J. J. Burdon, P. H. Thrall, and L. Ericson, The current and future dynamics of disease in plant communities, Annual Review of Phytopathology, vol.44, pp.19-39, 2006.

R. C. Cobb, J. Filipe, R. K. Meentemeyer, C. A. Gilligan, and D. M. Rizzo, Ecosystem transformation by emerging infectious disease: loss of large tanoak from California forests, Journal of Ecology, vol.100, pp.712-722, 2012.

R. N. Mack, D. Simberloff, W. M. Lonsdale, H. Evans, and M. Clout, Biotic invasions: Causes, epidemiology, global consequences, and control, Ecological Applications, vol.10, pp.689-710, 2000.

E. C. Oerke, Crop losses to pests, Journal of Agricultural Science, vol.144, pp.31-43, 2006.

J. M. Raaijmakers, T. C. Paulitz, C. Steinberg, C. Alabouvette, and Y. Moenne-loccoz, The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms, Plant and Soil, vol.321, pp.341-361, 2009.

M. J. Jeger, Theory and plant epidemiology, Plant Pathology, vol.49, pp.651-658, 2000.

J. Chadoeuf, J. Pierrat, D. Nandris, J. Geiger, and N. M. , Modeling rubber tree root disease epidemics with a Markov spatial process, Forest science, vol.39, pp.41-54, 1993.

C. A. Gilligan, An epidemiological framework for disease management, Advances in Botanical Research, vol.38, pp.1-64, 2002.

W. Otten, J. Filipe, D. J. Bailey, and C. A. Gilligan, Quantification and analysis of transmission rates for soilborne epidemics, Ecology, vol.84, pp.3232-3239, 2003.

P. H. Thrall, J. D. Bever, J. D. Mihail, and H. M. Alexander, The population dynamics of annual plants and soil-borne fungal pathogens, Journal of Ecology, vol.85, pp.313-328, 1997.

C. A. Gilligan, J. E. Truscott, and A. J. Stacey, Impact of scale on the effectiveness of disease control strategies for epidemics with cryptic infection in a dynamical landscape: an example for a crop disease, Journal of the Royal Society Interface, vol.4, pp.925-934, 2007.

P. Lucas, Diseases caused by soil-borne pathogens, The Epidemiology of Plant Diseases, 2006.

L. M. Quesada-ocampo, D. W. Fulbright, and M. K. Hausbeck, Susceptibility of Fraser Fir to Phytophthora capsici, Plant Disease, vol.93, pp.135-141, 2009.

S. Kiewnick, B. J. Jacobsen, A. Braun-kiewnick, J. Eckhoff, and J. W. Bergman, Integrated Control of Rhizoctonia Crown and Root Rot of Sugar Beet with Fungicides and Antagonistic Bacteria, Plant Disease, vol.85, pp.718-722, 2001.

L. Tsror, Epidemiology and Management of Rhizoctonia solani on Potato, Journal of Phytopathology, vol.158, pp.649-658, 2010.

L. V. Madden, G. Hughes, and F. Van-den-bosch, The study of plant disease epidemics, 2007.

A. Ogoshi, Ecology and pathogenicity of anastomosis and intraspecific groups of Rhizoctonia solani Kühn, Annual Review of Phytopathology, vol.25, pp.125-143, 1987.

J. Filipe, E. M. Riley, C. J. Drakeley, C. J. Sutherland, and A. C. Ghani, Determination of the Processes Driving the Acquisition of Immunity to Malaria Using a Mathematical Transmission Model, PLoS Comput Biol, vol.3, p.255, 2007.

M. J. Keeling and P. Rohani, Modeling Infectious Diseases in Humans and Animals. Princeton and Oxford, 2008.

A. Krä-mer, M. Kretzschmar, and K. Krickeberg, Modern Infectious Disease Epidemiology: Concepts, Methods, Mathematical Models, and Public Health, 2009.

C. Fraser, S. Riley, R. M. Anderson, and N. M. Ferguson, Factors that make an infectious disease outbreak controllable, Proceedings of the National Academy of Sciences of the United States of America, vol.101, pp.6146-6151, 2004.

M. Chan and M. A. Johansson, The Incubation Periods of Dengue Viruses, Plos One, vol.7, p.50972, 2012.

R. M. Anderson and R. M. May, Infectious Diseases of Humans: Dynamics and Control, 1992.

W. O. Kermack and A. G. Mckendrick, A Contribution to the Mathematical Theory of Epidemics, Proceedings of the Royal Society of London Series A, vol.115, pp.700-721, 1927.

J. E. Van-der-plank, Plant diseases: epidemics and control, 1963.

N. Motisi, S. Poggi, J. Filipe, P. Lucas, and T. Doré, Epidemiological analysis of the effects of biofumigation for biological control of root rot in sugar beet, Plant Pathology, vol.62, pp.69-78, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01186857

S. P. Blythe and R. M. Anderson, Distributed incubation and infectious periods in models of the transmission dynamics of the human immunodeficiency virus (HIV), Ima Journal of Mathematics Applied in Medicine and Biology, vol.5, pp.1-19, 1988.

A. Cairns, Epidemics in Heterogeneous Populations: II. Nonexponential Incubation Periods and Variable Infectiousness, Mathematical Medicine and Biology, vol.7, pp.219-230, 1990.

A. L. Lloyd, Realistic distributions of infectious periods in epidemic models: Changing patterns of persistence and dynamics, Theoretical Population Biology, vol.60, pp.59-71, 2001.

