Summary1. While teaching statistics to ecologists, the lead authors of this paper have noticed common statistical problems. If a random sample of their work (including scientific papers) produced before doing these courses were selected, half would probably contain violations of the underlying assumptions of the statistical techniques employed. 2. Some violations have little impact on the results or ecological conclusions; yet others increase type I or type II errors, potentially resulting in wrong ecological conclusions. Most of these violations can be avoided by applying better data exploration. These problems are especially troublesome in applied ecology, where management and policy decisions are often at stake. 3. Here, we provide a protocol for data exploration; discuss current tools to detect outliers, heterogeneity of variance, collinearity, dependence of observations, problems with interactions, double zeros in multivariate analysis, zero inflation in generalized linear modelling, and the correct type of relationships between dependent and independent variables; and provide advice on how to address these problems when they arise. We also address misconceptions about normality, and provide advice on data transformations. 4. Data exploration avoids type I and type II errors, among other problems, thereby reducing the chance of making wrong ecological conclusions and poor recommendations. It is therefore essential for good quality management and policy based on statistical analyses.

Summary 0[ Recent legislation designed to reduce air pollution has restricted Californian rice! farmers from burning rice stubble after harvest[ Intentional~ooding of _elds during winter to speed straw decomposition is becoming increasingly common as growers seek alternatives to burning residual straw[ The potential for~ooded _elds to act as a surrogate for destroyed wetland habitat may be an additional bene_t in a region that hosts a large proportion of North America|s wintering waterbirds[ We investigated the degree to which waterbirds use~ooded _elds and whether the method of~ooding a}ects their use[ Speci_cally\ we tested whether waterbird use "a# was greater in intentionally~ooded _elds than in un~ooded _elds\ "b# di}ered among~ooded _elds receiving di}erent straw manipulations and "c# varied with water depth[ 1[ Intentionally~ooded rice _elds received signi_cantly greater use by 13 of 20 species studied[ Only great blue herons Ardea herodias and sandhill cranes Grus canadensis were signi_cantly more common in un~ooded _elds[ Geese densities did not di}er between~ooded and un~ooded _elds[ 2[ We found no di}erences in the densities of most species in~ooded _elds that received di}erent straw manipulations to improve decomposition rates[ Exceptions included several small shorebirds which occurred at highest densities in _elds where straw was incorporated into the soil[ 3[ Species di}ered in their use of di}erent water depths[ For 03 species we tested whether preferred depths\ suggested in the literature\ received disproportionately higher use[ Most of these species were more likely to be encountered within the suggested depth ranges[ Depth\ however\ was a poor predictor of bird density[ Depths of 04Ð19 cm resulted in frequent use by the greatest number of species[ 4[ We conclude that~ooding rice _elds increased suitable habitat for most\ but not all\ species studied[ Di}erent straw manipulation methods had little e}ect on most species[ Water depth\ however\ was important in determining species occurrence[ During the _rst half of the winter\ water depths were greater than the median depths used by most species[ Key!words] agriculture\ shorebirds\ waterfowl\ water depth\ wetland management[

Evaluating the potential for anthropogenic habitats to act as surrogates for the natural habitats they replace is a key issue in conservation biology. In California, flooded rice fields are used by numerous aquatic birds during winter. If this habitat functions similarly to more natural wetlands, increased flooding may help replace the extensive wetlands that occurred in the region prior to agricultural development. I tested whether food abundance, perceived predation threat, foraging performance, and the way in which birds allocate their time to different behaviors differed between flooded rice fields and seminatural wetlands for several species of aquatic bird. When appropriate, I also compared flooded and unflooded fields. Invertebrate densities did not differ among habitats. Seminatural wetlands had less rice grain but more seeds from other plants than the two rice habitats. The frequency with which predators passed over a feeding area was lower in flooded fields than in unflooded fields or seminatural wetlands. Most differences in feeding performance and time allocation among habitats were small and statistically insignificant. For some species, feeding efficiency was greater in seminatural wetlands than in flooded fields. Increasing attack rates and the amount of time spent feeding when in flooded fields, however, may allow birds to compensate for reduced efficiency. Multivariate analyses showed that group size, predation threat, time of day, date, and water depth often were associated with behaviors, but that these variables rarely accounted for habitat differences. Flooded fields apparently provide equivalent foraging habitat to seminatural wetlands and, because of reduced predation threat, may be a safer habitat for waterbirds. Thus, if managed appropriately, one of the world's dominant forms of agriculture can provide valuable waterbird habitat. Equivalencia Funcional entre Hábitats de Arrozales y Humedales SeminaturalesResumen: La evaluación del potencial en hábitats antropogénicos para actuar como substitutos de los hábitats naturales que remplazaron es un tema clave en la biologíá de la conservación. En California, tierras inundadas para cultivo de arroz son utilizadas por numerosas aves acuáticas durante el invierno. Si estos hábitats funcionan en forma similar a humedales más naturales, el incremento de inundaciones podría ayudar a reemplazar los extensos humedales que existieron en la región antes del desarrollo agricultural. Analizé si la abundancia de alimento, la percepción del peligro de depredación, el rendimiento en forrajeo y la forma en que las aves distribuyen su tiempo hacia diferentes conductas difieren entre arrozales inundados y humedales seminaturales para diferentes especies de aves acuáticas. Cuando fue posible, también comparé arrozales inundados contra no inundados. Las densidades de invertebrados no difirieron entre hábitats. Los humedales seminaturales tuvieron menos grano de arróz, pero más semillas de otras plantas que los dos tipos de hábitats de arrozal. La frecuencia con l...

