Wrap Your Model!

Introduction Environmental models are often provided in the form of software solutions, with different levels of complexity. The simplest form is an executable file reading the model setup and boundary conditions from input files, doing the calculations and generating output files with model results. Preparing input files and reading output files requires to know and respect model specifics such as file formats and calling conventions. This user-unfriendliness may discourage the usage of models in this simplest form. However, these models may offer great opportunities since they are often freely available and contain the pure model core being fast in execution. This paper shows how specific requirements can be hidden from the user by wrapping the model software into packages for the software environment R . Methods and Results Two very different models have been wrapped : a groundwater drawdown and a sewer deterioration model. For each model an R package has been created, containing functions for writing input files, executing the model and reading output files. In one package, a function for reading model configurations from existing input files is also provided, thus allowing to manipulate existing model configurations and to rerun the model with the modified parameter set. By calling the functions in the R package repeatedly a sensitivity analysis identifying the most influential model parameters could be performed in an automated way. Conclusions Wrapping existing stand-alone model software into R packages provides the advantages of: - making models accessible from the R programming environment which is widely used in science, - using R\u27s methods and data structures for data preparation and analysis, - facilitating multiple model runs (e.g. for calibration, sensitivity analysis), - using R\u27s graphing capabilities to represent model results, - using R\u27s documentation standard to document the model\u27s usage, - facilitating the exchange of models between users

Examinations of the body temperature on experimental pigs, established with the transponder technique at different implantation sites in comparison to rectally measured body temperatures

