nlraa v0.53

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Nonlinear Regression for Agricultural Applications

Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Eighteen new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses nlsLM for fitting, but it is otherwise almost identical to 'nlme::nlsList'. One of the main benefits is that these functions can be integrated in the modeling framework of the 'nlme' package. It also provides three vignettes with extended examples.

Readme

nlraa: R pacakge for Nonlinear Regression for Agricultural

Applications

This package supports the following publications:

  1. 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

  2. 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

  3. 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

Other publications where we have used nonlinear mixed models:

  1. 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

  2. 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

  3. 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

Ideas for future versions:

  • Include more data and analysis code from the above examples
  • Include more SS functions

To install

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

Functions in nlraa

Name Description
barley Data from a paper by Arild Vold on response of barley to nitrogen fertilizer
SSnrh self start for non-rectangualr hyperbola (photosynthesis)
sm Sorghum and Maize growth in Greece
SSbg4rp self start for the reparameterized Beta growth function with four parameters
SSpexpf self start for plateau-exponential function
lfmc Live fuel moisture content
swpg Simulated data based on obseved data presented in Sinclair (1986) - Fig. 1A
SSplin self start for plateau-linear function
SSpquad self start for plateau-quadratic function
SSricker self start for Ricker Function
SSratio self start for a rational curve
nlsLMList Create a list of nls objects with the option of using nlsLM in addition to nls
SSprofd self start for profile decay function
SSquadp self start for quadratic-plateau function
nlsLMList.formula Formula method for nls 'LM' list method
SSexpfp self start for an exponential-plateau function
SSexpf self start for an exponential function
SSdlf self start for Declining Logistic Function
SSblin self start for a bilinear Function
SSbell self start for a bell-shaped curve
SSbgrp self start for the reparameterized Beta growth function
SSlinp self start for linear-plateau function
SSbgf self start for Beta Growth Function
SSbgf4 self start for Beta growth function with four parameters
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Vignettes of nlraa

Name
nlraa-AgronJ-paper.Rmd
nlraa-Oddi-LFMC.Rmd
nlraa.Rmd
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Details

License GPL-3
Encoding UTF-8
VignetteBuilder knitr
BugReports https://github.com/femiguez/nlraa/issues
LazyData true
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2020-01-09 21:39:02 UTC; fernandomiguez
Repository CRAN
Date/Publication 2020-01-13 16:20:02 UTC

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