Package: lactcurves
Type: Package
Title: Lactation Curve Parameter Estimation
Version: 1.1.0
Author: Eva M. Strucken
Maintainer: Eva M. Strucken <eva.strucken@gmail.com>
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).
      <www.plantphys.info/plant_physiology/copyright/MichaelisMentenTranslation2.pdf>
  (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).
      <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2140670/>
  (4) Schumacher: Schumacher, F.X. (1939) in Thornley, J.H.M. and J. France (2007).
      <https://books.google.com.au/books/about/Mathematical_Models_in_Agriculture.html?id=rlwBCRSHobcC&redir_esc=y>
  (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).
      <https://journal.interbull.org/index.php/ib/issue/view/11>
  (15) Mixed log model 3 (Guo and Swalve): Guo, Z. and H.H. Swalve (1995).
      <https://journal.interbull.org/index.php/ib/issue/view/11>
  (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).
      <http://www.aaabg.org/aaabghome/AAABG23papers/35Strucken23139.pdf>
  (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).
      <https://journal.interbull.org/index.php/ib/issue/view/11>
  (24) Ali and Schaeffer: Ali, T.E. and L.R. Schaeffer (1987).
      <https://cdnsciencepub.com/doi/pdf/10.4141/cjas87-067>
  (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).
      <https://journal.interbull.org/index.php/ib/article/view/417>
  (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).
      <https://link.springer.com/book/10.1007/978-3-319-19425-7>
  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.
License: GPL-3
Depends: polynom,orthopolynom,splines
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-01-14 23:10:36 UTC; estrucke
Repository: CRAN
Date/Publication: 2021-01-15 09:50:02 UTC
Built: R 4.1.0; ; 2021-05-26 05:39:40 UTC; unix
