CRAN/E | lactcurves

lactcurves

Lactation Curve Parameter Estimation

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About

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). doi:10.1017/S002185960007684X (1b) Michaelis-Menten + exponential (Rook): Rook, A.J., J. France, and M.S. Dhanoa (1993). doi:10.1017/S002185960007684X (2) Brody (1923): Brody, S., A.C. Ragsdale, and C.W. Turner (1923). doi:10.1085/jgp.5.6.777 (3) Brody (1924): Brody, S., C.W. Tuner, and A.C. Ragsdale (1924). (4) Schumacher: Schumacher, F.X. (1939) in Thornley, J.H.M. and J. France (2007). (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). doi:10.3168/jds.2014-8132 (5) Parabolic exponential (Adediran): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). doi:10.3168/jds.2011-4663 (6) Wood: Wood, P.D.P. (1967). doi:10.1038/216164a0 (6a) Wood reparameterized (Dhanoa): Dhanoa, M.S. (1981). doi:10.1017/S0003356100027276 (6b) Wood non-linear (Cappio-Borlino): Cappio-Borlino, A., G. Pulina, and G. Rossi (1995). doi:10.1016/0921-4488(95)00713-U (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). doi:10.3168/jds.2011-4663 (8) Cobby and Le Du (Vargas): Vargas, B., W.J. Koops, M. Herrero, and J.A.M Van Arendonk (2000). doi:10.3168/jds.S0022-0302(00)75005-3 (9) Papajcsik and Bodero 1: Papajcsik, I.A. and J. Bodero (1988). doi:10.1017/S0003356100003275 (10) Papajcsik and Bodero 2: Papajcsik, I.A. and J. Bodero (1988). doi:10.1017/S0003356100003275 (11) Papajcsik and Bodero 3: Papajcsik, I.A. and J. Bodero (1988). doi:10.1017/S0003356100003275 (12) Papajcsik and Bodero 4: Papajcsik, I.A. and J. Bodero (1988). doi:10.1017/S0003356100003275 (13) Papajcsik and Bodero 6: Papajcsik, I.A. and J. Bodero (1988). doi:10.1017/S0003356100003275 (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). doi:10.3168/jds.2011-4663 (17) Wilmink: J.B.M. Wilmink (1987). doi:10.1016/0301-6226(87)90003-0 (17a) modified Wilmink (Jakobsen): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002). doi:10.3168/jds.S0022-0302(02)74231-8 (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). doi:10.3168/jds.2011-4663 (19) Dijkstra: Dijkstra, J., J. France, M.S. Dhanoa, J.A. Maas, M.D. Hanigan, A.J. Rook, and D.E. Beever (1997). doi:10.3168/jds.S0022-0302(97)76185-X (20) Morant and Gnanasakthy (Pollott et al 2000): Pollott, G.E. and E. Gootwine (2000). doi:10.1017/S1357729800055028 (21) Morant and Gnanasakthy (Vargas et al 2000): Vargas, B., W.J. Koops, M. Herrero, and J.A.M Van Arendonk (2000). doi:10.3168/jds.S0022-0302(00)75005-3 (22) Morant and Gnanasakthy (Adediran et al. 2012): Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). doi:10.3168/jds.2011-4663 (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). doi:10.1017/S175173111200239X (26) Pollott multiplicative (Elvira): Elvira, L., F. Hernandez, P. Cuesta, S. Cano, J.-V. Gonzalez-Martin, and S. Astiz (2012). doi:10.1017/S175173111200239X (27) Pollott modified: Adediran, S.A., D.A. Ratkowsky, D.J. Donaghy, and A.E.O. Malau-Aduli (2012). doi:10.3168/jds.2011-4663 (28) Monophasic Grossman: Grossman, M. and W.J. Koops (1988). doi:10.3168/jds.S0022-0302(88)79723-4 (29) Monophasic Power Transformed (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999). doi:10.3168/jds.S0022-0302(99)75464-0 (30) Diphasic (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999). doi:10.3168/jds.S0022-0302(99)75464-0 (31) Diphasic Power Transformed (Grossman 1999): Grossman, M., S.M. Hartz, and W.J. Koops (1999). doi:10.3168/jds.S0022-0302(99)75464-0 (32) Legendre Polynomial (3th order): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002). doi:10.3168/jds.S0022-0302(02)74231-8 (33) Legendre Polynomial (4th order): Jakobsen J.H., P. Madsen, J. Jensen, J. Pedersen, L.G. Christensen, and D.A. Sorensen (2002). doi:10.3168/jds.S0022-0302(02)74231-8 (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). doi:10.3168/jds.S0022-0302(99)75277-X (36) Natural Cubic Spline (4 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999). doi:10.3168/jds.S0022-0302(99)75277-X (37) Natural Cubic Spline (5 percentiles): White, I.M.S., R. Thompson, and S. Brotherstone (1999) doi:10.3168/jds.S0022-0302(99)75277-X (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.

Key Metrics

Version 1.1.0
Published 2021-01-15 1200 days ago
Needs compilation? no
License GPL-3
CRAN checks lactcurves results

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Maintainer

Maintainer

Eva M. Strucken

eva.strucken@gmail.com

Authors

Eva M. Strucken

Material

README
NEWS
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

lactcurves archive

Depends

polynom
orthopolynom
splines