[131] R. W. Rayner. Germination and penetration studies on coffee rust (Hemileia vastatrix B. & Br.). *Annals of Applied Biology*, 49(3):497-505, 1961. doi:10.1111/j.1744-7348.1961.tb03641.x. (Cited on pages 36, 64, 100 and 126.)

[132] R. Razafindramamba. Biologie de la rouille du caféier. *Revue de Mycologie*, 23:177-200, 1958. URL: https://www/documentation.ird.fr/hor/fdi:11779. (Cited on page 33.)

[133] L. Rimbaud, F. Fabre, J. Papaïx, B. Moury, C. Lannou, L. G. Barrett, and P. H. Thrall. Models of plant resistance deployment. *Annual Review of Phytopathology*, 59:125-152, 2021. doi:10.1146/annurev-phyto-020620-122134. (Cited on page 121.)

[134] L. Rimbaud, J. Papaïx, L. G. Barrett, J. J. Burdon, and P. H. Thrall. Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance? *Evolutionary Applications*, 11(10):1791-1810, 2018. doi:10.1111/eva.12681. (Cited on pages 12, 33 and 91.)

[135] C. Rodrigues Jr, A. Bettencourt, and L. Rijo. Races of the pathogen and resistance to coffee rust. *Annual review of phytopathology*, 13(1):49-70, 1975. doi:10.1146/annurev.py.13.090175.000405. (Cited on page 10.)

[136] C. J. Rodrigues Jr. Coffee rusts: history, taxonomy, morphology, distribution and host resistance. *Fitopatologia Brasileira*, 15:5-9, 1990. (Cited on pages 9 and 62.)

[137] R. Ross. *The prevention of malaria*. John Murray, 1911. (Cited on page 11.)

[138] M. A. Rutherford and N. Phiri. Pests and diseases of coffee in eastern Africa: A technical and advisory manual. *Wallingford, UK: CAB International*, 2006. URL: https://fa2q.net/sites/cooperativeknowledge.info/files/resource/U3071CoffeeManual.pdf. (Cited on pages 2, 3 and 4.)

[139] E. Santiago-Elena, E. J. Zamora-Macorra, M. Zamora-Macorra, and K. G. Elizalde-Gaytan. Interaction between mycodiplosis and hemileia vastatrix in three scenarios of coffee crop management (coffea arabica). *Revista mexicana de fitopatología*, 38(3):320-336, 2020. doi:10.18781/r.mex.fit.2005-2. (Cited on pages 10, 92 and 120.)

[140] N. Sapoukhina, Y. Tyutyunov, I. Sache, and R. Arditi. Spatially mixed crops to control the stratified dispersal of airborne fungal diseases. *Ecological Modelling*, 221(23):2793-2800, 2010. doi:10.1016/j.ecolmodel.2010.08.020. (Cited on pages 12, 33, 61 and 62.)

[141] M. Saubin, S. de Mita, X. Zhu, B. Sudret, and F. Halkett. Impact of ploidy and pathogen life cycle on resistance durability. *Peer Community in Evolutionary Biology*, Aug. 2021. URL: https://hal.archives-ouvertes.fr/hal-03610230, doi:10.24072/pcjournal.10. (Cited on page 10.)

[142] G. H. Sera, C. H. S. de Carvalho, J. C. de Rezende Abrahão, E. A. Pozza, J. B. Matiello, S. R. de Almeida, L. Bartelega, and D. M. dos Santos Botelho. Coffee leaf rust in brazil: Historical events, current situation, and control measures. *Agronomy*, 12(2), 2022. doi:10.3390/agronomy12020496. (Cited on pages 10 and 11.)
[143] R. Setiawati, A. Widiastuti, A. Wibowo, and A. Priyatmojo. Variability of lecanicillium spp. mycoparasite of coffee leaf rust pathogen (hemileia vastatrix) in Indonesia. *Pakistan Journal of Biological Sciences: PJBS*, 24(5):588-598, 2021. doi:10.3923/pjbs.2021.588.598. (Cited on page 117.)

[144] J. Shafi, H. Tian, and M. Ji. Bacillus species as versatile weapons for plant pathogens: a review. *Biotechnology & Biotechnological Equipment*, 31(3):446-459, 2017. doi:10.1080/13102818.2017.1286950. (Cited on page 92.)

[145] E. G. Sharvelle. *Plant disease control*. The AVI Publishing Company, 1979. (Cited on pages 9, 10 and 91.)

[146] H. F. Shiomi, H. S. A. Silva, I. S. d. Melo, F. V. Nunes, and W. Bettiol. Bioprospecting endophytic bacteria for biological control of coffee leaf rust. *Scientia Agricola*, 63:32-39, 2006. doi:10.1590/S0103-90162006000100006. (Cited on pages 10 and 75.)

[147] H. S. A. Silva, J. P. Tozzi, C. R. F. Terrasan, and W. Bettiol. Endophytic microorganisms from coffee tissues as plant growth promoters and biocontrol agents of coffee leaf rust. *Biological Control*, 63(1):62-67, 2012. doi:10.1016/j.biocontrol.2012.06.005. (Cited on page 75.)