Summary 1.Methods papers play a crucial role in advancing applied ecology. Counting organisms, in particular, has a rich history of methods development with many key advances both in field sampling and the treatment of resulting data. 2. Most counts, however, have associated errors due to portions of the population of interest being unavailable for detection (e.g. target population not fully sampled; individuals present but not detectable), detection mistakes (e.g. detectable individuals missed; non-existent individuals recorded), or erroneous counts (e.g. large groups miscounted; individuals misidentified). 3. Developments in field methods focus on reducing biases in the actual counts. Simultaneously, statisticians have developed many methods for improving inference by quantifying and correcting for biases retrospectively. Prominent examples of methods used to account for detection errors include distance sampling and multiple-observer methods. 4. Simulations, in which population characteristics are set by the investigator, provide an efficient means of testing methods. With good estimates of sampling biases, computer simulations can be used to evaluate how much a given counting problem affects estimates of parameters such as population size and decline, thereby allowing applied ecologists to test the efficacy of sampling designs. Combined with cost estimates for each field method, such models would allow the cost-effectiveness of alternative protocols to be assessed. 5. Synthesis and applications . Major advances are likely to come from research that looks for systematic patterns, across studies, in the effects of different types of bias and assumption violation on the ecological conclusions drawn. Specifically, determining how often, and under what circumstances, errors contribute to poor management and policy would greatly enhance future application of ecological knowledge.

Systematic review, meta‐analysis and other forms of evidence synthesis are critical to strengthen the evidence base concerning conservation issues and to answer ecological and evolutionary questions. Synthesis lags behind the pace of scientific publishing, however, due to time and resource costs which partial automation of evidence synthesis tasks could reduce. Additionally, current methods of retrieving evidence for synthesis are susceptible to bias towards studies with which researchers are familiar. In fields that lack standardized terminology encoded in an ontology, including ecology and evolution, research teams can unintentionally exclude articles from the review by omitting synonymous phrases in their search terms. To combat these problems, we developed a quick, objective, reproducible method for generating search strategies that uses text mining and keyword co‐occurrence networks to identify the most important terms for a review. The method reduces bias in search strategy development because it does not rely on a predetermined set of articles and can improve search recall by identifying synonymous terms that research teams might otherwise omit. When tested against the search strategies used in published environmental systematic reviews, our method performs as well as the published searches and retrieves gold‐standard hits that replicated versions of the original searches do not. Because the method is quasi‐automated, the amount of time required to develop a search strategy, conduct searches, and assemble results is reduced from approximately 17–34 hr to under 2 hr. To facilitate use of the method for environmental evidence synthesis, we implemented the method in the R package litsearchr, which also contains a suite of functions to improve efficiency of systematic reviews by automatically deduplicating and assembling results from separate databases.

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Climate change and sea-level rise pose an imminent threat to the survival of coastal ecosystems, but the mechanisms by which animals inhabiting these areas may be affected by these changes are not well studied. During 2007-2009, we quantified the frequency of nest-flooding events at two salt marshes located in the northeastern United States that are of global importance to Saltmarsh Sparrow {Ammodramus caudacutus) conservation. Although nest flooding is a major cause of nest failure in this species, we lack a detailed understanding of exactly how flooding affects success, so it is difficult to determine the magnitude of the threat posed by sea-level rise. We tested whether variables associated with the timing of nest initiation, tide height, and flooding frequency can be used to estimate three aspects of nest fate: the probability of nest success, the probability of nest failure due to flooding, and the number of ofl^spring lost to flooding. Of the 191 nests that we monitored, only 15% were never flooded and 18% were successful; the mean (± SD) number of flooding events observed per nest was 2.8 ± 2.1 (range: 0-10). The top-performing model for each measure of nest fate included variables related to tidal metrics, but model composition for the three measures differed in the importance of particular tide variables. Both tide height and flooding frequency emerged as important drivers of nest fate in this system. Saltmarsh Sparrow nests appear to be extremely vulnerable to even slight increases in sea level. Planiñcación para un Aumento del Nivel del Mar: Cuantifícación de los Patrones de Inundación de los Nidos de Ammodramus caudacutus bajo Condiciones Actuales del Nivel del MarRESUMEN.-El cambio climático y el aumento del nivel del mar plantean una amenaza inminente a la supervivencia de los ecosistemas costeros, pero los mecanismos por los cuales los animales que habitan estas áreas pueden ser afectados por estos cambios no han sido bien estudiados. Durante 2007-2009, cuantificamos la frecuencia de eventos de inundación de nidos en dos marismas saladas localizadas en el noreste de Estados Unidos que son de importancia global para la conservación de Ammodramus caudacutus. Aunque la inundación de nidos es una de las causas principales de fracaso de los nidos en esta especie, nos falta comprender en detalle cómo exactamente afecta la inundación al éxito, por lo que es difícil determinar la magnitud de la amenaza que plantea el aumento del nivel del mar. Evaluamos si las variables asociadas con la fecha de inicio de los nidos, la altura de la marea y la frecuencia de anidación pueden ser usadas para estimar tres aspectos del destino de los nidos: la probabilidad de éxito de los nidos, la probabilidad de fracaso de los nidos por inundación y el número de crias perdidas por inundación. De los 191 nidos que monitoreamos, sólo el 15% no se inundaron nunca y el 18% fueron exitosos; el número medio (± DE) de eventos de inundación observados por nido fue de 2.8 ± 2.1 (rango: 0-10). El modelo que se desempeñó mejor para cada...