Ziel der vorliegenden Arbeit war es, zu prüfen, ob ein Zusammenhang zwischen der digital gemessenen Rektaltemperatur und der subcutan gemessenen Temperatur mittels eines Temperaturtranspondersystems existiert. Des Weiteren sollte geklärt werden, inwieweit das Transpondersystem im Rahmen der Gesundheitsüberwachung von grossen Versuchstieren (Schweinen), die aus landwirtschaftlicher Produktion stammen, geeignet ist. Die Temperaturtransponder (IPTT- 100, Firma PLEXX, Elst, Niederlande) wurden an insgesamt 21 Läuferschweinen (14 weibliche und sieben männliche Tiere) getestet. Für die Lokalisationen der Temperaturtransponder wurden folgende vier Positionen ausgewählt: unter dem Scutulum (cartilago scutiformis) am linken Ohr, und jeweils an der rechten Körperseite am Ohrgrund, am Ansatz der letzten Rippe sowie am Schwanzansatz. Alle Tiere wurden vor der Applikation der Transponder mit Azaperon und Ketamin narkotisiert, was eine sehr gute Handhabung der Tiere zur Folge hatte. Anschliessend wurden die Tiere gereinigt und die vier Injektionsorte für die Transponder desinfiziert. Bei nur einem Tier konnte nach der Injektion der Transponder an nur einer Position (Scutulum) eine lokal entzündliche Reaktion festgestellt werden. Die Ergebnisse dieser Arbeit lassen die Schlussfolgerung zu, dass hygienisches Arbeiten einen positiven Effekt auf die Einheilung der Transponder hat und so entzündliche Reaktionen, Abszessbildungen und Transponderverluste minimiert werden können. Beim Applizieren der Transponder hat es sich als hilfreich herausgestellt, die Injektionskanüle ca. einen cm subcutan vorzuschieben und dann den Transponder abzulegen. Auch sollte die Einstichwunde nach dem Entfernen der Injektionskanüle zusammengedrückt werden. Die Untersuchungen wurden unter praxisnahen Bedingungen durchgeführt. Zu einem definierten Zeitpunkt wurden einmal täglich mit einem mobilen Lesegerät die Temperaturtransponder ausgelesen. Zeitgleich erfolgte die Messung der Rektaltemperatur mittels eines handelsüblichen digitalen Thermometers als Referenztemperatur. Die rektal gemessenen Temperaturen lieferten plausible Werte und stimmen mit denen in der Literatur beschriebenen Werten überein. Die Werte der Temperaturtransponder variierten in vielen Fällen sehr stark. Bei nur 20 Korrelationsberechnungen konnte eine signifikante Korrelation aufgedeckt werden und auch unter diesen variierten die Korrelationskoeffizienten stark. Bei den restlichen Korrelationen kann nicht vom Zufall unterschieden werden. Mittels der Korrelationsanalyse lässt sich keine generelle Bestimmung für einen Zusammenhang der jeweiligen Transponderposition mit der Rektaltemperatur beschreiben. Bei der Berechnung der Regression stellte sich heraus, dass bei den Regressionsparametern a und b die Spannweiten aber auch die Lagebereiche der Konfidenzintervalle stark schwankten und dadurch keine generelle Regressionsgleichung für die Beziehung der jeweiligen Transponderpositionen zur Rektaltemperatur beschrieben werden kann. Von 84 Transpondern zeigten 27 Funktionsausfälle. Von diesen 27 Funktionsausfällen konnten fünf auf Transponderverluste und 14 auf Beschädigungen oder Glasbruch der Transponderhülle zurückgeführt werden. Für acht Transponder konnte kein Grund festgestellt werden. Für die Funktionsausfälle gibt es verschiedene Erklärungen, z.B. mechanische Einflüsse auf den Transponder oder Herausdrücken des Transponders aus dem Injektionskanal. Schwankungen der Hauttemperatur sind u.a. bedingt durch Umwelteinflüsse, Verhalten der Tiere und physikalische Prozesse, wie z.B. Konvektion, Konduktion, Radiation und Verdunstung. Abschliessend kann in der von mir durchgeführten Arbeit als Ergebnis festgestellt werden, dass die Messung der Hauttemperatur mit Hilfe eines Temperaturtranspondersystems eine zu ungenaue Methode darstellt, um Rückschlüsse auf die Rektaltemperatur schliessen zu können. Die Hauttemperaturmessung mittels eines Transpondersystems ist ein hochsensibles Verfahren, wobei jedoch zu viele Faktoren den zu messenden Temperaturwert beeinflussen können. Diese Faktoren zu kontrollieren und eventuell zu neutralisieren erscheint zu aufwendig und kaum durchführbar. Beim Schwein spielen tierartspezifische Besonderheiten wie z.B. das Verhalten sowie erhöhte Stressanfälligkeit eine wichtige Rolle. Die Ergebnisse der vorliegenden Arbeit gelten somit nur für Schweine und sind nicht auf andere Tierarten mit den entsprechenden arttypischen Umweltbedingungen bzw. Verhalten anwendbar.Aim of the current study was to determine a correlation between the digitally measured rectal temperature and the subcutaneously measured temperature, by means of a temperature transponder system, in pigs. In addition it was examined to what degree the transponder system would be valuable in the supervision of the health status of large laboratory animals (e.g. pigs) originating from agricultural production systems. The temperature transponders (IPTT- 100, Company PLEXX, Elst, Netherlands), were tested on 21 pigs (14 females, seven males). For the localization of the transponders the following four sites were chosen: under the scutulum (cartilago scutiformis) of the left ear, and, all on the right side of the body, at the base of the ear, articulation of the last rib, and at the base of the tail. All animals were anaesethised with azaperon and ketamine before transponder implantation, which resulted in an easy handling of the animals afterwards. After implantation the animals were cleaned and the implantation sites disinfected. Only one animal, and only at one site (scutulum), developed a local inflammatory reaction after injection of the transponder. The results of this study propose that hygiene has a positive effect on the healing of the transponder sites, and minimizes inflammatory reactions and abscess formations at the transponder site as well as transponder losses. It proofed to be helpful to advance the injection needle approximately one cm subcutaneously before depositing the transponder and to apply pressure on the injection site after removal of the needle. The examinations were conducted under practice like condition. Once a day, at a set time, the transponders were red via a mobile reader and concurrently the rectal temperature was measured with a commercial digital thermometer as a reference temperature. The rectally measured temperatures were within normal limits according to published literature. The values of the temperature transponders varied in many of the measurements. Out of only 20 correlation measurements one correlation could be determined as significant, and even in between these the correlation coefficients varied greatly. The other correlations could not be set apart from coincidence. Using the correlation analysis, at different positions measured transponder temperatures, could not be put into context with the rectally measured temperatures. When calculating the regression it turned out that, looking at the regression parameters a and b, the range as well as the position of the confidence intervals varied greatly making it impossible to determine a general regression formula for the relationship between the transponder sites and the rectal temperatures. Out of 84 transponders 27 showed functional failures. Out of those 27 failures five were due to transponder losses and14 due to damage or breaking of the glass casing of the transponder. In eight cases the cause of failure could not be determined but possible explanations could be mechanical influences on the transponder or pushing of the transponder out of the injection canal. Variation of the skin temperature can be due to environmental influences, animal behaviour and physical processes like convection, conduction, radiation and evaporation. In conclusion, it can be determined with this current study, that the measurement of the skin temperatures via a transponder system does not provide an accurate method to draw conclusions about the rectal temperature. The measurement of the skin temperature with the transponder system is a very sensitive procedure which can still be influenced by too many factors. It seems too difficult to control or neutralize these factors and, in pigs, species specific features, such as behaviour and stress susceptibility play an important role. The results of this study are only valid for pigs and are not applicable to other species with species specific environmental and behavioural conditions