[148] V. Singh and B. Deverall. Bacillus subtilis as a control agent against fungal pathogens of citrus fruit. *Transactions of the British Mycological Society*, 83(3):487-490, 1984. doi:10.1016/S0007-1536(84)80045-5. (Cited on page 92.)

[149] R. L. Steyaert. Cladosporium hemileiae n. spec. un parasite de l'hemileia vastatrix berk. et br. *Bulletin de la Société Royale de Botanique de Belgique/Bulletin van de Koninklijke Belgische Botanische Vereniging*, 63(Fasc. 1):46-48, 1930. URL: https://www.jstor.org/stable/20791606. (Cited on pages 10 and 92.)

[150] C. Struck. Infection strategies of plant parasitic fungi. In B. Cooke, D. G. Jones, and B. Kaye, editors, *The Epidemiology of Plant Diseases*, pages 117-137. Springer, Dordrecht, 2006. doi:10.1007/1-4020-4581-6_4. (Cited on page 11.)

[151] J.-B. Suchel. Quelques remarques à propos de la répartition des pluies au Cameroun durant la période sèche 1969-1973. *Hommes et Terres du Nord*, 3(1):24-28, 1983. (Cited on pages 62, 99 and 100.)

[152] C. Tadmon and S. Foko. Modeling and mathematical analysis of an initial boundary value problem for hepatitis b virus infection. *Journal of Mathematical Analysis and Applications*, 474(1):309-350, 2019. doi:10.1016/j.jmaa.2019.01.047. (Cited on page 72.)

[153] P. Talhinhas, D. Batista, I. Diniz, A. Vieira, D. N. Silva, A. Loureiro, S. Tavares, A. P. Pereira, H. G. Azinheira, L. Guerra-Guimarães, et al. The coffee leaf rust pathogen hemileia vastatrix: one and a half centuries around the tropics. *Molecular plant pathology*, 18(8):1039, 2017. doi:10.1111/mpp.12512. (Cited on page 7.)

[154] A. T. Tamen, Y. Dumont, J.-J. Tewa, S. Bowong, and P. Couteron. A minimalistic model of tree-grass interactions using impulsive differential equations and non-linear feedback
functions of grass biomass onto fire-induced tree mortality. *Mathematics and Computers in Simulation*, 133:265-297, 2017. doi:10.1016/j.matcom.2016.03.008. (Cited on page 124.)

[155] I. Tankam-Chedjou, F. Grognard, J. J. Tewa, and S. Touzeau. Optimal and sustainable management of a soilborne banana pest. *Applied Mathematics and Computation*, 397:125883, 2021. doi:10.1016/j.amc.2020.125883. (Cited on pages 13 and 91.)

[156] I. Tankam-Chedjou, S. Touzeau, L. Mailleret, J. J. Tewa, and F. Grognard. Modelling and control of a banana soilborne pest in a multi-seasonal framework. *Mathematical biosciences*, 322:108324, 2020. doi:10.1016/j.mbs.2020.108324. (Cited on page 124.)

[157] B. S. Tchienkou-Tchiengang, I. Tankam-Chedjou, I. V. Yatat-Djeumen, and J. J. Tewa. Multi-seasonal modelling of the african maize stalk borer with assessment of crop residue management. *Applied Mathematical Modelling*, 114:379-407, 2023. URL: https://www.sciencedirect.com/science/article/pii/S0307904X22004474, doi:https://doi.org/10.1016/j.apm.2022.09.025. (Cited on page 13.)

[158] V. M. Toledo and P. Moguel. Coffee and sustainability: the multiple values of traditional shaded coffee. *Journal of Sustainable Agriculture*, 36(3):353-377, 2012. (Cited on page 61.)

[159] N. E. Torres Castillo, E. M. Melchor-Martínez, J. S. Ochoa Sierra, R. A. Ramirez-Mendoza, R. Parra-Saldívar, and H. M. Iqbal. Impact of climate change and early development of coffee rust – an overview of control strategies to preserve organic cultivars in mexico. *Science of The Total Environment*, 738:140225, 2020. doi:10.1016/j.scitotenv.2020.140225. (Cited on pages 5, 99 and 100.)

[160] V. Valencia, L. García-Barrios, E. J. Sterling, P. West, A. Meza-Jiménez, and S. Naeem. Smallholder response to environmental change: Impacts of coffee leaf rust in a forest frontier in mexico. *Land Use Policy*, 79:463-474, 2018. doi:10.1016/j.landusepol.2018.08.020. (Cited on page 3.)

[161] F. Van den Bosch, J. Metz, and J. Zadoks. Pandemics of focal plant disease, a model. *Phytopathology*, 89(6):495-505, 1999. doi:10.1094/PHYTO.1999.89.6.495. (Cited on page 12.)

[162] P. Van den Driessche and J. Watmough. Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. *Mathematical biosciences*, 180(1-2):29-48, 2002. doi:10.1016/s0025-5564(02)00108-6. (Cited on pages 21, 22, 40 and 42.)

