What Biases Could Your Sampling Methods Add to Your Data?

Post provided by ROGER HO LEE

這篇博客文章也有中文版

Have you ever gone fishing? If so, you may have had the experience of not catching any fish, while the person next to you got plenty. If you walked along the pier or bank, you may have seen that other fishermen and -women caught fish of various shapes and sizes. You’d soon realise that each person was using a different set of equipment and baits, and of course, that the anglers differed in their skills and experience. Beneath the water were many fish, but whether you could catch them, or which species could even be caught, all depended on your fishing method, as well as where and how the fish you were targeting lived.

Designing Sampling Protocols

Head view of different ant species found in Hong Kong and further in SE Asia.

Head view of different ant species found in Hong Kong and further in South East Asia.

This is a lot like the situation that ecologists often face when designing sampling protocols for field surveys. While a comprehensive survey will yield the most complete information, few of us have the resources to capture every member of the community we’re studying. So, we take representative samples instead. But the method(s) used for sampling will only allow us to collect a subset of the species which are present. This selection of the species is not random per se – it’s dependent on species’ life history. Continue reading

採樣方法會帶來怎樣的數據偏差?

作者:李灝

This blog post is also available in English

你有釣魚的經驗嗎?若有的話,以下的經歷對你應該不會陌生。自己釣了大半天,魚杆動也沒動過,但身旁的釣手卻滿載而歸。感到灰心時,你沿著碼頭或岸邊巡視,你看到其他人的魚獲大大小小的也有﹑形態不同的的也有。心裡被疑惑與不甘的思緒纏繞著的一刻,你突然意識到每個人都在使用不同的釣具和魚餌(當然每位垂釣者的技能和經驗也不同)。在水中有各種各樣的魚,但你能否釣到牠們,或者釣到那一些品種,都取決於你釣魚的方法,以及你目標魚種的活動範圍和生活方式。

採樣方案的設計

Head view of different ant species found in Hong Kong and further in SE Asia.

香港和東南亞地區的螞蟻品種。

上述的經歷與生態學家在設計野外調查時所遇到的情況非常相似。雖然全面的調查能取得最完整的資料,但我們很少會有充足的資源去完整地採集整個物種群落。取而代之的是我們只能採集一部份的物種來作寫照。值得我們留意的是每種採樣方法只允許我們收集到群落中的某些物種;這些物種不是隨機地被選中,而是取決於物種的生活史。 Continue reading

Field Work on a Shoestring: Using Consumer Technology as an Early Career Researcher

Post provided by CARLOS A. DE LA ROSA

Esta entrada de blog también está disponible en español

Champagne Tastes on a Beer Budget

Freshly outfitted with a VACAMS camera and GPS unit, #1691 heads off into the forest with her calf. ©Carlos A. de la Rosa

Freshly outfitted with a VACAMS camera and GPS unit, #1691 heads off into the forest with her calf. ©Carlos A. de la Rosa

There’s a frustrating yin and yang to biological research: motivated by curiosity and imagination, we often find ourselves instead defined by limitations. Some of these are fundamental human conditions. The spectrum of light detectable by human eyes, for example, means we can never see a flower the way a bee sees it. Others limitations, like funding and time, are realities of modern-day social and economic systems.

Early career researchers (ECRs) starting new projects and delving into new research systems must be especially creative to overcome the odds. Large grants can be transformative, giving a research group the equipment and resources to complete a study, but they’re tough to get. Inexperienced ECRs are at a disadvantage when competing against battle-hardened investigators with years of grant writing experience. Small grants of up to about $5000 USD, on the other hand, are comparatively easy to find. So, how can ECRs make the most of small, intermittent sources of funding?

