Saving our Species: Guidelines for estimating a evaluating species' response to management

Provides guidance to species' managers within the Saving our Species program on how to estimate a species’ response to management for the purpose of setting targets for adaptive management. These guidelines were developed through a series of end user workshops and are designed as a\ua0tool for using expert judgement in the absence of quantitative data. This is a acheived using a combination of conceptual modelling\ua0and a structured elicitiation protocol. This work was commissioned by the NSW Department on Planning Industry and the Environment (formerly Office of Environment and Heritage) and carried out in conjunction with the National Environmental Science Program Threatened Species Recovery Hub

Afterschool Program Effects on English Learners\u27 Reading and Teachers\u27 Reading Curriculum Perceptions

This project study addressed the problem of 3rd grade English language learners (ELLs) not passing the state mandated reading test at the same rate as other students between 2009 and 2013 in Georgia. The purpose of the study was to examine the effects of an elementary school\u27s afterschool program (ASP) on ELLs\u27 reading achievements and to investigate 3rd grade afterschool teachers\u27 perceptions of the reading curriculum using a mixed methods explanatory sequential design. Schema theory, the framework used to guide this study, indicated prior knowledge and experiences are necessary to comprehend new ideas or concepts. Prior knowledge and experiences can be gained from the instruction provided during ASPs. During the quantitative phase, a paired-samples t test was conducted using archived data from 2014 on 43 ELLs. The result was a significant increase in reading from pre- to posttest. In the qualitative phase, two 3rd grade ASP teachers were interviewed about their perceptions of the reading curriculum and those interviews were then analyzed using In Vivo coding and 2 cycle analysis. Themes revealed were professional development (PD), curriculum presentation, instructional strategies, and ASP modifications. A 4-day PD was designed for teachers providing plans to teach ELLs academic content and literacy. PD would provide teachers with reading instructional strategies to teach ELLs, which may increase their achievement on state tests to decrease the ELL reading achievement gap. Implications for positive social change include using an ASP and PD to increase ELLs\u27 reading achievements and to increase success on state mandated tests

Use of a structure aware discretisation algorithm for Bayesian networks applied to water quality predictions

Bayesian networks have become a popular modelling technique in many fields, however there are several design decisions that, if poorly made, can result in models with insufficient evidence to make good predictions. One such decision is how to discretise the continuous nodes. The lack of a commonly accepted algorithm for achieving this makes it a difficult task for novice data modellers. We present a structure aware discretisation algorithm that minimises the number of missing values in the conditional probability tables by taking into account the network structure. It also prevents users from having to specify the exact number of bins. Results from two water quality case studies in south-east Queensland showed that the algorithm has potential to improve the discretisation process over equal case discretisation and demonstrates the suitability of Bayesian networks for this field

Use of freely available datasets and machine learning methods in predicting deforestation

The range and quality of freely available geo-referenced datasets is increasing. We evaluate the usefulness of free datasets for deforestation prediction by comparing generalised linear models and generalised linear mixed models (GLMMs) with a variety of machine learning models (Bayesian networks, artificial neural networks and Gaussian processes) across two study regions. Freely available datasets were able to generate plausible risk maps of deforestation using all techniques for study zones in both Mexico and Madagascar. Artificial neural networks outperformed GLMMs in the Madagascan (average AUC 0.83 vs 0.80), but not the Mexican study zone (average AUC 0.81 vs 0.89). In Mexico and Madagascar, Gaussian processes (average AUC 0.89, 0.85) and structured Bayesian networks (average AUC 0.88, 0.82) performed at least as well as GLMMs (average AUC 0.89, 0.80). Bayesian networks produced more stable results across different sampling methods. Gaussian processes performed well (average AUC 0.85) with fewer predictor variables

Structurally aware discretisation for Bayesian networks

Bayesian networks represent a versatile probabilistic modelling technique widely used to tackle a range of problems in many different domains. However, they are discrete models, and a significant decision when designing a BN is how to split the continuous variables into discrete bins. Default options offered in most BN packages include assigning an equal number of cases to each bin or assigning equal sized bins. However, these methods discretise nodes independently of each other. When learning probabilities from data, this can result in conditional probability tables (CPTs) with missing or uninformed probabilities because data for particular bin combinations (scenarios) is either missing or scarce. This can result in poor model performance

Use of geographically weighted logistic regression to quantify spatial variation in the environmental and sociodemographic drivers of leptospirosis in Fiji: a modelling study.