[163] J. Van der Plank. Chapter 7 - analysis of epidemics. In J. HorsfallO and A. Dimond, editors, *Plant Pathology*, pages 229-289. Academic Press, 1960. doi:10.1016/B978-0-12-395678-1.50013-8. (Cited on pages 11 and 12.)

[164] J. Van der Plank. Dynamics of epidemics of plant disease: Population bursts of fungi, bacteria, or viruses in field and forest make an interesting dynamical study. *Science*, 147(3654):120-124, 1965. (Cited on page 11.)
[165] J. Vandermeer, Z. Hajian-Forooshani, and I. Perfecto. The dynamics of the coffee rust disease: an epidemiological approach using network theory. *European Journal of Plant Pathology*, 150(4):1001-1010, 2018. doi:10.1007/s10658-017-1339-x. (Cited on pages 17, 34, 61, 116 and 124.)

[166] J. Vandermeer, D. Jackson, and I. Perfecto. Qualitative dynamics of the coffee rust epidemic: educating intuition with theoretical ecology. *BioScience*, 64(3):210-218, 2014. doi:10.1007/s10658-017-1339-x. (Cited on pages 17, 61 and 120.)

[167] J. Vandermeer and A. King. Consequential classes of resources: Subtle global bifurcation with dramatic ecological consequences in a simple population model. *Journal of theoretical biology*, 263(2):237-241, 2010. doi:10.1016/j.jtbi.2009.12.006. (Cited on page 17.)

[168] J. Vandermeer, I. Perfecto, and H. Liere. Evidence for hyperparasitism of coffee rust (Hemileia vastatrix) by the entomogenous fungus, Lecanicillium lecanii, through a complex ecological web. *Plant Pathology*, 58(4):636-641, 2009. doi:10.1111/j.1365-3059.2009.02067.x. (Cited on pages 10, 75, 92, 117, 120 and 132.)

[169] J. Vandermeer and P. Rohani. The interaction of regional and local in the dynamics of the coffee rust disease. *arXiv*, 1407.8247, 2014. doi:10.48550/arXiv.1407.8247. (Cited on pages 17, 61 and 116.)

[170] J. Waller. Control of coffee diseases. In *Coffee*, pages 219-229. Springer, 1985. (Cited on page 2.)

[171] J. Waller, M. Bigger, and R. Hillocks. World coffee production. In *Coffee pests, diseases and their management*, pages 17-33. CABI Wallingford UK, 2007. (Cited on pages 2, 3 and 4.)

[172] J. M. Waller. Coffee rust—epidemiology and control. *Crop Protection*, 1(4):385-404, 1982. doi:10.1016/0261-2194(82)90022-9. (Cited on pages 33, 36, 62 and 64.)

[173] H. Wang. *Mathematical modeling I-preliminary*. Bookboon, 2012. (Cited on pages 25, 98 and 128.)

[174] J. Wang, J. Yang, and T. Kuniya. Dynamics of a pde viral infection model incorporating cell-to-cell transmission. *Journal of Mathematical Analysis and Applications*, 444(2):1542-1564, 2016. (Cited on page 72.)

[175] R. Ward, D. Gonthier, and C. Nicholls. Ecological resilience to coffee rust: Varietal adaptations of coffee farmers in copán, honduras. *Agroecology and Sustainable Food Systems*, 41(9-10):1081-1098, 2017. doi:10.1080/21683565.2017.1345033. (Cited on page 3.)

[176] Wikipedia. Hemileia vastatrix. [accessed 12/9/2022]. URL: https://en.wikipedia.org/wiki/Hemileia_vastatrix. (Cited on page 7.)

[177] J. N. Wintgens, editor. *Coffee: Growing, processing, sustainable production. A guide-book for growers, processors, traders and researchers*. Wiley, 2009. doi:10.1002/9783527619627. (Cited on pages 2, 4, 5, 10 and 33.)
[178] K. Wong and W. Tang. Optimal control of switched impulsive systems with time delay. *The ANZIAM Journal*, 53(4):292-307, 2012. doi:10.1017/S1446181112000284. (Cited on page 124.)

[179] A. Yagi. *Abstract parabolic evolution equations and their applications*. Springer Science & Business Media, 2009. (Cited on page 70.)

[180] L. Zambolim. Current status and management of coffee leaf rust in brazil. *Tropical Plant Pathology*, 41(1):1-8, 2016. doi:10.1007/s40858-016-0065-9. (Cited on pages 33, 36, 100 and 116.)

[181] B. Zewdie, A. J. Tack, B. Ayalew, G. Adugna, S. Nemomissa, and K. Hylander. Temporal dynamics and biocontrol potential of a hyperparasite on coffee leaf rust across a landscape in arabica coffee's native range. *Agriculture, Ecosystems & Environment*, 311:107297, 2021. doi:10.1016/j.agee.2021.107297. (Cited on pages 10, 17 and 18.)

[182] W. Zhu. Global exponential stability of impulsive reaction-diffusion equation with variable delays. *Applied Mathematics and Computation*, 205(1):362-369, 2008. doi:10.1016/j.amc.2008.08.018. (Cited on page 80.)