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lactcurves
Lactation Curve Parameter Estimation
View on CRAN: Click
here
Download and install lactcurves package within the R console
Install from CRAN:
install.packages("lactcurves")
Install from Github:
library("remotes")
install_github("cran/lactcurves") Install by package version:
library("remotes")
install_version("lactcurves", "1.1.0") Attach the package and use:
library("lactcurves")
Maintained by
Eva M. Strucken
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-08-20
Latest Update: 2021-01-15
Description:
AllCurves() runs multiple lactation curve models and extracts selection criteria for each model.
This package summarises the most common lactation curve models from the last century and provides a tool
for researchers to quickly decide on which model fits their data best to proceed with their analysis.
Start parameters were optimized based on a dataset with 1.7 million Holstein-Friesian cows. If convergence fails,
the start parameters need to be manually adjusted.
The models included in the package are taken from:
(1) Michaelis-Menten: Michaelis, L. and M.L. Menten (1913).
(1a) Michaelis-Menten (Rook): Rook, A.J., J. France, and M.S. Dhanoa (1993).
(1b) Michaelis-Menten + exponential (Rook): Rook, A.J., J. France, and M.S. Dhanoa (1993).
(2) Brody (1923): Brody, S., A.C. Ragsdale, and C.W. Turner (1923).
(3) Brody (1924): Brody, S., C.W. Tuner, and A.C. Ragsdale (1924).
(4a) Schumacher (Lopez et al. 2015): Lopez, S. J. France, N.E. Odongo, R.A. McBride, E. Kebreab, O. AlZahal, B.W. McBride, and J. Dijkstra (2015).
(5) Parabolic exponential (Adediran): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012).
(6) Wood: Wood, P.D.P. (1967).
(6a) Wood reparameterized (Dhanoa): Dhanoa, M.S. (1981).
(6b) Wood non-linear (Cappio-Borlino): Cappio-Borlino, A., G. Pulina, and G. Rossi (1995).
(7) Quadratic Polynomial (Dave): Dave, B.K. (1971) in Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012).
(8) Cobby and Le Du (Vargas): Vargas, B., W.J. Koops, M. Herrero, and J.A.M Van Arendonk (2000).
(9) Papajcsik and Bodero 1: Papajcsik, I.A. and J. Bodero (1988).
(10) Papajcsik and Bodero 2: Papajcsik, I.A. and J. Bodero (1988).
(11) Papajcsik and Bodero 3: Papajcsik, I.A. and J. Bodero (1988).
(12) Papajcsik and Bodero 4: Papajcsik, I.A. and J. Bodero (1988).
(13) Papajcsik and Bodero 6: Papajcsik, I.A. and J. Bodero (1988).
(14) Mixed log model 1 (Guo and Swalve): Guo, Z. and H.H. Swalve (1995).
(15) Mixed log model 3 (Guo and Swalve): Guo, Z. and H.H. Swalve (1995).
(16) Log-quadratic (Adediran et al. 2012): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012).
(17) Wilmink: J.B.M. Wilmink (1987).
(17a) modified Wilmink (Jakobsen): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002).
(17b) modified Wilmink (Laurenson & Strucken): Strucken E.M., Brockmann G.A., and Y.C.S.M. Laurenson (2019).
(18) Bicompartemental (Ferguson and Boston 1993): Ferguson, J.D., and R. Boston (1993) in Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012).
(19) Dijkstra: Dijkstra, J., J. France, M.S. Dhanoa, J.A. Maas, M.D. Hanigan, A.J. Rook, and D.E. Beever (1997).
(20) Morant and Gnanasakthy (Pollott et al 2000): Pollott, G.E. and E. Gootwine (2000).
(21) Morant and Gnanasakthy (Vargas et al 2000): Vargas, B., W.J. Koops, M. Herrero, and J.A.M Van Arendonk (2000).
(22) Morant and Gnanasakthy (Adediran et al. 2012): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012).
(23) Khandekar (Guo and Swalve): Guo, Z. and H.H. Swalve (1995).
(24) Ali and Schaeffer: Ali, T.E. and L.R. Schaeffer (1987).
(25) Fractional Polynomial (Elvira et al. 2013): Elvira, L., F. Hernandez, P. Cuesta, S. Cano, J.-V. Gonzalez-Martin, and S. Astiz (2012).
(26) Pollott multiplicative (Elvira): Elvira, L., F. Hernandez, P. Cuesta, S. Cano, J.-V. Gonzalez-Martin, and S. Astiz (2012).
(27) Pollott modified: Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012).
(28) Monophasic Grossman: Grossman, M. and W.J. Koops (1988).
(29) Monophasic Power Transformed (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999).
(30) Diphasic (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999).
(31) Diphasic Power Transformed (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999).
(32) Legendre Polynomial (3th order): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002).
(33) Legendre Polynomial (4th order): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002).
(34) Legendre + Wilmink (Lidauer): Lidauer, M. and E.A. Mantysaari (1999).
(35) Natural Cubic Spline (3 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999).
(36) Natural Cubic Spline (4 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999).
(37) Natural Cubic Spline (5 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999)
(38) Natural Cubic Spline (defined knots according to Harrell 2001): Jr. Harrell, F.E. (2001).
The selection criteria measure the goodness of fit of the model and include:
Residual standard error (RSE),
R-square (R2),
log likelihood,
Akaike information criterion (AIC),
Akaike information criterion corrected (AICC),
Bayesian Information Criterion (BIC),
Durbin Watson coefficient (DW).
The following model parameters are included:
Residual sum of squares (RSS),
Residual standard deviation (RSD),
F-value (F) based on F-ratio test.
How to cite:
Eva M. Strucken (2019). lactcurves: Lactation Curve Parameter Estimation. R package version 1.1.0, https://cran.r-project.org/web/packages/lactcurves. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.0 (2019-08-20 18:30)
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Some associated R codes: lactcurves_R-package.R . Full lactcurves package functions and examples
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