Generalized additive models for location, scale and shape in the analysis of common bean productivity
DOI:
https://doi.org/10.5902/2179460X85223Keywords:
Distributional regression models, Model selection, Phaseolus vulgaris LAbstract
The common bean (Phaseolus vulgaris L.) is a leguminous plant and one of the world’s most important crops, with substantial economic relevance. Hence, the main aim of this paper is to analyze the productivity of common beans, establishing relationships with specific variables. For this purpose, the following candidate explanatory variables were considered: plant height, number of branches per plant, days to flowering, days to maturity, number of seeds per pod, number of pods per plant, and seed mass. Because of its flexibility in explaining the behaviour of a response variable, the generalized additive models for location, scale, and shape (GAMLSS) were used for statistical modelling. Initially, three distinct distributions for the response variable (productivity) were considered: the inverse gamma (IGAMMA), the generalized gamma (GG), and the inverse Gaussian (IG). The covariates for the regression structures were selected using the so-called Strategy A, a stepwise-based method. Based on both Akaike and Schwarz criteria, the GAMLSS based on the IG distribution was chosen as the best fit. The variables number of pods per plant and days to maturity had a positive significant effect on average productivity, whereas the number of branches per plant presents a negative effect on its variability. Based on a residual analysis, we can conclude that the fitted GAMLSS based on the IG distribution is appropriate to explain the data.
Downloads
References
Abdollahi, A.; Tahmasebpour, B.; Dehghanian, H. Factor analysis of Phonological and Morphological Traits in Common bean (Phaseolus vulgaris L.). Biological Forum-An International Journal, v. 8, n.1, p. 132–134, 2016.
Akaike, H. A new look at the statistical model identification.IEEE Transactions on Automatic Control. Notre Dame, v.19, n.6, p.716-723, 1974.
Amanullah, K. A.; Nawab, K.; Sohail, Q. Performance of promising common bean (Phaseolus vulgaris L.) germplasm at Kalam-Swat. Pakistan. J. Biol. Sci. v. 9, n. 14, p. 2642–2646, 2006.
Arevalo, A. C. M.; Cardoso, D. L.; Kraeski, M. J.; Santana D. C.; Arguelho S. G. Parâmetros genéticos, correlações e componentes principais para caracteres agronômicos em genótipos de feijoeiro comum do grupo carioca. Research, Society and Development, v. 9, n. 11, e3179119831, 2020.
Biscaro, G. A.; Junior, S. A. R. G.; Soratto, R. P.; Júnior, N. A. F.; Motomiya, A. V. A. M.; Filho, G. C. C. Molibdênio via semente e nitrogênio em cobertura no feijoeiro irrigado em solo de cerrado. Ciênc. agrotec., v. 33, n. 5, p. 1280-1287, 2009.
Bisognin, M. B.; Pias, O. H. C.; Vian, A. L.; Basso, C. J.; Santi, A. L. Seed spacing variability reduces common bean yield. Pesq. Agropec. Trop., Goiânia, v. 49, e55134, 2019.
CONAB. 2023. Acompanhamento da Safra Brasileira, Feijão,2022/23, 4° levantamento. Available at: https://www.conab.gov.br. Accessed on June 2, 2023.
Correa, A. M.; Ceccon, G.; Correa, C. M. A.; Delben, D. S. Estimativas de parâmetros genéticos e correlações entre caracteres fenológicos e morfoagronômicos em feijão-caupi. Rev. Ceres, Viçosa, v. 59, n.1, p. 88 – 94, 2012.
Dunn, P.k.; Smyth, G.k. Randomized quantile residuals. J. Comput. Graph Stat. v. 5, p. 236–244, 1996.
Eilers, P.h.c.; Marx, B.d. Flexible smoothing with B-splines and penalties. Statistical Science, v. 11, p. 89–121 1996.
FAOSTAT-Food and Agriculture Organization Corporate Statistical Database. 2020. Available at: https://www.fao.org/faostat/en/. Accessed on July 28, 2023.
Federer, W.t. Augmented (or Hoonuiaku) Designs. Hawaiian Planters’ Record, v. 55, p. 191-208, 1956.
Fernandes, D. S.; Soratto, R. P.; Kulczynski, S. M.; Biscaro, G. A.; Dos Reis, C. G. Produtividade e qualidade fisiológica de sementes de feijão em conseqüência da aplicação foliar de manganês. Pesq. agropec. bras., v.42, n.3, p.419-426, 2007.
Harikrishnan, R.; Del Río, L. E. A Logistic Regression Model for Predicting Risk of White Mold Incidence on Dry Bean in North Dakota. Plant Disease, v. 92, n. 1, 2008.
IPGRI. Descritores para Phaseolus vulgaris. International Plant Genetic Resources Institute, Rome. 2001.
Jannat, S.; Shah, A. H.; Hassan, M.; Sher, A.; Fiaz, S.; Elesawy, B. H.; Ismail, K. A.; El Askary, A.; Gharib, A. F.; Qayyum, A. Genetic diversity of common bean (Phaseolus vulgaris L.) ecotypes from Pakistan using Simple Sequence Repeats. Saudi Journal of Biological Sciences, v. 29, 2022.