I found myself faced with this question in the second year of my PhD field work. Continue reading

Trabajo de Campo a lo Barato: Uso de Tecnología de Productos de Consumo Para un Investigador al Inicio de su Carrera de Investigación

Contribución de CARLOS A. DE LA ROSA

This blog post is available in English

Gusto por champaña con presupuesto de cerveza

Recientemente equipada con una unidad de cámara y GPS VACAMS, la vaca No. 1691 se dirige al bosque con su becerro. ©Carlos A. de la Rosa

Recientemente equipada con una unidad de cámara y GPS VACAMS, la vaca No. 1691 se dirige al bosque con su becerro. ©Carlos A. de la Rosa

Hay un frustrante toma-y-dame en el campo de la investigación biológica: motivados por la curiosidad y la imaginación, a menudo nos encontramos definidos por limitaciones. Algunas de estas, como nuestros sentidos, son condiciones humanas fundamentales. El espectro de luz detectable por los ojos humanos, por ejemplo, significa que nunca podremos ver a una flor de la misma forma en que la ve una abeja. Otras limitaciones, como financiamiento y tiempo, representan las realidades de los sistemas sociales y económicos de hoy día.

Los investigadores al comienzo de sus carreras (Early Career Researchers, o ECRs en sus siglas en inglés) que se embarcan en nuevos proyectos y se involucran con sistemas nuevos de investigación deben ser especialmente creativos para poder superar las probabilidades. Una generosa beca puede ser transformativa, pero un ECR con poca experiencia está en desventaja cuando compite con investigadores ya endurecidos por la batalla, quienes tienen años de experiencia escribiendo propuestas de financiamiento. Por otra parte, las pequeñas becas en el rango de $2.000 a $5.000 son comparativamente fáciles de encontrar. ¿Cómo puede un ECR aprovechar al máximo estas pequeñas e intermitentes fuentes de financiamiento?

En el segundo año del trabajo de campo de mi doctorado me enfrenté con este enigma. Continue reading

Limitations and Benefits of the Unmatched Count Technique: Considering How We Use New Methods in Conservation

Post provided by Amy Hinsley and Ana Nuno

Esta publicação no blogue também está disponível em português

A New Conservation Toolbox

It is widely accepted that many conservation challenges are directly related to human behaviour. Whether it is the over-collection of a rare orchid by harvesters in Southeast Asia, or the decisions by collectors in Europe to buy and smuggle these orchids home, understanding the extent and nature of these behaviours is essential to addressing the threats they might cause. This has led conservation researchers and practitioners to start looking outside of their discipline, to find methods and approaches from across the social sciences to improve our understanding of these complex issues.

A research assistant carrying out a UCT survey about the use of Traditional Medicine products containing bear bile in China. © Chen Haochun.

A research assistant carrying out a UCT survey about the use of Traditional Medicine products containing bear bile in China. © Chen Haochun.

While this interdisciplinarity is a positive move for conservation, it is important that we treat these ‘new’ methods carefully and understand their limitations. If we don’t, there is a risk that our new toolbox full of exciting methods that sound great on a funding application, may in fact not be making what we do any better, or in extreme cases they may even be making it worse.

With this in mind, a group of conservation social scientists, led by researchers at the Universities of Oxford and Exeter, decided to look in depth into one of these ‘new’ methods, to provide recommendations on when and how it should be used, and when it shouldn’t. Our Open Access article – ‘Asking sensitive questions using the unmatched count technique: Applications and guidelines for conservation‘ – looks at the Unmatched Count Technique (UCT – also called the list experiment), which is increasingly being used in conservation to ask questions about ‘sensitive’ topics. Continue reading

Limitações e benefícios da técnica de contagem de itens: considerações sobre o uso de novos métodos em Conservação

publicação no blogue FORNECIDO POR AMY HINSLEY E ANA NUNO

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Novas ferramentas de conservação

Muitos desafios em conservação estão diretamente relacionados com o comportamento humano. Quer seja a recolha excessiva de uma orquídea rara no Sudeste Asiático, ou a compra e contrabando dessas orquídeas por colecionadores na Europa, entender a magnitude e a natureza desses comportamentos é essencial para lidar com as ameaças que eles podem causar. Isso levou os investigadores e profissionais da área de conservação a começarem a olhar para fora da sua própria disciplina, de modo a encontrar métodos e abordagens das ciências sociais para melhorar a nossa compreensão sobre estas questões complexas.

