Overview of Random Forest Methodology and Practical Guidance with Emphasis on Computational Biology and Bioinformatics

The Random Forest (RF) algorithm by Leo Breiman has become a standard data analysis tool in bioinformatics. It has shown excellent performance in settings where the number of variables is much larger than the number of observations, can cope with complex interaction structures as well as highly correlated variables and returns measures of variable importance. This paper synthesizes ten years of RF development with emphasis on applications to bioinformatics and computational biology. Special attention is given to practical aspects such as the selection of parameters, available RF implementations, and important pitfalls and biases of RF and its variable importance measures (VIMs). The paper surveys recent developments of the methodology relevant to bioinformatics as well as some representative examples of RF applications in this context and possible directions for future research

Vegetation Dynamics in Ecuador

Global forest cover has suffered a dramatic reduction during recent decades, especially in tropical regions, which is mainly due to human activities caused by enhanced population pressures. Nevertheless, forest ecosystems, especially tropical forests, play an important role in the carbon cycle functioning as carbon stocks and sinks, which is why conservation strategies are of utmost importance respective to ongoing global warming. In South America the highest deforestation rates are observed in Ecuador, but an operational surveillance system for continuous forest monitoring, along with the determination of deforestation rates and the estimation of actual carbon socks is still missing. Therefore, the present investigation provides a functional tool based on remote sensing data to monitor forest stands at local, regional and national scales. To evaluate forest cover and deforestation rates at country level satellite data was used, whereas LiDAR data was utilized to accurately estimate the Above Ground Biomass (AGB; carbon stocks) at catchment level. Furthermore, to provide a cost-effective tool for continuous forest monitoring of the most vulnerable parts, an Unmanned Aerial Vehicle (UAV) was deployed and equipped with various sensors (RBG and multispectral camera). The results showed that in Ecuador total forest cover was reduced by about 24% during the last three decades. Moreover, deforestation rates have increased with the beginning of the new century, especially in the Andean Highland and the Amazon Basin, due to enhanced population pressures and the government supported oil and mining industries, besides illegal timber extractions. The AGB stock estimations at catchment level indicated that most of the carbon is stored in natural ecosystems (forest and páramo; AGB ~98%), whereas areas affected by anthropogenic land use changes (mostly pastureland) lost nearly all their storage capacities (AGB ~2%). Furthermore, the LiDAR data permitted the detection of the forest structure, and therefore the identification of the most vulnerable parts. To monitor these areas, it could be shown that UAVs are useful, particularly when equipped with an RGB camera (AGB correlation: R² > 0.9), because multispectral images suffer saturation of the spectral bands over dense natural forest stands, which results in high overestimations. In summary, the developed operational surveillance systems respective to forest cover at different spatial scales can be implemented in Ecuador to promote conservation/ restoration strategies and to reduce the high deforestation rates. This may also mitigate future greenhouse gas emissions and guarantee functional ecosystem services for local and regional populations

Forest biodiversity maintenance

The global biodiversity loss within forest ecosystems has attracted attention during the last decades. Awareness increased both world-wide and in Sweden, which led to changes in the Swedish forests policy. In the Swedish Forestry Act of 1993 the environmental and production goals became equally important, and several new policy implementation instruments were taken into use. One of these was the Woodland Key Habitat Survey, in which indicator species are used to identify sites with conservation values. The first two papers in this thesis assess the relationships between the lichen indicator species found in the study area (in South-Central Sweden) and their growing-substrates and habitats, respectively. Both studies confirm that the indicator species showed habitat preferences which included old or deciduous trees. In Paper II also the habitat preferences of sedentary birds were assessed and the mixed deciduous habitats showed to be the more species rich, compared to pure coniferous forest. Paper III and IV evaluate the forest owners’ intentions and knowledge of nature conservation, as well as their attitudes towards it. In paper III the conservation intentions of the forest owners were estimated on the harvest registration form and compared to the actual retention at the clear-cuts. The intentions were followed by associated practices, however, the retained amounts of stand structures were overall low. I conclude that the intentions did not increase over the study period, the retained amounts were too low to meet, e.g., the Forest Stewardship Council standards, and, also, that such forms could become important information instruments to the forestry authorities concerning intentions and practices of the forest owners. In Paper IV the results of a questionnaire sent to non-industrial private forest (NIPF) owners within the study area, showed that knowledge about conservation and attendance to a recent educational programme, which included conservation information, were positively related to the attitude towards it. However, those occupied with land-use had a more negative attitude towards conservation than others. Also, in the ranking of operational goals for their own conservation efforts, only 7% of the respondents ranked ‘long-term species survival’ as their first priority, while the vast majority ranked ‘forest health’ as number one. In the fifth and last paper the usefulness of indicator species in monitoring systems adapted to NIPF owners, is discussed. In the questionnaire used in paper IV, NIPF owners were asked to mark all species that they could recognise, from a list of 12 forest species. The results showed that they had a weak knowledge of the listed lichens and fungi, but all four birds were recognised by more than 50%. Thus, in indicator species based monitoring systems for NIPF owners and the public only a few easily communicated and conspicuous species of documented indicator value should be used, e.g. vertebrates

