seed food resources on the distribution of introduced bird species on New Zealand farmland in winter. Methods Birds were counted on 90 ha of mixed cropping farmland during mid- and late-winter periods, 2004. The presence or absence of six introduced species (Blackbird Turdus merula, Skylark Alauda arvensis, House Sparrow Passer domesticus, Goldfinch Carduelis carduelis, Yellowhammer Emberiza citrinella and Starling Sturnus vulgaris) in fields was investigated in relation to crop composition and structure and seed abundance. Results Species–habitat associations varied over time and between species. Blackbird, House Sparrow, Yellowhammer and Starling were associated more frequently with grassland than arable crops during at least one survey. Seed abundance was a significant predictor of the occurrence of all species except House Sparrow, while crop structure was a predictor of only Goldfinch, Yellowhammer and Starling occurrence. Conclusion During the winter, the distribution of six introduced bird species in the lowland cropping area was related to habitat composition, vegetation structure, and seed food resources. The preference for grassland habitats was probably determined by the vegetation structure and seed resources in these areas. The trend for increased use of supplementary animal feed in livestock farming in New Zealand may help sustain introduced bird populations. A larger-scale study is needed to investigate the generality of the species–habitat associations detected in this study at the landscape scale.

Do Yellowhammers Emberiza citrinella achieve higher breeding productivity in their introduced range than in their native range

Capsule Success in New Zealand is not from enhanced reproductive productivity, but may be from better winter food supplies and fewer natural predators.

Variation in productivity of Grey-faced Petrels (Pterodroma gouldi) with local burrow density and breeding island

Abstract For long-lived birds, estimates of productivity can be effective indicators of environmental change or responses to management. Such estimates are also valuable in modelling population growth. We report estimates of nest survival for burrow-nesting Grey-faced Petrels (Pterodroma gouldi) from four islands off the north-eastern coast of New Zealand. We surveyed the contents of breeding burrows for up to four breeding seasons and followed the fates of 1371 eggs. We used a logistic-exposure modelling approach to investigate the effects of island, year, local burrow density and occupancy rate on nest survival. Daily nest survival varied between years and islands but declined with increasing local burrow density across all islands. Local burrow occupancy rate had no detectable effect. We estimated overall rates of breeding success on our island groups of 11% (95% confidence interval 9–14%) to 28% (26–30%). The negative density-dependent relationships between local burrow densities and productivity add to the growing evidence for this effect in burrow-nesting seabirds worldwide, in contrast to trends in surface-breeding species. The variation in productivity between our study colonies may be linked to the restoration histories of the islands and suggests that data from one location should be used cautiously when guiding management of the same species elsewhere.