README.md
In nlraa: Nonlinear Regression for Agricultural Applications

nlraa: R package for Nonlinear Regression for Agricultural

Applications

NOTE: the vignettes (nlraa-Oddi-LFMC and nlraa-AgronJ-paper) that used to be distributed with the package have been moved to the documentation above because of CRAN size limits.

Nonlinear Models (video) - part I

Nonlinear Models (video) - part II

Nonlinear Models (video) - part III

To install

library(remotes) \ remotes::install_github("femiguez/nlraa") \ library(nlraa)

This package supports the following publications:

Archontoulis, S. V., and F. E. Miguez. 2015. Nonlinear Regression Models and Applications in Agricultural Research. Agron. J. 107:786-798. \ https://doi.org/10.2134/agronj2012.0506
Miguez, F., S. Archontoulis, H. Dokoohaki 2018. Chapter 15: Nonlinear Regression Models and Applications. In: B. Glaz, K. M. Yeater, editors, Applied Statistics in Agricultural, Biological, and Environmental Sciences, ASA, CSSA, and SSSA, Madison, WI. p. 401-448. \ https://doi.org/10.2134/appliedstatistics.2016.0003
Oddi et. al. (2019). A nonlinear mixed-effects modelling approach for ecological data: Using temporal dynamics of vegetation moisture as an example. Ecology and Evolution. \ https://doi.org/10.1002/ece3.5543

Some recent publications that cite this package:

51. Moisture and nutrient management for sustainable dryland sun ower production. Loza et al. 2023. https://doi.org/10.21203/rs.3.rs-3697663/v1

50. Nitrogen fertilizer and pronitridine rates for corn production in the Midwest U.S. Kaur et al. 2023. https://doi.org/10.1016/j.fcr.2023.109200

49. The changing landscape of paddy cultivation in Andhra Pradesh: A statistical assessment of area, production, and productivity. https://dx.doi.org/10.22271/maths.2023.v8.i6Sc.1373

48. Assessment of Tissue Phosphorus Concentrations and Diagnostic Tools for Phosphorus Nutrition in Corn. Roa and Ruiz Diaz. 2023.

47. A New Scenario Framework for Equitable and Climate-Compatible Futures. Ranjan et al. 2023

46. Microbial race to colonise leaf litter in a littoral-lake environment and its relation to nutrient dynamics. Madaschi et al. 2023. https://doi.org/10.1111/fwb.14173

45. Enhancing Our Understanding of Optimal Nitrogen Fertilizer Rates for Maize: A Synthesis of Long-Term Experimentation and Crop Modeling. Baum. PhD Thesis. 2023.

44. Spatial Applications for Improved Nutrient and Agronomic Management in Minnesota Cropping Systems. Nigon, Leanna. PhD Thesis. 2023.

43. Genetic improvement of winter wheat (Triticum aestivum L.) grain yield in the Northern Great Plains of North America, 1959–2021, Boehm et al. 2023. https://doi.org/10.1002/csc2.21065

42. Background matching through fast and reversible melanin-based pigmentation plasticity in tadpoles comes with morphological and antioxidant changes. Liedtke et al. 2023. https://doi.org/10.1038/s41598-023-39107-4

41. Determining cardinal temperatures for eight cover crop species. Pessotto et al. 2023. https://doi.org/10.1002/agg2.20393

40. Maximizing winter wheat yield through planting date and seeding rate management. Copeland et al. 2023. https://doi.org/10.1002/cft2.20240

39. Accelerated leaf appearance and flowering in maize after four decades of commercial breeding. dos Santos et al. 2023. https://doi.org/10.1002/csc2.21044

38. Irrigated corn grain yield prediction in Florida using active sensors and plant height. Leitao et al. 2023. https://doi.org/10.1016/j.atech.2023.100276

37. Patterns of regional site index across a North American boreal forest gradient. Montesano et al. 2023. https://doi.org/10.1088/1748-9326/acdcab

36. Methods for Improving Potassium Fertilizer Recommendations for Corn in South Dakota. Andrew j. Ahlersmeyer. MS Thesis. 2023

35. Hemp yield and cannabinoid concentrations under variable nitrogen and potassium fertilizer rates. James et al. 2023. https://doi.org/10.1002/csc2.20966

34. Physical Modes of Action of Fungicides Against Apple Scab: Timing Is Everything, but Dose Matters. Vincent Philion, Valentin Joubert, Marc Trapman, and Arne Stensvand. https://doi.org/10.1094/PDIS-11-22-2758-RE

33. nlive: an R Package to facilitate the application of the sigmoidal and random change point mixed models. Capuano and Wagner. https://arxiv.org/pdf/2302.10836.pdf

32. The Effect of Harvest Date on Temporal Cannabinoid and Biomass Production in the Floral Hemp (Cannabis sativa L.) Cultivars BaOx and Cherry Wine. Linder et al. 2022. . https://doi.org/10.3390/horticulturae8100959

31. Establishing Transplant Date, Plant Spacing and Harvest Date Recommendations for Floral Hemp Production. Eric Linder. MS Thesis. 2022.