Towards national reporting on agricultural land use change in Australia

This report provides the latest available information on national land use and land use change in Australia.SummaryLand use describes the purposes assigned to land. It refers to the purpose for which the land is committed. It is fundamental to understanding landscapes, agricultural production and the management of natural resources. Land use can include the production of goods (such as crops, timber and manufactures) and services (such as defence, recreations, biodiversity and natural resources protection). It also includes urban and rural settlement. Land use choices have a major effect on food production, the natural environment and communities.Land use change is central to much current debate in Australia around agriculture and food and fibre security, forestry, water management, mining, climate change mitigation and adaptation, population, urban expansion, biodiversity protection, community development and landscape aesthetics.This report provides the latest available information on national land use and land use change. It draws heavily on the ABARES time series of national scale land use maps and Australian Bureau of Statistics (ABS) agricultural statistics as these are the most reliable and consistent for reporting on land use change at the national level. The strength of the ABARES national scale land use maps is that they combine ABS agricultural statistics with other land use information into one complete spatial dataset for Australia.The broad trends in agricultural land use change are as follows:Agriculture remains Australia\u27s dominant land use, covering around 456 million hectares (ha) or 59 per cent of the continent in 2005‐06, a decrease of around 18.8 million ha (4 per cent of the agricultural area) since 1992‐93.The most common agricultural land use by area is grazing on native vegetation and modified pastures which occupies 428 million ha or around 56 per cent of Australia and occurs mostly in the arid and semi‐arid regions of inland Australia.The area of grazing decreased by 6 per cent between 1992‐93 and 2005‐06. Over the same period, the area of land used for cropping increased by 39 per cent to 27 million ha (3.5 per cent of Australia’s land area). These changes vary across the country, see Maps S1 and S2.In 2005‐06, areas of minimal use, nature conservation and other protected areas including Indigenous uses occupied around 282 million hectares or 37 per cent of Australia. Based on the Collaborative Australian Protected Area Database (CAPAD), between 1992‐93 and 2005‐ 06, the area of formal nature conservation increased by 15 million ha (37 per cent). In some regions, decreases in the area of land used for grazing are associated with increases in the area of land used for cropping and nature conservation although locations where direct conversions from one land use to another have occurred cannot be identified from the national‐scale data reviewed in this report.The number of farm businesses decreased from 144 860 in 1997‐98 to 135 447 in 2010‐11. However, decreases by farm size were only reflected in the medium (50 to 2 500 ha) category. The number of large farms (greater than 2 500 ha) and small farms (less than 50 ha) both increased between 1997‐98 and 2010‐11. Changes in farm size can arise from a range of factors including pressures to increase economic productivity and efficiency as well as sub‐division for peri‐urban lifestyle blocks or for more intensive production.While the growth in peri‐urban areas (those that lie on the fringe of the major built‐up areas of cities) can compete with agricultural land and the loss of agricultural land to urban growth is important, these changes do not necessarily translate into a decrease in the value of agricultural production. The Melbourne Statistical Division, for example, had only 2 per cent of the total area of Victoria\u27s agricultural holdings in 2010‐11, but this area produced 13.4 per cent ($1.2 billion) of the State’s agricultural commodities by value. Mining is also expanding into agricultural lands and some new coal seam gas developments occur in areas of high value agricultural activity.While the national picture suggests relatively modest changes in area for key land uses (grazing, cropping and nature conservation) over the period 1992‐93 to 2005‐06, regional land use change patterns can vary significantly from national trends. Over the longer term the impacts of increased climate variability and population pressure may strongly impact the location of agricultural and non‐agricultural activities. Changes in the location of traditional agricultural activities (grazing and cropping) are already emerging. Australia is improving its capacity to track land use change, drawing on information sources including satellite remote sensing and statistical collections. The next national scale land use map, based on 2010‐11 agricultural census information, is due for release by ABARES late in 2013 and will provide the opportunity to analyse change across the country for a number of key land uses (grazing, cropping and conservation) from 1992‐93 to 2010‐11. It will also be possible to analyse change for a wider range of land uses between 2005‐06 and 2010‐11. This is being developed by the Australian Collaborative Land Use and Management Program (ACLUMP), a consortium of national and state agencies coordinated by ABARES. Authored by Jodie Mewett, Justyna Paplinska, Georgina Kelley, Rob Lesslie, Phil Pritchard and Christine Atyeo

