<b>simecol</b>: An Object-Oriented Framework for Ecological Modeling in<i>R</i>

Petzoldt, Thomas; Rinke, Karsten

doi:10.18637/jss.v022.i09

Cited by 70 publications

(48 citation statements)

References 36 publications

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“…Micro-kinetic modelling of the extracted absorbance bands was performed with the Simecol package [29]. The Runge-Kutta forth order integration solver (rk4), as implemented in to the deSolve package, was used for least-square fitting of model parameters to experimental data [30].…”

Section: Data Processing and Micro-kinetic Modellingmentioning

confidence: 99%

Adsorption and photo-oxidation of acetaldehyde on TiO2 and sulfate-modified TiO2: Studies by in situ FTIR spectroscopy and micro-kinetic modeling

Topalian

Stefanov

Granqvist

et al. 2013

Journal of Catalysis

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Adsorption and photocatalytic oxidation of acetaldehyde have been investigated on TiO 2 and sulphate-modified TiO 2 films (denoted SO 4 -TiO 2 ). In situ Fourier transform infrared spectroscopy was used to study surface reactions as a function of time and number of experimental cycles. Spectral analysis and micro-kinetic modelling show that crotonaldehyde formation occurs spontaneously on TiO 2 but is impeded on SO 4 -TiO 2 , where instead acetaldehyde desorption is significant. Photo-oxidation yields significant amounts of formate on TiO 2 , and was identified as the rate-determining step and associated with site blocking.Significantly smaller amounts of formate were observed on SO 4 -TiO 2 , which is due to the acidity of this surface resulting in weaker bonding of aldehyde and carboxylate intermediate species. Our results are of considerable interest for applications to photocatalytic air purification and to surfaces with controlled wettability.

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Section: Data Processing and Micro-kinetic Modellingmentioning

confidence: 99%

Adsorption and photo-oxidation of acetaldehyde on TiO2 and sulfate-modified TiO2: Studies by in situ FTIR spectroscopy and micro-kinetic modeling

Topalian

Stefanov

Granqvist

et al. 2013

Journal of Catalysis

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“…The R package simecol (Petzoldt and Rinke, 2007) To show the amount of effort needed for each management scenario, a value of one was assigned to each cell where buckthorn was removed and 0.5 for cells that were surveyed but buckthorn was not removed. This reflects the scenario where all mature buckthorns were removed from the patch before the beginning of the simulation and therefore buckthorn removal will only require hand pulling and will not require a large amount of effort relative to surveying.…”

Section: ~ 57 ~mentioning

confidence: 99%

Modelling the spread of European buckthorn in the Region of Waterloo

2017

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European buckthorn (Rhamnus cathartica L.) is a common invasive species in the Region of Waterloo. Management of buckthorn is expensive and time consuming and as a result it has continued to spread in the Region of Waterloo despite being on the Ontario noxious weed list.Control of buckthorn will require long term management to prevent reinvasion of managed areas.Therefore this project seeks to provide land managers with a model to predict the likely spread of buckthorn over time and space so that the cost of management can be predicted and different management strategies can be compared.A generalized linear mixed-effects model was used to create a habitat suitability model and a spread model for the probability of buckthorn presence for cells in a grid. The habitat suitability model predicts the presence of buckthorn based on environmental characteristics while the spread model predicts the likelihood of buckthorn invasion based on the suitability of habitat and the presence of buckthorn in the surrounding area. The spread model indicates that the invasion of buckthorn is influenced by the suitability of habitat and the presence of buckthorn in neighbouring cells. The success of the spread model suggests that this approach can be used to create a spatiotemporally explicit model with limited sampling effort. To explore the utility of the spread model for conservation management purposes, a simulation model was created that is based on the spread model. Simulations were performed to test the spread of buckthorn in a sample forest patch and to test different management strategies. The simulations showed that buckthorn can be controlled within a patch with a limited amount of effort. ~ iv ~ Acknowledgements

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“…It contains several optimization methods; we have chosen the Nelder--Mead algorithm for the presented computations. The procedure fitOdeModel is described in the report [9].…”

Section: Simulationsmentioning

confidence: 99%

Deterministic models and identification of their parameters

Pink¹

2011

Tatra Mountains Mathematical Publications

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ABSTRACT. This article deals with a possibility to identify parameters of a selected growth model of two populations coupled by a predator-prey interaction from a set of observed data. It starts with a brief description of the Gause-type model and of a property (interior equilibrium stability) important from a point of view of an application. Subsequently, data for four forms of the trophic function are simulated and then, a noise was added to the simulated data such that the coefficients of variation equal to 0.2, 0.3 and 0.4. For each data set, the parameters are estimated using a procedure implemented in the R-language package and the coordinates of equilibrium are computed. Then we can evaluate the effect of changing variation to the values of parameters and (un)stability of the equilibrium.

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simecol: An Object-Oriented Framework for Ecological Modeling inR

Cited by 70 publications

References 36 publications

Adsorption and photo-oxidation of acetaldehyde on TiO2 and sulfate-modified TiO2: Studies by in situ FTIR spectroscopy and micro-kinetic modeling

Adsorption and photo-oxidation of acetaldehyde on TiO2 and sulfate-modified TiO2: Studies by in situ FTIR spectroscopy and micro-kinetic modeling

Modelling the spread of European buckthorn in the Region of Waterloo

Deterministic models and identification of their parameters

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