30. Estimating optimal sampling area for monitoring tropical forest restoration. Londe et al. (2022). Biological Conservation. https://doi.org/10.1016/j.biocon.2022.109532

29. Establishment, Growth, and Morphology of Miscanthus× Giganteus in Farmed Ephemeral Wetlands. Alex Steiner. MS Thesis. 2021.

28. Anything but Simple: Using Models and Field Studies to Explore the Effects of Cropping System Diversification in the Upper Midwestern United States. Virginia Nichols. PhD Thesis. 2021.

27. Love under lockdown: How changes in time with partner impacted stress and relationship outcomes during the COVID-19 pandemic. https://doi.org/10.1177/02654075231162599

26. Mitchell E. Baum, John E. Sawyer, Emerson D. Nafziger, Isaiah Huber, Peter J. Thorburn, Michael J. Castellano, Sotirios V. Archontoulis. Evaluating and improving APSIM's capacity in simulating long-term corn yield response to nitrogen in continuous- and rotated-corn systems, Agricultural Systems, Volume 207, 2023, https://doi.org/10.1016/j.agsy.2023.103629.

25. Physical Modes of Action of Fungicides Against Apple Scab: Timing is Everything, but Dose Matters Vincent Philion, Valentin Joubert, Marc Trapman, and Arne Stensvand. Published Online:23 Feb 2023https://doi.org/10.1094/PDIS-11-22-2758-RE

24. Song, S., Ding, Y., Li, W. et al. Mangrove reforestation provides greater blue carbon benefit than afforestation for mitigating global climate change. Nat Commun 14, 756 (2023). https://doi.org/10.1038/s41467-023-36477-1

23. Bonansea, S.; Ernst, O.R.; Mazzilli, S.R. Baseline for Brassica carinata Components of Nitrogen-Use Efficiency in Southern South America. Agronomy 2023, 13, 412. https://doi.org/10.3390/agronomy13020412

22. Gonzalo Carracelas, Nicolas Guilpart, Kenneth G. Cassman, Patricio Grassini, Distinguishing between yield plateaus and yield ceilings: A case study of rice in Uruguay, Field Crops Research, https://doi.org/10.1016/j.fcr.2023.108808.

21. McMaster ES, Chen SH, Yap J-YS, Rossetto M (2022) Conservation genomics of Persoonia hirsuta support of management. Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney.

20. Alejo Ruiz, Sotirios V. Archontoulis, Lucas Borrás, Kernel weight relevance in maize grain yield response to nitrogen fertilization, Field Crops Research, Volume 286, 2022, 108631, https://doi.org/10.1016/j.fcr.2022.108631.

19. Miguez, F. E., & Poffenbarger, H. (2022). How can we estimate optimum fertilizer rates with accuracy and precision? Agricultural & Environmental Letters, 7, e20075. https://doi.org/10.1002/ael2.20075

18. Pearce, A.W., Slaton, N.A., Lyons, S.E., Bolster, C.H., Bruulsema, T.W., Grove, J.H., Jones, J.D., McGrath, J.M., Miguez, F.E., Nelson, N.O., Osmond, D.L., Parvej, M.R., Pena-Yewtukhiw, E.M. and Spargo, J.T. (2022), Defining relative yield for soil test correlation and calibration trials in the fertilizer recommendation support tool. Soil Sci. Soc. Am. J.. Accepted Author Manuscript. https://doi.org/10.1002/saj2.20450

17. Rebecca L. Atkins, Kathleen M. Clancy, William T. Ellis, and Craig W. Osenberg. Thermal Traits Vary with Mass and across Populations of the Marsh Periwinkle, Littoraria irrorata. The Biological Bulletin. 2022. https://doi.org/10.1086/719850

16. Guamani-Quimis, Lenin A., Ariolfo L. Solís-Bowen, Diego Portalanza, and Felipe R. Garcés-Fiallos. 2022. Can Mathematical Models Describe Spear Rot Progress in Oil Palm Trees? A Five-Year Black Weevil-Disease Assessment from Ecuador. Agriculture 12, no. 2: 257. https://doi.org/10.3390/agriculture12020257

15. Nichols, V. A., Moore, E. B., Gailans, S., Kaspar, T. C., & Liebman, M. (2022). Site-specific effects of winter cover crops on soil water storage. Agrosyst Geosci Environ, 5:e220238. https://doi.org/10.1002/agg2.20238

14. Positive associations of soil organic matter and crop yields across a regional network of working farms. Emily E. Oldfield, Mark A. Bradford, Abigail J. Augarten, Eric T. Cooley, Amber M. Radatz, Timothy Radatz, Matthew D. Ruark. Soil Science Society of America. 2021. https://doi.org/10.1002/saj2.20349

13. Improvement of the Mass-Rearing Protocols for the South American Fruit Fly for Application of the Sterile Insect Technique. Mastrangelo et al. Insects 2021, 12(7), 622; https://doi.org/10.3390/insects12070622

12. High-yielding sugarcane in tropical Brazil – Integrating field experimentation and modelling approach for assessing variety performances. Henrique Boriolo Dias, Geoff Inman-Bamber, Paulo Cesar Sentelhas, Yvette Everingham, Rodrigo Bermejo, Diomedes Christodoulou. Field Crops Research. 2021. https://doi.org/10.1016/j.fcr.2021.108323.