A Forest of Blue - Canada's Boreal Forest, the World's Waterkeeper

Describes how the lakes, rivers, and wetlands comprising the boreal forest preserve biodiversity, mitigate global climate change effects, and offer food and cultural benefits to rural communities. Suggests policies to limit damaging industrial activities

Crisis in Indonesia: Forests, fires and finances

The jewel in the East Asian "economic miracle" of the 1980s and 1990s came crashing to earth during late 1997 with a collapse of the currency and disintegration of the banking system. By mid-1998 Suharto was forced out of office by a tidal wave of street protests, and raging fires were ablaze throughout the land. In this paper we draw attention to the fundamentals of the finance crisis and the environmental crisis as they relate to the state of tropical rainforests in Indonesia. It is concluded that, somewhat ironically, the dramatic collapse of the Indonesian economy and the devastating forest fires of the late 1990s may lead to the preservation of one of the earth's most significant heritage sites, the tropical rainforests and biodiversity of Indonesia

Freshwater ecosystem services in mining regions : modelling options for policy development support

The ecosystem services (ES) approach offers an integrated perspective of social-ecological systems, suitable for holistic assessments of mining impacts. Yet for ES models to be policy-relevant, methodological consensus in mining contexts is needed. We review articles assessing ES in mining areas focusing on freshwater components and policy support potential. Twenty-six articles were analysed concerning (i) methodological complexity (data types, number of parameters, processes and ecosystem-human integration level) and (ii) potential applicability for policy development (communication of uncertainties, scenario simulation, stakeholder participation and management recommendations). Articles illustrate mining impacts on ES through valuation exercises mostly. However, the lack of ground-and surface-water measurements, as well as insufficient representation of the connectivity among soil, water and humans, leave room for improvements. Inclusion of mining-specific environmental stressors models, increasing resolution of topographies, determination of baseline ES patterns and inclusion of multi-stakeholder perspectives are advantageous for policy support. We argue that achieving more holistic assessments exhorts practitioners to aim for high social-ecological connectivity using mechanistic models where possible and using inductive methods only where necessary. Due to data constraints, cause-effect networks might be the most feasible and best solution. Thus, a policy-oriented framework is proposed, in which data science is directed to environmental modelling for analysis of mining impacts on water ES

Ecological models at fish community and species level to support effective river restoration