Support Vector Machines Used for the Prediction of the Structural Conditions of Pipes in Bogota’s Sewer System

Objective: this paper focused on: (i) developing a deterioration model based on support vector machines (SVM) from its regression approach to separate the prediction of the structural condition of sewer pipes from a classification by grades and predict the scores obtained by failures found in CCTV inspections; and (ii) comparing the prediction results of the proposed model with the ones obtained by a deterioration model based on SVM classification tasks to explore the advantages and disadvantages of their predictions from different perspectives. Materials and methods: The sewer network of Bogota was the case study for this work in which a dataset consisting of the characteristics of 5031 pipes inspected by CCTV (obtained by GIS) was considered, as well as information on external variables (e.g., age, sewerage, and road type). Probability density functions (PDF) were used to convert the scores given by failures found in CCTV into structural grades. In addition, three techniques were used to evaluate the predictions from different perspectives: positive likelihood rate (PLR), performance curve and deviation analysis. Results: it was found that: (i) SVM-based deterioration model used from its regression approach is suitable to predict critical structural conditions of uninspected sewer pipes because this model showed a PLR value around 6.8 (the highest value among the predictions of all structural conditions for both models) and 74 % of successful predictions for the first 100 pipes with the highest probability of being in critical conditions; and (ii) SVM-based deterioration model used from its classification approach is suitable to predict other structural conditions because this model showed homogeneous PLR values for the prediction of all structural conditions (PLR values between 1.67 and 3.88) and deviation analysis results for all structural conditions are lower than the ones for the SVM-based model from its regression approachObjetivo: este artículo se centra en: (i) desarrollar un modelo de deterioro basado en máquinas de soporte vectorial (SVM) a partir de su enfoque regresivo para desligar la predicción de la condición estructural del alcantarillado de los grados de clasificación y predecir los puntajes dados por las fallas encontradas en las inspecciones CCTV; y (ii) comparar los resultados de predicción del modelo propuesto con aquellos resultados obtenidos de un modelo basado en SVM a partir de su enfoque de clasificación con el fin de explorar las ventajas y desventajas en sus predicciones bajo diferentes perspectivas. Materiales y métodos: el caso de estudio considerado fue la red de alcantarillado de Bogotá, el cual contaba con 5031 tuberías inspeccionadas, información de las características físicas de las tuberías e información de factores externos (p. e., edad, tipo de afluente y tipo de vía). Las funciones de densidad de probabilidad (FDP) se utilizaron para convertir los puntajes de las fallas encontradas en las inspecciones de CCTV en grados estructurales. Además, se utilizaron tres técnicas para evaluar las predicciones mediante diferentes perspectivas: tasas de verosimilitud positiva (TPR), curvas de rendimiento y análisis de desviación. Resultados: se encuentra que: (i) el modelo de deterioro basado en SVM a partir de su enfoque de regresión es apropiado para predecir condiciones estructurales críticas, ya que este modelo muestra valores de TPR alrededor de 6.8 (el valor más alto entre la predicción de todas las condiciones estructurales en ambos modelos) y 74 % de predicciones exitosas en las primeras 100 tuberías con más altas probabilidades de estar en condición crítica; y (ii) el modelo de deterioro basado en SVM a partir de su enfoque de clasificación es apropiado para predecir las otras condiciones estructurales, ya que este modelo muestra valores de PLR homogéneos para la predicción de todas las condiciones estructurales (entre 1.67 y 3.88) y las desviaciones entre lo observado y lo predicho son menores que aquellos resultados obtenidos del modelo SVM a partir de su enfoque de regresió

