{ "_id": "6a1edd7ab401979e734100e7", "Package": "nlraa", "Version": "1.9.11", "Authors@R": "c(person(\"Fernando\", \"Miguez\", email = \"femiguez@iastate.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4627-8329\")),\nperson(\"Caio\", \"dos Santos\", role = c(\"ctb\"), comment = \"author of SSscard\"),\nperson(\"José\", \"Pinheiro\", role = c(\"ctb\",\"cph\"), comment = \"author of nlme::nlsList, nlme::predict.gnls, nlme::predict.nlme\"),\nperson(\"Douglas\", \"Bates\", role = c(\"ctb\",\"cph\"), comment = \"author of nlme::nlsList, nlme::predict.gnls, nlme::predict.nlme\"),\nperson(\"R-core\", email = \"R-core@R-project.org\", role = c(\"ctb\", \"cph\")))", "Title": "Nonlinear Regression for Agricultural Applications", "Description": "Additional nonlinear regression functions using self-start\n(SS) algorithms. One of the functions is the Beta growth\nfunction proposed by Yin et al. (2003)\n. There are several other functions\nwith breakpoints (e.g. linear-plateau, plateau-linear,\nexponential-plateau, plateau-exponential, quadratic-plateau,\nplateau-quadratic and bilinear), a non-rectangular hyperbola\nand a bell-shaped curve. Twenty eight (28) new self-start (SS)\nfunctions in total. This package also supports the publication\n'Nonlinear regression Models and applications in agricultural\nresearch' by Archontoulis and Miguez (2015)\n, a book chapter with similar\nmaterial and a\npublication by Oddi et. al. (2019) in Ecology and Evolution\n. The function 'nlsLMList' uses 'nlsLM'\nfor fitting, but it is otherwise almost identical to\n'nlme::nlsList'.In addition, this release of the package\nprovides functions for conducting simulations for 'nlme' and\n'gnls' objects as well as bootstrapping. These functions are\nintended to work with the modeling framework of the 'nlme'\npackage. It also provides four vignettes with extended\nexamples.", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "BugReports": "https://github.com/femiguez/nlraa/issues", "LazyData": "true", "LazyDataCompression": "xz", "RoxygenNote": "7.3.2", "Repository": "https://femiguez.r-universe.dev", "Date/Publication": "2025-08-22 21:58:46 UTC", "RemoteUrl": "https://github.com/femiguez/nlraa", "RemoteRef": "HEAD", "RemoteSha": "d6afbf815a423077286821acc97ce44184ecb039", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 08:16:07 UTC", "User": "root" }, "Author": "Fernando Miguez [aut, cre] (ORCID:\n),\nCaio dos Santos [ctb] (author of SSscard),\nJosé Pinheiro [ctb, cph] (author of nlme::nlsList, nlme::predict.gnls,\nnlme::predict.nlme),\nDouglas Bates [ctb, cph] (author of nlme::nlsList, nlme::predict.gnls,\nnlme::predict.nlme),\nR-core [ctb, cph]", "Maintainer": "Fernando Miguez ", "MD5sum": "3dda2f30555a3e1601ef272da26e5426", "_user": "femiguez", "_type": "src", 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"topics": [ "boot_lm" ] }, { "page": "boot_lme", "title": "Bootstraping for linear mixed models", "topics": [ "boot_gls", "boot_lme" ] }, { "page": "boot_nlme", "title": "Bootstraping for generalized nonlinear models and nonlinear mixed models", "topics": [ "boot_gnls", "boot_nlme" ] }, { "page": "boot_nls", "title": "Bootstrapping for nonlinear models", "topics": [ "boot_nls" ] }, { "page": "confidence_intervals", "title": "Confidence interval methods for (non)-linear models", "topics": [ "confidence_intervals" ] }, { "page": "fm1.P.at.x.0.4", "title": "object for confidence bands vignette fm1.P.at.x.0.4", "topics": [ "fm1.P.at.x.0.4" ] }, { "page": "fm1.P.bt", "title": "object for confidence bands vignette fm1.P.bt", "topics": [ "fm1.P.bt" ] }, { "page": "fm1.P.bt.ft", "title": "object for confidence bands vignette fm1.P.bt.ft", "topics": [ "fm1.P.bt.ft" ] }, { "page": "fm2.Lob.bt", "title": "object for confidence bands vignette fm2.Lob.bt", "topics": [ "fm2.Lob.bt" ] }, { "page": "fmm1.bt", "title": "object for confidence bands vignette fmm1.bt", "topics": [ "fmm1.bt" ] }, { "page": "IA_tab", "title": "Indexes of Agreement Table", "topics": [ "IA_tab", "plot.IA_tab", "print.IA_tab" ] }, { "page": "IC_tab", "title": "Information Criteria Table", "topics": [ "IC_tab" ] }, { "page": "lfmc", "title": "Live fuel moisture content", "topics": [ "lfmc" ] }, { "page": "Lob.bt.pe", "title": "object for confidence bands vignette Lob.bt.pe", "topics": [ "Lob.bt.pe" ] }, { "page": "maizeleafext", "title": "Maize leaf extension rate as a response to temperature", "topics": [ "maizeleafext" ] }, { "page": "nlraa.env", "title": "Environment to store options and data for nlraa", "topics": [ "nlraa.env" ] }, { "page": "nlsLMList", "title": "Create a list of nls objects with the option of using nlsLM in addition to nls", "topics": [ "nlsLMList", "nlsLMList.selfStart" ] }, { "page": "nlsLMList.formula", "title": "Formula method for nls 'LM' list method", "topics": [ "nlsLMList.formula" ] }, { "page": "predict_gam", "title": "Modified prediciton function based on predict.gam", "topics": [ "predict_gam" ] }, { "page": "predict_nlme", "title": "Average predictions from several (non)linear models based on IC weights", "topics": [ "predict_gls", "predict_gnls", "predict_lme", "predict_nlme" ] }, { "page": "predict_nls", "title": "Average predictions from several (non)linear models based on IC weights", "topics": [ "predict2_gam", "predict_nls" ] }, { "page": "predict2_nls", "title": "Prediction Bands for Nonlinear Regression", "topics": [ "predict2_nls" ] }, { "page": "R2M", "title": "R-squared for nonlinear mixed models", "topics": [ "R2M", "R2M.gls", "R2M.gnls", "R2M.lm", "R2M.lme", "R2M.nlme", "R2M.nls" ] }, { "page": "simulate_gam", "title": "Simulate responses from a generalized additive linear model 'gam'", "topics": [ "simulate_gam" ] }, { "page": "simulate_gls", "title": "Simulate fitted values from an object of class 'gls'", "topics": [ "simulate_gls" ] }, { "page": "simulate_gnls", "title": "Simulate fitted values from an object of class 'gnls'", "topics": [ "simulate_gnls" ] }, { "page": "simulate_lm", "title": "Simulate responses from a linear model 'lm'", "topics": [ "simulate_lm" ] }, { "page": "simulate_lme", "title": "Simulate values from an object of class 'lme'", "topics": [ "simulate_lme" ] }, { "page": "simulate_nlme", "title": "Simulate samples from a nonlinear mixed model from fixed effects", "topics": [ "simulate_nlme" ] }, { "page": "simulate_nlme_one", "title": "Simulate fitted values from an object of class 'nlme'", "topics": [ "simulate_nlme_one" ] }, { "page": "simulate_nls", "title": "Simulate fitted values from an object of class 'nls'", "topics": [ "simulate_nls" ] }, { "page": "sm", "title": "Sorghum and Maize growth in Greece", "topics": [ "sm" ] }, { "page": "SSagauss", "title": "self start for an asymmetric Gaussian bell-shaped curve", "topics": [ "agauss", "SSagauss" ] }, { "page": "SSbell", "title": "self start for a bell-shaped curve", "topics": [ "bell", "SSbell" ] }, { "page": "SSbeta5", "title": "self