BACKGROUND: Leptospirosis is a globally important zoonotic disease, with complex exposure pathways that depend on interactions between human beings, animals, and the environment. Major drivers of outbreaks include flooding, urbanisation, poverty, and agricultural intensification. The intensity of these drivers and their relative importance vary between geographical areas; however, non-spatial regression methods are incapable of capturing the spatial variations. This study aimed to explore the use of geographically weighted logistic regression (GWLR) to provide insights into the ecoepidemiology of human leptospirosis in Fiji. METHODS: We obtained field data from a cross-sectional community survey done in 2013 in the three main islands of Fiji. A blood sample obtained from each participant (aged 1-90 years) was tested for anti-Leptospira antibodies and household locations were recorded using GPS receivers. We used GWLR to quantify the spatial variation in the relative importance of five environmental and sociodemographic covariates (cattle density, distance to river, poverty rate, residential setting [urban or rural], and maximum rainfall in the wettest month) on leptospirosis transmission in Fiji. We developed two models, one using GWLR and one with standard logistic regression; for each model, the dependent variable was the presence or absence of anti-Leptospira antibodies. GWLR results were compared with results obtained with standard logistic regression, and used to produce a predictive risk map and maps showing the spatial variation in odds ratios (OR) for each covariate. FINDINGS: The dataset contained location information for 2046 participants from 1922 households representing 81 communities. The Aikaike information criterion value of the GWLR model was 1935·2 compared with 1254·2 for the standard logistic regression model, indicating that the GWLR model was more efficient. Both models produced similar OR for the covariates, but GWLR also detected spatial variation in the effect of each covariate. Maximum rainfall had the least variation across space (median OR 1·30, IQR 1·27-1·35), and distance to river varied the most (1·45, 1·35-2·05). The predictive risk map indicated that the highest risk was in the interior of Viti Levu, and the agricultural region and southern end of Vanua Levu. INTERPRETATION: GWLR provided a valuable method for modelling spatial heterogeneity of covariates for leptospirosis infection and their relative importance over space. Results of GWLR could be used to inform more place-specific interventions, particularly for diseases with strong environmental or sociodemographic drivers of transmission. FUNDING: WHO, Australian National Health & Medical Research Council, University of Queensland, UK Medical Research Council, Chadwick Trust

Predictive risk mapping of an environmentally-driven infectious disease using spatial Bayesian networks: A case study of leptospirosis in Fiji

Introduction Leptospirosis is a zoonotic disease responsible for over 1 million severe cases and 60,000 deaths annually. The wide range of animal hosts and complex environmental drivers of transmission make targeted interventions challenging, particularly when restricted to regression-based analyses which have limited ability to deal with complexity. In Fiji, important environmental and socio-demographic factors include living in rural areas, poverty, and livestock exposure. This study aims to examine drivers of transmission under different scenarios of environmental and livestock exposures. Methods Spatial Bayesian networks (SBN) were used to analyse the influence of livestock and poverty on the risk of leptospirosis infection in urban compared to rural areas. The SBN models used a combination of spatially-explicit field data from previous work and publically available census information. Predictive risk maps were produced for overall risk, and for scenarios related to poverty, livestock, and urban/rural setting. Results While high, rather than low, commercial dairy farm density similarly increased the risk of infection in both urban (12% to 18%) and rural areas (70% to 79%), the presence of pigs in a village had different impact in rural (43% to 84%) compared with urban areas (4% to 24%). Areas with high poverty rates were predicted to have 26.6% and 18.0% higher probability of above average seroprevalence in rural and urban areas, respectively. In urban areas, this represents >300% difference between areas of low and high poverty, compared to 43% difference in rural areas. Conclusions Our study demonstrates the use of SBN to provide valuable insights into the drivers of leptospirosis transmission under complex scenarios. By estimating the risk of leptospirosis infection under different scenarios, such as urban versus rural areas, these subgroups or areas can be targeted with more precise interventions that focus on the most relevant key drivers of infection

A community survey of coverage and adverse events following country-wide triple-drug mass drug administration for lymphatic filariasis elimination, Samoa 2018

The Global Programme to Eliminate Lymphatic Filariasis has made considerable progress but is experiencing challenges in meeting targets in some countries. Recent World Health Organization guidelines have recommended two rounds of triple-drug therapy with ivermectin, diethylcarbamazine (DEC), and albendazole (IDA), in areas where mass drug administration (MDA) results with two drugs (DEC and albendazole) have been suboptimal, as is the case in Samoa. In August 2018, Samoa was the first country in the world to implement countrywide triple-drug MDA. This paper aims to describe Samoa’s experience with program coverage and adverse events (AEs) in the first round of triple-drug MDA. We conducted a large cross-sectional community survey to assess MDA awareness, reach, compliance, coverage and AEs in September/October 2018, 7–11 weeks after the first round of triple-drug MDA. In our sample of 4420 people aged ≥2 years (2.2% of the population), age-adjusted estimates indicated that 89.0% of the eligible population were offered MDA, 83.9% of the eligible population took MDA (program coverage), and 80.2% of the total population took MDA (epidemiological coverage). Overall, 83.8% (2986/3563) reported that they did not feel unwell at all after taking MDA. Mild AEs (feeling unwell but able to do normal everyday things) were reported by 13.3% (476/3563) and moderate or severe AEs (feeling unwell and being unable to do normal everyday activities such as going to work or school) by 2.9% (103/3563) of participants. This study following the 2018 triple-drug MDA in Samoa demonstrated a high reported program awareness and reach of 90.8% and 89.0%, respectively. Age-adjusted program coverage of 83.9% of the total population showed that MDA was well accepted and well tolerated by the community