Assistente de investigação a realizar um estudo recorrendo a TCI sobre o uso de produtos de medicina tradicional com bílis de urso na China. © Chen Haochun.

Assistente de investigação a realizar um estudo recorrendo a TCI sobre o uso de produtos de medicina tradicional com bílis de urso na China. © Chen Haochun.

Embora esta interdisciplinaridade seja um passo positivo para a conservação, é importante tratar esses “novos” métodos com cuidado e entender as suas limitações. Se não o fizermos, existe o risco da nossa nova caixa de ferramentas, repleta de métodos interessantes que soam bem em candidaturas a financiamento, na verdade não melhorar aquilo que nós geralmente já fazemos ou, em casos extremos, até piorá-lo.

Tendo isto em conta, um grupo de cientistas sociais em conservação, liderado por investigadores das Universidades de Oxford e Exeter, decidiu examinar em profundidade um desses “novos” métodos, fornecer recomendações sobre quando e como ele deveria ser usado, e quando não deveria. O artigo, disponível gratuitamente na revista científica Methods in Ecology and Evolution nesta semana, examina a Técnica de Contagem de Itens (TCI), que tem sido cada vez mais usada em conservação para fazer perguntas sobre tópicos “sensíveis”. Continue reading

Spatial Cross-Validation of Species Distribution Models in R: Introducing the blockCV Package

Post provided by Roozbeh Valavi

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Modelling species distributions involves relating a set of species occurrences to relevant environmental variables. An important step in this process is assessing how good your model is at figuring out where your target species is. We generally do this by evaluating the predictions made for a set of locations that aren’t included in the model fitting process (the ‘testing points’).

Random splitting of the species occurrence data into training and testing points

Random splitting of the species occurrence data into training and testing points

The normal, practical advice people give about this suggests that, for reliable validation, the testing points should be independent of the points used to train the model. But, truly independent data are often not available. Instead, modellers usually split their data into a training set (for model fitting) and a testing set (for model validation), and this can be done to produce multiple splits (e.g. for cross-validation). The splitting is typically done randomly. So testing points sometimes end up located close to training points. You can see this in the figure to the right: the testing points are in red and training points are in blue. But, could this cause any problem? Continue reading

اعتبارسنجی متقاطع مکانی در مدلسازی توزیع گونه‌‌ها

نویسنده: روزبه وَلَوی

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مدلسازی توزیع گونه‌ها به تخمین و برآورد ارتباط بین مجموعه‌ای از نقاط حضور گونه با متغیرهای زیست‌محیطی مرتبط می پردازد. یکی از مراحل اساسی این فرایند، ارزیابی قدرت مدل برای پیش­بینی مکان‌هایی است که احتمال حضورگونه در آنجا وجود دارد. این کار اغلب با ارزیابی پیش­بینی انجام شده در مجموعه‌ای ازنقاط که در فرآیند مدلسازی مورد استفاده قرار نگرفته اند (نقاط آزمایشی) صورت می‌گیرد.