start for Beta 5-parameter function", "topics": [ "beta5", "SSbeta5" ] }, { "page": "SSbg4rp", "title": "self start for the reparameterized Beta growth function with four parameters", "topics": [ "bg4rp", "SSbg4rp" ] }, { "page": "SSbgf", "title": "self start for Beta Growth Function", "topics": [ "bgf", "bgf2", "SSbgf" ] }, { "page": "SSbgf4", "title": "self start for Beta growth function with four parameters", "topics": [ "bgf4", "SSbgf4" ] }, { "page": "SSbgrp", "title": "self start for the reparameterized Beta growth function", "topics": [ "bgrp", "SSbgrp" ] }, { "page": "SSblin", "title": "self start for a bilinear Function", "topics": [ "blin", "SSblin" ] }, { "page": "SScard3", "title": "self start for cardinal temperature response", "topics": [ "card3", "SScard3" ] }, { "page": "SSdlf", "title": "self start for Declining Logistic Function", "topics": [ "dlf", "SSdlf" ] }, { "page": "SSexpf", "title": "self start for an exponential function", "topics": [ "expf", "SSexpf" ] }, { "page": "SSexpfp", "title": "self start for an exponential-plateau function", "topics": [ "expfp", "SSexpfp" ] }, { "page": "SSexplin", "title": "self start for the exponential-linear growth equation", "topics": [ "explin", "SSexplin" ] }, { "page": "SSgmicmen", "title": "self start for a generalized Michaelis-Menten function", "topics": [ "gmicmen", "SSgmicmen" ] }, { "page": "SSharm", "title": "self start for a harmonic regression model", "topics": [ "harm1", "SSharm1" ] }, { "page": "SShill", "title": "self start for Hill Function", "topics": [ "hill1", "hill2", "hill3", "SShill", "SShill1", "SShill2", "SShill3" ] }, { "page": "SSlinp", "title": "self start for linear-plateau function", "topics": [ "linp", "SSlinp" ] }, { "page": "SSlogis5", "title": "self start for five-parameter logistic function", "topics": [ "logis5", "SSlogis5" ] }, { "page": "SSmoh", "title": "self start for modified hyperbola (photosynthesis)", "topics": [ "moh", "SSmoh" ] }, { "page": "SSnrh", "title": "self start for non-rectangular hyperbola (photosynthesis)", "topics": [ "nrh", "SSnrh" ] }, { "page": "SSpexpf", "title": "self start for plateau-exponential function", "topics": [ "pexpf", "SSpexpf" ] }, { "page": "SSplin", "title": "self start for plateau-linear function", "topics": [ "plin", "SSplin" ] }, { "page": "SSpquad", "title": "self start for plateau-quadratic function", "topics": [ "pquad", "SSpquad" ] }, { "page": "SSpquad3", "title": "self start for plateau-quadratic function", "topics": [ "pquad3", "SSpquad3" ] }, { "page": "SSprofd", "title": "self start for profile decay function", "topics": [ "profd", "SSprofd" ] }, { "page": "SSquadp", "title": "self start for quadratic-plateau function", "topics": [ "quadp", "SSquadp" ] }, { "page": "SSquadp3", "title": "self start for quadratic-plateau function", "topics": [ "quadp3", "SSquadp3" ] }, { "page": "SSquadp3xs", "title": "self start for quadratic-plateau function (xs)", "topics": [ "quadp3xs", "SSquadp3xs" ] }, { "page": "SSquadpq", "title": "self start for quadratic-plateau-quadratic (QPQ) function", "topics": [ "quadpq", "SSquadpq" ] }, { "page": "SSratio", "title": "self start for a rational curve", "topics": [ "ratio", "SSratio" ] }, { "page": "SSricker", "title": "self start for Ricker Function", "topics": [ "ricker", "SSricker" ] }, { "page": "SSscard3", "title": "self start for smooth cardinal temperature response", "topics": [ "scard3", "SSscard3" ] }, { "page": "SSsharp", "title": "self start for temperature response", "topics": [ "sharp", "SSsharp" ] }, { "page": "SSspherical", "title": "self start for spherical function", "topics": [ "spherical", "SSspherical" ] }, { "page": "SStemp", "title": "self start for Collatz temperature response", "topics": [ "SStemp3", "temp3" ] }, { "page": "SStrlin", "title": "self start for a trilinear Function", "topics": [ "SStrlin", "trlin" ] }, { "page": "summary_simulate", "title": "Summarize a matrix of simulations by their mean (median), sd (mad), and quantiles", "topics": [ "summary_simulate" ] }, { "page": "swpg", "title": "Water limitations for Soybean growth", "topics": [ "swpg" ] }, { "page": "var_cov", "title": "Variance Covariance matrix of for g(n)ls and (n)lme models", "topics": [ "var_cov" ] } ], "_readme": "https://github.com/femiguez/nlraa/raw/HEAD/README.md", "_rundeps": [ "boot", "evaluate", "highr", "knitr", "lattice", "MASS", "Matrix", "mgcv", "nlme", "xfun", "yaml" ], "_vignettes": [ { "source": "Confidence-Bands.Rmd", "filename": "Confidence-Bands.html", "title": "Confidence and Prediction Bands Methods for Nonlinear Models", "author": "Fernando Miguez", "engine": "knitr::rmarkdown", "headings": [ "Motivation", "Confidence and Prediciton Bands in Regression", "Linear Example", "Nonlinear Example: Loblolly", "Nonlinear Example: Puromycin", "Nonlinear Example: Maize Leaf Extension Rate", "Nonlinear Example: Theoph", "Nonlinear Example: Prediction bands for an observation within a subject", "Nonlinear Example: Prediction bands for an mean function (new subject)", "References" ], "created": "2021-05-13 21:54:15", "modified": "2023-06-09 15:33:33", "commits": 8 }, { "source": "nlraa.Rmd", "filename": "nlraa.html", "title": "nlraa: An R package for Nonlinear Regression Applications in Agricultural Research", "author": "Fernando Miguez", "engine": "knitr::rmarkdown", "headings": [ "Nonlinear Regression", "Index of self starting functions", "Functions in 'base' R", "Functions in this package (nlraa)", "Documentation", "References", "List of available SS (self-start) functions.", "Prediction, Simulation and Bootstrap", "Datasets", "What to do when convergence fails?", "Some common error messages", "Barley example", "Other modeling approaches", "Contributed packages", "FlexParamCurve package", "sicegar package", "drc package", "investr", "easynls pacakge", "chngpt pacakge", "mcp package", "nlsr package", "propagate package", "car package", "HydroMe package", "Nonlinear mixed models packages", "Additional material on growth models" ], "created": "2019-08-12 21:04:32", "modified": "2025-08-11 13:08:15", "commits": 43 }, { "source": "Models-and-Functions.Rmd", "filename": "Models-and-Functions.html", "title": "nlraa: Models and Functions for Mixed Models", "author": "Fernando Miguez", "engine": "knitr::rmarkdown", "headings": [ "Intro", "Linear Model", "Generalized least squares (gls)" ], "created": "2020-06-12 12:56:14", "modified": "2020-11-09 13:23:08", "commits": 2 }, { "source": "nlraa-AgronJ-paper.Rmd", "filename": "nlraa-AgronJ-paper.html", "title": "Nonlinear Regression (Archontoulis and Miguez) paper", "author": "Fernando Miguez", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example" ], "created": "2019-08-12 21:04:32", "modified": "2020-11-09 13:23:08", "commits": 8 }, { "source": "Bootstrapping.Rmd", "filename": 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