11. Evaluation of mehlich-3 for determination of cation exchange capacity in Kansas soils. Edmond Bryan Rutter, Dorivar Ruiz Diaz,Lynn M. Hargrave. 2021. Soil Science Society of America. https://doi.org/10.1002/saj2.20354

10. Effects of human disturbance on postnatal growth and baseline corticosterone in a long-lived bird. Hannah Watson, Pat Monaghan, Britt J Heidinger, Mark Bolton. Conservation Physiology, Volume 9, Issue 1, 2021. https://doi.org/10.1093/conphys/coab052

9. The use of R in photosynthesis research. Yasi Liu, Xiangping Wang, Dayong Fan and Jiangshan Lai. Functional Plant Biology 1-8 https://doi.org/10.1071/FP21102

8. Topographic effects on soil microclimate and surface cover crop residue decomposition in rolling cropland. Sam J. Leuthold, Dan Quinn, Fernando Miguez, Ole Wendroth, Monsterrat Salmerón, Hanna Poffenbarger. Agriculture, Ecosystems & Environment, Volume 320, 2021. https://doi.org/10.1016/j.agee.2021.107609.

7. Long-term no-till increases soil nitrogen mineralization but does not affect optimal corn nitrogen fertilization practices relative to inversion tillage. Lucas Pecci Canisares, John Grove, Fernando Miguez and Hanna Poffenbarger. Soil and Tillage Research. Volume 213. 2021. 105080. https://doi.org/10.1016/j.still.2021.105080.

6. Rotating maize reduces the risk and rate of nitrate leaching. Heather Randolph Pasley, Nichols Virginia, Michael J Castellano, Matthew J Helmers, Mitchell E Baum, Eileen J Kladivko and Sotirios Archontoulis. 2021. Environmental Research Letters. https://doi.org/10.1088/1748-9326/abef8f

5. Abendroth, L.J., Miguez, F.E., Castellano, M.J., Carter, P.R., Messina, C.D., Dixon, P.M. and Hatfield, J.L. (2021), Lengthening of maize maturity time is not a widespread climate change adaptation strategy in the US Midwest. Glob Change Biol. https://doi.org/10.1111/gcb.15565

4. Interactive effect of glyphosate-based herbicides and organic soil layer thickness on growth and reproduction of the tropical earthworm Pontoscolex corethrurus (Müller, 1857). Garcia-Perez et al. (2020). https://doi.org/10.1016/j.apsoil.2020.103648

3. Cuando la variabilidad varía: Heterocedasticidad y funciones de varianza. Oddi, F. J., Miguez, F. E., Benedetti, G. G., & Garibaldi, L. A. (2020). Ecología Austral; 30; 438-453.

2. Short-term effects of integrated tillage systems and cover crop on agronomic response and soil health in North Central Iowa. Alex Cleveringa. 2020. MS Thesis. Iowa State University.

1. The Effects of Agronomic Management and 40 Years of Variety Release on Soybean Seed Fill and Yield Components. Kathryn Graf. 2018. MS thesis. Purdue University.

Other publications where we have used nonlinear mixed models:

Fernando E. Miguez, María Bonita Villamil, Stephen P. Long, Germán A. Bollero, Meta-analysis of the effects of management factors on Miscanthus × giganteus growth and biomass production, Agricultural and Forest Meteorology, Volume 148, Issues 8–9, 2008, Pages 1280-1292, ISSN 0168-1923, \ https://doi.org/10.1016/j.agrformet.2008.03.010. \ Supporting information: \ http://miguezlab.agron.iastate.edu/OldWebsite/Research/Miscanthus/MetaMiscan.tar.gz
Eichenberger, S., F. Miguez, J. Edwards, and A. Knapp. 2015. Changes in Kernel Filling with Selection for Grain Yield in a Maize Population. Crop Sci. 55:521-526. \ https://doi.org/10.2135/cropsci2014.07.0462
Stein, M., F. Miguez, and J. Edwards. 2016. Effects of Plant Density on Plant Growth before and after Recurrent Selection in Maize. Crop Sci. 56:2882-2894. \ https://doi.org/10.2135/cropsci2015.09.0599

Talks:

2008 ACS meeting.

Slides: \ http://miguezlab.agron.iastate.edu/OldWebsite/Research/Talks/ASA_Miguez.pdf

Data and code: \ http://miguezlab.agron.iastate.edu/OldWebsite/Research/Talks/Barley.zip