تقسیم تصادفی داده‌های حضور گونه به نقاط آزمایشی و آموزشی

تقسیم تصادفی داده‌های حضور گونه به نقاط آزمایشی و آموزشی

مطالعات پیشین بر این نکته تاکید دارند که به منظور ارزیابی معتبر، نقاط آزمایشی باید مستقل از نقاط آموزشی باشند، این درحالیست که داده مستقل واقعی به ندرت در دسترس می باشد. به همین دلیل، در فرایند مدلسازی معمولا داده‌های موجود را به دو قسمت داده‌های آموزشی (برای کالیبره کردن مدل) و داده های آزمایشی (برای ارزیابی دقت مدل) تقسیم می‌کنند، این استراتژی می‌تواند چند قسمتی هم باشد (برای مثال اعتبارسنجی متقاطع یا cross-validation). از آنجاییکه این تقسیم بندی معمولا بصورت تصادفی انجام می‌شود، بنابراین گاهی اوقات نقاط آزمایشی در فواصل نزدیک به نقاط آموزشی قرار می‌گیرند. شکل زیر این مساله را به خوبی نشان می دهد که در آن نقاط آزمایشی به رنگ قرمز و نقاط آموزشی آبی هستند. اما آیا این مساله می‌تواند مشکلی ایجاد کند؟ Continue reading

In Conservation Planning, Some Data are More Important Than Others

Provided by Heini Kujala and José Lahoz-Monfort

Esta entrada de blog también está disponible en español

Spatial Conservation Planning and the Quest for Perfect Data

Conservation planners and managers often need to make decisions with imperfect information. When deciding what action to take or how to divide resources between candidate locations, we rarely have all the information we’d like on what species are present at a site or which areas are most critical for supporting their population viability. A large volume of ecological research focuses on answering these very questions.

To make conservation decisions, we need other types of data as well. These include information on things like the cost of carrying out a given conservation action, current condition of sites, the distribution and intensity of threats in a region, and much more. Many conservation problems are spatial, meaning that we often need to decide between multiple candidate locations and that there are spatial dependencies between sites that need to be accounted for. All these different pieces of information are needed to make cost-efficient and effective conservation decisions.

Ecologists and conservation biologists are usually concerned about the completeness and accuracy of the ecological data used to make these decisions (understandably). But less effort has been spent in researching and verifying the accuracy of the types of data mentioned above. At the same time, we have relatively poor understanding of how data gaps influence solutions optimised across multiple species and locations, and the relative importance of gaps in different types of data. This is what we set out to find in ‘Not all data are equal: Influence of data type and amount in spatial conservation prioritisation’. Continue reading

En la planificación de la conservación, algunos datos son más importantes que otros

Por Heini Kujala y José Lahoz-Monfort

This blog post is also available in English

La planificación espacial de la conservación y la búsqueda de datos perfectos

Los planificadores y administradores de la conservación a menudo necesitan tomar decisiones con información imperfecta. Al decidir qué acción tomar o cómo dividir recursos entre diferentes localizaciones, rara vez tenemos toda la información que nos gustaría sobre qué especies están presentes en un lugar o qué áreas son las más críticas para respaldar su viabilidad poblacional. Un gran volumen de investigación ecológica se focaliza en responder a estas preguntas.

Para tomar decisiones de conservación, también necesitamos otros tipos de datos, incluyendo, entre otros, información sobre el costo de llevar a cabo una acción de conservación determinada, la condición actual de los diferentes sitios, y la distribución e intensidad de las amenazas en una región. Muchos problemas de conservación son espaciales, es decir que a menudo tenemos que decidir entre varias ubicaciones candidatas, con dependencias espaciales entre ellas. Todas estas diferentes piezas de información son necesarias para tomar decisiones de conservación rentables y efectivas.

Los ecólogos y los biólogos de la conservación suelen estar preocupados por la integridad y exactitud de los datos ecológicos utilizados para tomar estas decisiones (comprensiblemente). Pero se ha dedicado menos esfuerzo a investigar y verificar la exactitud de los otros tipos de datos mencionados anteriormente. Además, tenemos una comprensión relativamente pobre de cómo las lagunas en los datos influyen en las soluciones optimizadas en múltiples especies y ubicaciones, y la importancia relativa de las lagunas en los diferentes tipos de datos. Es esto precisamente lo que nos propusimos investigar en el artículo ‘Not all data are equal: Influence of data type and amount in spatial conservation prioritisation’. Continue reading