Influence of local calibration on the quality of online wet weather discharge monitoring: feedback from five international case studies

International audienceThis paper reports about experiences gathered from five online monitoring campaigns in the sewer systems of Berlin (Germany), Graz (Austria), Lyon (France) and Bogota (Colombia) using ultraviolet–visible (UV–VIS) spectrometers and turbidimeters. Online probes are useful for the measurement of highly dynamic processes, e.g. combined sewer overflows (CSO), storm events, and river impacts. The influence of local calibration on the quality of online chemical oxygen demand (COD) measurements of wet weather discharges has been assessed. Results underline the need to establish local calibration functions for both UV–VIS spectrometers and turbidimeters. It is suggested that practitioners calibrate locally their probes using at least 15–20 samples. However, these samples should be collected over several events and cover most of the natural variability of the measured concentration. For this reason, the use of automatic peristaltic samplers in parallel to online monitoring is recommended with short representative sampling campaigns during wet weather discharges. Using reliable calibration functions, COD loads of CSO and storm events can be estimated with a relative uncertainty of approximately 20%. If no local calibration is established, concentrations and loads are estimated with a high error rate, questioning the reliability and meaning of the online measurement. Similar results have been obtained for total suspended solids measurements

Quantifying the effects of urban stormwater management - towards a novel approach for integrated planning

ABSTRACT Integrated planning of stormwater management requires a quantitative description of positive and negative effects of possible measures. We suggest quantifying these effects with generic performance indicators within eight categories: building physics and services, landscape quality, urban climate, biodiversity, groundwater, surface water, direct costs and indirect environmental costs. First results indicate that the defined performance indicators allow an objective pre-selection of measures based on their ability to reach local stormwater management goals. The final selection of measures should be based on an evaluation for a specific city quarter (to reduce indicator uncertainty) and reviewed by local stake holders

Multicenter Prospective Cohort Study of the Patient-Reported Outcome Measures PRO-CTCAE and CAT EORTC QLQ-C30 in Major Abdominal Cancer Surgery (PATRONUS): A Student-Initiated German Medical Audit (SIGMA) Study

Background!#!The patient-reported outcomes (PRO) version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE) and the computerized adaptive testing (CAT) version of the EORTC quality-of-life questionnaire QLQ-C30 have been proposed as new PRO measures in oncology; however, their implementation in patients undergoing cancer surgery has not yet been evaluated.!##!Methods!#!Patients undergoing elective abdominal cancer surgery were enrolled in a prospective multicenter study, and postoperative complications were recorded according to the Dindo-Clavien classification. Patients reported PRO data using the CAT EORTC QLQ-C30 and the PRO-CTCAE to measure 12 core cancer symptoms. Patients were followed-up for 6 months postoperatively. The study was carried out by medical students of the CHIR-Net SIGMA study network.!##!Results!#!Data of 303 patients were obtained and analyzed across 15 sites. PRO-CTCAE symptoms 'poor appetite', 'fatigue', 'exhaustion' and 'sleeping problems' increased after surgery and climaxed 10-30 days postoperatively. At 3-6 months postoperatively, no PRO-CTCAE symptom differed significantly to baseline. Patients reported higher 'social functioning' (p = 0.021) and overall quality-of-life scores (p < 0.05) 6 months after cancer surgery compared with the baseline level. There was a lack of correlation between postoperative complications or death and any of the PRO items evaluated. Feasibility endpoints for student-led research were met.!##!Conclusion!#!The two novel PRO questionnaires were successfully applied in surgical oncology. Postoperative complications do not affect health-reported quality-of-life or common cancer symptoms following major cancer surgery. The feasibility of student-led multicenter clinical research was demonstrated, but might be enhanced by improved student training