The Accuracy and Reliability of Traditional Surface Flow Type Mapping: Is It Time for A New Method of Characterising Physical River Habitat?

Surface flow types (SFT) are advocated as ecologically relevant hydraulic units, often mapped visually from the bankside to characterise rapidly the physical habitat of rivers. SFT mapping is simple, non-invasive and cost-efficient. However, it is also qualitative, subjective and plagued by difficulties in recording accurately the spatial extent of SFT units. Quantitative validation of the underlying physical habitat parameters is often lacking, and does not consistently differentiate between SFTs. Here, we investigate explicitly the accuracy, reliability and statistical separability of traditionally mapped SFTs as indicators of physical habitat, using independent, hydraulic and topographic data collected during three surveys of a c. 50m reach of the River Arrow, Warwickshire, England. We also explore the potential of a novel remote sensing approach, comprising a small unmanned aerial system (sUAS) and Structure-from-Motion photogrammetry (SfM), as an alternative method of physical habitat characterisation. Our key findings indicate that SFT mapping accuracy is highly variable, with overall mapping accuracy not exceeding 74%. Results from analysis of similarity (ANOSIM) tests found that strong differences did not exist between all SFT pairs. This leads us to question the suitability of SFTs for characterising physical habitat for river science and management applications. In contrast, the sUAS-SfM approach provided high resolution, spatially continuous, spatially explicit, quantitative measurements of water depth and point cloud roughness at the microscale (spatial scales ≤1m). Such data are acquired rapidly, inexpensively, and provide new opportunities for examining the heterogeneity of physical habitat over a range of spatial and temporal scales. Whilst continued refinement of the sUAS-SfM approach is required, we propose that this method offers an opportunity to move away from broad, mesoscale classifications of physical habitat (spatial scales 10-100m), and towards continuous, quantitative measurements of the continuum of hydraulic and geomorphic conditions which actually exists at the microscale.

Validation of Electronic Health Record Phenotyping of Bipolar Disorder Cases and Controls

Objective: The study was designed to validate use of elec-tronic health records (EHRs) for diagnosing bipolar disorder and classifying control subjects. Method: EHR data were obtained from a health care system of more than 4.6 million patients spanning more than 20 years. Experienced clinicians reviewed charts to identify text features and coded data consistent or inconsistent with a diagnosis of bipolar disorder. Natural language processing was used to train a diagnostic algorithm with 95% specificity for classifying bipolar disorder. Filtered coded data were used to derive three additional classification rules for case subjects and one for control subjects. The positive predictive value (PPV) of EHR-based bipolar disorder and subphenotype di- agnoses was calculated against diagnoses from direct semi- structured interviews of 190 patients by trained clinicians blind to EHR diagnosis. Results: The PPV of bipolar disorder defined by natural language processing was 0.85. Coded classification based on strict filtering achieved a value of 0.79, but classifications based on less stringent criteria performed less well. No EHR- classified control subject received a diagnosis of bipolar dis- order on the basis of direct interview (PPV=1.0). For most subphenotypes, values exceeded 0.80. The EHR-based clas- sifications were used to accrue 4,500 bipolar disorder cases and 5,000 controls for genetic analyses. Conclusions: Semiautomated mining of EHRs can be used to ascertain bipolar disorder patients and control subjects with high specificity and predictive value compared with diagnostic interviews. EHRs provide a powerful resource for high-throughput phenotyping for genetic and clinical research.