Jannat, S.; Shah, A. H.; Sabir, S. M. Nutraceutical characterisation of common bean (Phaseolus vulgaris L.) germplasm from Pakistan. International Food Research Journal, v. 26, n. 2, p. 1835–1843, 2019.
Kakhki, S. H. N.; Taghaddosi, M. V.; Moini, M. R.; Naseri, B. Predict bean production according to bean growth, root rots, fly and weed development under different planting dates and weed control treatments. heliyon journal, v. 8, n. 11, 2022.
Kneib, T. Beyond mean regression. Statistical Modelling, v.13, p. 275–303, 2013.
Machado, C. F.; Teixeira, N. J.; Filho, F. R. F.; Rocha, M. R.; Gomes, R. L. F. Identificação de genótipos de feijão-caupi quanto à precocidade, arquitetura da planta e produtividade de grãos. Revista Ciência Agronômica, 39:114-123, 2008.
MADER-Ministério da Agricultura e Desenvolvimento Rural. 2021. Inquérito Integrado Agrário 2020. Maputo, Mocambique. Available at: https://www.agricultura.gov.mz/wp_content/uploads/2021/06/MADER_Inquerito_Agrario_2020.pdf. Accessed on June 20, 2023.
Nakamura, L. R.; Ramires, T. G.; Righetto, A. J.; Pescim, R. R.; Roquim, F. V.; Savian, T. V.; Stasinopoulos, D. M. Cattle reference growth curves based on centile estimation: A GAMLSS approach. Computers and Electronics in Agriculture, v. 192, p. 106572, 2022.
Nakamura, L. R.; Rigby, R. A.; Stasinopoulos, D. M.; Leandro, R. A.; Villegas, C.; Pescim, R. R. Modelling location, scale and shape parameters of the Birnbaum-Saunders generalized t distribution. Journal of Data Science, v. 15, p. 221–237, 2017.
Pedro, C.; Donça, M. C. B; Somueque, S. I.; Dique, J. E. L.; Bambo, E. C.; Colial; H. V.; Alexandre, D. C.; Gimo, S. T.; Divage, B. A. F.; Rico, D. M. R.; Barbosa, I. V.; Felizmino, V.; Serrote, R. I.; Moisés, Y. A. A.; Amós, N. R. Variability, Similarity Network and Genotypic Path Analysis of Common bean yield traits. FPBJ - Scientific Journal, v. 4, n. 2, p. 13–22, 2022a.
Pedro, C.; Donça, M. C. B.; Colial, H. V.; Dique, J. E. L.; Bambon, E. C.; Somueque, S. I.; Divage, B. A. F.; Rico, D. M. R.; Barbosa, I. P. Morpho-agronomic genetic diversity in common bean landraces based on blup values. FPBJ - Scientific Journal, v. 5, n. 3, 2022b.
Pereira, R. F.; Cavalcante, S. N.; Lima, A. S.; Filho, F. C. F. M; Santos, J. G. R. Crescimento e rendimento de feijão vigna submetido à adubação orgânica. Revista Verde (Mossoró – RN - Brasil), v. 8, n. 3, p. 91 - 96, 2013.
Ramires, T. G.; Nakamura, L. R.; Righetto, A. J.; Pescim, R. R.; Mazucheli, J.; Rigby, R. A.; Stasinopoulos, D. M. Validation of Stepwise-Based Procedure in GAMLSS. Journal of Data Science, v. 19, n. 1, p. 96–110, 2021.
Ribeiro, N. D.; Mello, R. M.; Dalla, R. C.; Sluszz, T. Correlações genéticas de caracteres agromorfológicos e suas implicações na seleção de genótipos de feijão carioca. Revista Brasileira de Agrociência, v. 7, n. 2, p. 93-99, 2001.
Rigby, R. A.; Stasinopoulos, D. M. Generalized additive models for location, scale and shape (with discussion). Appl. Statist. v. 54, p. 507–554, 2005.
Rigby, R. A.; Stasinopoulos, D. M.; Heller, G. Z.; De Bastiani, F. Distributions for Modeling Location, Scale, and Shape: Using GAMLSS in R. Chapman and Hall/CRC, 2019.
Righetto, A. J.; Ramires, T. G.; Nakamura, L. R.; Castanho, P. L. D. B.; Faes, C.; Savian, T. V. Predicting weed invasion in a sugarcane cultivar using multispectral image. Journal of Applied Statistics, v. 46, p. 1–12, 2019.
Rosse, L. N.; Vencovsky, R. Modelo de regressão não-linear aplicado ao estudo da estabilidade fenotípica de genótipo de feijão no estado do paraná. Bragantia, Campinas, v. 59, n. 1, p. 99 – 107, 2000.