RESUMEN Los peces nativos son indicadores de la salud de los ecosistemas acuáticos, y se han convertido en un elemento de calidad clave para evaluar el estado ecológico de los ríos. La comprensión de los factores que afectan a las especies nativas de peces es importante para la gestión y conservación de los ecosistemas acuáticos. El objetivo general de esta tesis es analizar las relaciones entre variables biológicas y de hábitat (incluyendo la conectividad) a través de una variedad de escalas espaciales en los ríos Mediterráneos, con el desarrollo de herramientas de modelación para apoyar la toma de decisiones en la restauración de ríos. Esta tesis se compone de cuatro artículos. El primero tiene como objetivos modelar la relación entre un conjunto de variables ambientales y la riqueza de especies nativas (NFSR), y evaluar la eficacia de potenciales acciones de restauración para mejorar la NFSR en la cuenca del río Júcar. Para ello se aplicó un enfoque de modelación de red neuronal artificial (ANN), utilizando en la fase de entrenamiento el algoritmo Levenberg-Marquardt. Se aplicó el método de las derivadas parciales para determinar la importancia relativa de las variables ambientales. Según los resultados, el modelo de ANN combina variables que describen la calidad de ribera, la calidad del agua y el hábitat físico, y ayudó a identificar los principales factores que condicionan el patrón de distribución de la NFSR en los ríos Mediterráneos. En la segunda parte del estudio, el modelo fue utilizado para evaluar la eficacia de dos acciones de restauración en el río Júcar: la eliminación de dos azudes abandonados, con el consiguiente incremento de la proporción de corrientes. Estas simulaciones indican que la riqueza aumenta con el incremento de la longitud libre de barreras artificiales y la proporción del mesohabitat de corriente, y demostró la utilidad de las ANN como una poderosa herramienta para apoyar la toma de decisiones en el manejo y restauración ecológica de los ríos Mediterráneos. El segundo artículo tiene como objetivo determinar la importancia relativa de los dos principales factores que controlan la reducción de la riqueza de peces (NFSR), es decir, las interacciones entre las especies acuáticas, variables del hábitat (incluyendo la conectividad fluvial) y biológicas (incluidas las especies invasoras) en los ríos Júcar, Cabriel y Turia. Con este fin, tres modelos de ANN fueron analizados: el primero fue construido solamente con variables biológicas, el segundo se construyó únicamente con variables de hábitat y el tercero con la combinación de estos dos grupos de variables. Los resultados muestran que las variables de hábitat son los ¿drivers¿ más importantes para la distribución de NFSR, y demuestran la importancia ecológica de los modelos desarrollados. Los resultados de este estudio destacan la necesidad de proponer medidas de mitigación relacionadas con la mejora del hábitat (incluyendo la variabilidad de caudales en el río) como medida para conservar y restaurar los ríos Mediterráneos. El tercer artículo busca comparar la fiabilidad y relevancia ecológica de dos modelos predictivos de NFSR, basados en redes neuronales artificiales (ANN) y random forests (RF). La relevancia de las variables seleccionadas por cada modelo se evaluó a partir del conocimiento ecológico y apoyado por otras investigaciones. Los dos modelos fueron desarrollados utilizando validación cruzada k-fold y su desempeño fue evaluado a través de tres índices: el coeficiente de determinación (R2 ), el error cuadrático medio (MSE) y el coeficiente de determinación ajustado (R2 adj). Según los resultados, RF obtuvo el mejor desempeño en entrenamiento. Pero, el procedimiento de validación cruzada reveló que ambas técnicas generaron resultados similares (R2 = 68% para RF y R2 = 66% para ANN). La comparación de diferentes métodos de machine learning es muy útil para el análisis crítico de los resultados obtenidos a través de los modelos. El cuarto artículo tiene como objetivo evaluar la capacidad de las ANN para identificar los factores que afectan a la densidad y la presencia/ausencia de Luciobarbus guiraonis en la demarcación hidrográfica del Júcar. Se utilizó una red neuronal artificial multicapa de tipo feedforward (ANN) para representar relaciones no lineales entre descriptores de L. guiraonis con variables biológicas y de hábitat. El poder predictivo de los modelos se evaluó con base en el índice Kappa (k), la proporción de casos correctamente clasificados (CCI) y el área bajo la curva (AUC) característica operativa del receptor (ROC). La presencia/ausencia de L. guiraonis fue bien predicha por el modelo ANN (CCI = 87%, AUC = 0.85 y k = 0.66). La predicción de la densidad fue moderada (CCI = 62%, AUC = 0.71 y k = 0.43). Las variables más importantes que describen la presencia/ausencia fueron: radiación solar, área de drenaje y la proporción de especies exóticas de peces con un peso relativo del 27.8%, 24.53% y 13.60% respectivamente. En el modelo de densidad, las variables más importantes fueron el coeficiente de variación de los caudales medios anuales con una importancia relativa del 50.5% y la proporción de especies exóticas de peces con el 24.4%. Los modelos proporcionan información importante acerca de la relación de L. guiraonis con variables bióticas y de hábitat, este nuevo conocimiento podría utilizarse para apoyar futuros estudios y para contribuir en la toma de decisiones para la conservación y manejo de especies en los en los ríos Júcar, Cabriel y Turia.Olaya Marín, EJ. (2013). Ecological models at fish community and species level to support effective river restoration [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/28853TESI