J. Filipe, R. C. Cobb, R. K. Meentemeyer, C. A. Lee, and Y. S. Valachovic, Landscape Epidemiology and Control of Pathogens with Cryptic and LongDistance Dispersal: Sudden Oak Death in Northern Californian Forests, PLoS Computational Biology, vol.8, p.1002328, 2012.

N. J. Cunniffe, R. Stutt, F. Van-den-bosch, and C. A. Gilligan, TimeDependent Infectivity and Flexible Latent and Infectious Periods in Compartmental Models of Plant Disease, Phytopathology, vol.102, pp.365-380, 2012.

E. Vergu, H. Busson, and P. Ezanno, Impact of the Infection Period Distribution on the Epidemic Spread in a Metapopulation Model, Plos One, vol.5, 2010.

H. J. Wearing, P. Rohani, and M. J. Keeling, Appropriate models for the management of infectious diseases, Plos Medicine, vol.2, pp.813-813, 2005.

C. E. Windels and D. J. Nabben, Characterization and pathogenicity of anastomosis groups of Rhizoctonia solani isolated from Beta vulgaris, Phytopathology, vol.79, pp.83-88, 1989.

M. Leclerc, T. Doré, C. A. Gilligan, P. Lucas, and J. Filipe, Host Growth Can Cause Invasive Spread of Crops by Soilborne Pathogens, Plos One, vol.8, p.63003, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01186843

D. J. Lovell, S. J. Powers, S. J. Welham, and S. R. Parker, A perspective on the measurement of time in plant disease epidemiology, Plant Pathology, vol.53, pp.705-712, 2004.

E. L. Kaplan and P. Meier, Nonparametric Estimation from Incomplete Observations, Journal of the American Statistical Association, vol.53, pp.457-481, 1958.

, R: A language and environment for statistical computing, R Foundation for Statistical Computing, 2008.

O. C. Ibe, Markov Processes for Stochastic Modeling, 2009.

D. Lunn, D. Spiegelhalter, A. Thomas, and N. Best, The BUGS project: Evolution, critique and future directions, Statistics in Medicine, vol.28, pp.3049-3067, 2009.

N. Bailey, The Elements of Stochastic Processes with Applications to the Natural Sciences, 1964.

R. Durrett and S. A. Levin, Stochastic spatial models: a user's guide to ecological applications, Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, vol.343, pp.329-350, 1994.

J. Filipe and G. J. Gibson, Studying and approximating spatio-temporal models for epidemic spread and control, Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, vol.353, pp.2153-2162, 1998.

J. Filipe, W. Otten, G. J. Gibson, and C. A. Gilligan, Inferring the dynamics of a spatial epidemic from time-series data, Bulletin of Mathematical Biology, vol.66, pp.373-391, 2004.

T. Aoyagi, K. Kageyama, and M. Hyakumachi, Characterization and survival of Rhizoctonia solani AG2-2 LP associated with large patch disease of zoysia, Plant Disease, vol.82, pp.857-863, 1998.

D. J. Wilkinson, Stochastic Modelling for Systems Biology, 2006.

K. B. Johnson and P. S. Teng, Coupling a Disease Progress Model for Early Blight to a Model of Potato Growth, Phytopathology, vol.80, pp.416-425, 1990.

T. R. Gottwald, Current Epidemiological Understanding of Citrus Huanglongbing, Annual Review of Phytopathology, vol.48, pp.119-139, 2010.

C. Hillnhuetter, R. A. Sikora, E. C. Oerke, and D. Van-dusschoten, Nuclear magnetic resonance: a tool for imaging belowground damage caused by, 2012.

, Heterodera schachtii and Rhizoctonia solani on sugar beet, Journal of Experimental Botany, vol.63, pp.319-327

G. J. Reynolds, C. E. Windels, I. V. Macrae, and S. Laguette, Remote Sensing for Assessing Rhizoctonia Crown and Root Rot Severity in Sugar Beet, Plant Disease, vol.96, pp.497-505, 2012.

L. B. Brown, A. , and B. , Forest stand dynamics and sudden oak death: Mortality in mixed-evergreen forests dominated by coast live oak, Forest Ecology and Management, vol.257, pp.1271-1280, 2009.

K. B. Newman, S. T. Buckland, S. T. Lindley, L. Thomas, and C. Fernãndez, Hidden Process Models For Animal Population Dynamics, Ecological Applications, vol.16, pp.74-86, 2006.

R. S. Schick, S. R. Loarie, F. Colchero, B. D. Best, and A. Boustany, Understanding movement data and movement processes: current and emerging directions, Ecology Letters, vol.11, pp.1338-1350, 2008.

S. Soubeyrand, S. Neuvonen, and A. Penttinen, Mechanical-Statistical Modeling in Ecology: From Outbreak Detections to Pest Dynamics, Bulletin of Mathematical Biology, vol.71, pp.318-338, 2009.

G. J. Gibson and E. Renshaw, Estimating parameters in stochastic compartmental models using Markov chain methods, Mathematical Medicine and Biology, vol.15, pp.19-40, 1998.

F. J. Pérez-reche, F. M. Neri, S. N. Taraskin, and C. A. Gilligan, Prediction of invasion from the early stage of an epidemic, Journal of the Royal Society Interface, vol.9, pp.2085-2096, 2012.

D. Nandris, J. Chadoeuf, J. C. Pierrat, H. Joannes, and J. P. Geiger, Modelling rubber-tree root diseases, simulations of various inoculum rates and methods of control, European Journal of Forest Pathology, vol.26, pp.25-44, 1996.