Schmutz, J.; Mcclean, P. E.; Mamidi, S.; Wu, G. A.; Cannon, S. B.; Grimwood, J.; Jenkins, J.; Shu, S.; Song, Q.; Chavarro, C.; Torres-Torres, M.; Geffroy, V.; Moghaddam, S. M.; Gao, D.; Abernathy, B.; Barry, K.; Blair, M.; Brick, M. A.; Chovatia, M.; Gepts, P.; Goodstein, D. M.; Gonzales, M.; Hellsten, U.; Hyten, D. L.; Jia, G.; Kelly, J. D.; Kudrna, D.; Lee, R.; Richard, M. M. S.; Miklas, P. N.; Osorno, J. M.; Rodrigues, J.; Thareau, V.; Urrea, C. A.; Wang, M.; Yu, Y.; Zhang, M.; Wing, R. A.; Cregan, P. B.; Rokhsar, D. S.; Jackson, S. A. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, v. 46, n. 7, p. 707–713, 2014.
Schwarz, G. Estimating the dimension of a model. Ann. Stat., v. 6, n. 2, p. 461–464,1978.
Shahid, A.; Kamaluddin, S. Correlation and path analysis for agro-morphological traits in rajmash beans under Baramulla- Kashmir region. African Journal of Agricultural Research, v. 8, n. 18, pp. 2027-2032, 2013.
Sofi, P. A.; Zargar, M. Y.; Debouk, D.; Graner, A. Evaluation of common bean (Phaseolus vulgaris L.) germplasm under temperate conditions of Kashmir Valley. J. Phytol., n. 3, v. 8, p. 47-52, 2011.
Stasinopoulos, D. M.; Rigby, R. A.; Heller, G. Z.; Voudouris, V.; De Bastiani, F. Flexible Regression and Smoothing: Using GAMLSS in R. Chapman and Hall/CRC, 2017.
Stoilova, T.; Pereira, G.; Tavares-De-Sousa, M. Morphological characterization of a small common bean (Phaseolus vulgaris L.) collection under different environments. Journal of Central European Agriculture. v. 14, n. 3, p. 1–11, 2013.
Van Buuren, S.; Fredriks, M. Worm plot: a simple diagnostic device for modelling growth reference curves. Statistics in medicine, v. 20, p. 1259 – 1277, 2001.
Voudouris, V.; Gilchrist, R.; Rigby, R.; Sedgwick, J.; Stasinopoulos, D. Modelling skewness and kurtosis with the BCPE density in GAMLSS. Journal of Applied Statistics, v. 39, n. 6, p. 1279–1293, 2012.
Zilio, M.; Coelho, C. M. M.; Souza, C. A.; Santos, J. C. P.; Miquelluti, D. J. Contribuição dos componentes de rendimento na produtividade de genótipos crioulos de feijão (Phaseolus vulgaris L.). Rev. Ciênc. Agron., v. 42, n. 2, p. 429 – 438, 2011.
Published
How to Cite
Issue
Section
License
Copyright (c) 2025 Ciência e Natura

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
To access the DECLARATION AND TRANSFER OF COPYRIGHT AUTHOR’S DECLARATION AND COPYRIGHT LICENSE click here.
Ethical Guidelines for Journal Publication
The Ciência e Natura journal is committed to ensuring ethics in publication and quality of articles.
Conformance to standards of ethical behavior is therefore expected of all parties involved: Authors, Editors, Reviewers, and the Publisher.
In particular,
Authors: Authors should present an objective discussion of the significance of research work as well as sufficient detail and references to permit others to replicate the experiments. Fraudulent or knowingly inaccurate statements constitute unethical behavior and are unacceptable. Review Articles should also be objective, comprehensive, and accurate accounts of the state of the art. The Authors should ensure that their work is entirely original works, and if the work and/or words of others have been used, this has been appropriately acknowledged. Plagiarism in all its forms constitutes unethical publishing behavior and is unacceptable. Submitting the same manuscript to more than one journal concurrently constitutes unethical publishing behavior and is unacceptable. Authors should not submit articles describing essentially the same research to more than one journal. The corresponding Author should ensure that there is a full consensus of all Co-authors in approving the final version of the paper and its submission for publication.
Editors: Editors should evaluate manuscripts exclusively on the basis of their academic merit. An Editor must not use unpublished information in the editor's own research without the express written consent of the Author. Editors should take reasonable responsive measures when ethical complaints have been presented concerning a submitted manuscript or published paper.
Reviewers: Any manuscripts received for review must be treated as confidential documents. Privileged information or ideas obtained through peer review must be kept confidential and not used for personal advantage. Reviewers should be conducted objectively, and observations should be formulated clearly with supporting arguments, so that Authors can use them for improving the paper. Any selected Reviewer who feels unqualified to review the research reported in a manuscript or knows that its prompt review will be impossible should notify the Editor and excuse himself from the review process. Reviewers should not consider manuscripts in which they have conflicts of interest resulting from competitive, collaborative, or other relationships or connections with any of the authors, companies, or institutions connected to the papers.


